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See detailDynamic change of the human gastrointestinal microbiome in relation to mucosal barrier effects during chemotherapy and immune ablative intervention
Kaysen, Anne UL

Doctoral thesis (2017)

Numerous studies have demonstrated that the gastrointestinal tract (GIT) microbiota plays important roles for the human host. Since the GIT microbiota interfaces with the immune system and represents a ... [more ▼]

Numerous studies have demonstrated that the gastrointestinal tract (GIT) microbiota plays important roles for the human host. Since the GIT microbiota interfaces with the immune system and represents a first line of defense against infectious agents, interest has grown in whether the GIT microbiota may influence the outcome of different anticancer treatments. In this study, the GIT of pediatric patients with different cancer types as well as adult patients with hematologic malignancies undergoing an allogeneic hematopoietic stem cell transplantation were sampled throughout their treatment. In order to deeply profile not only the composition of the community, but also the functional capacity and expression, recently developed wet- and dry-lab methodologies for integrated multi-omic analyses were applied. The trajectories of the prokaryotic and microeukaryotic GIT communities of the patients were described in detail using 16S, 18S rRNA gene amplicon sequencing, as well as metagenomic and metatranscriptomic shotgun sequencing. Indeed, changes in the GIT microbiome in response to treatment were detected. Some changes that are generally thought to be detrimental for human health were detected during treatment, such as a decrease in alpha-diversity, a decrease in relative abundance of bacteria associated with health-promoting properties (such as Blautia spp., Roseburia spp. and Faecalibacterium spp.), as well as an increase in the relative abundance of antibiotic resistance genes. These changes were more pronounced in the adult hematology patients than in the pediatric patients, which is likely due to the more intensive treatment. Some observations need further investigation in order to explain their implication in human health. For example, in the pediatric patients, lower relative abundance of Akkermansia muciniphila was associated with mucositis and functional gene categories that are linked to bacteriophages or the bacterial defense mechanism against bacteriophages were associated with the overall status of the patient and mucositis development. Importantly, in both cohorts, high inter-individual but also high intra-individual variation in the prokaryotic communities were detected while the microeukaryotic community did not exhibit drastic changes. In conclusion, the employed integrated multi-omics analysis allowed detailed profiling of the GIT community including archaea, bacteria, eukaryotes and viruses as well as the functional potential including antibiotic resistance genes. In the future, analysis of the individual-specific processes within the GIT microbial community of patients throughout treatment might allow to adjust therapy regimens accordingly and improve the overall outcome of the therapy. [less ▲]

Detailed reference viewed: 258 (66 UL)
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See detailDynamic composition of solvers for coupled problems in DOLFINx
Rehor, Martin UL; Hale, Jack UL

Presentation (2021, March 22)

Recent developments in DOLFINx allow for the block assembly of linear algebraic systems arising from discretisations of coupled partial differential equations. Each algebraic block represents a subproblem ... [more ▼]

Recent developments in DOLFINx allow for the block assembly of linear algebraic systems arising from discretisations of coupled partial differential equations. Each algebraic block represents a subproblem associated with a coupling of the unknown fields. Designing and implementing robust and scalable solution and preconditioning strategies for block-structured linear systems is an active area of research. In this contribution we show how DOLFINx can now exploit one of the most significant features of PETSc; the dynamic composition of the hierarchical solver and preconditioner options at runtime, see Brown et al [1]. The idea is inspired by the work of Kirby and Mitchell [2] that was originally implemented in the Firedrake Project. One of the most significant benefits of the approach is the possibility to construct advanced preconditioners that require structure beyond a purely algebraic problem description, eg the pressure-convection-diffusion (PCD) approximation of the Schur complement for the Navier–Stokes equations, see Silvester et al [3]. We illustrate the capabilities of our implementation on examples ranging from incompressible flow of a viscous fluid, through temperature-driven convection, to flows described by rate-type viscoelastic fluid models. References [1] J. Brown, M. G. Knepley, D. A. May, L. C. McInnes, and B. Smith, "Composable Linear Solvers for Multiphysics," in 2012 11th International Symposium on Parallel and Distributed Computing, Munich, Germany, Jun. 2012, pp. 55–62, doi: 10.1109/ISPDC.2012.16. [2] R. C. Kirby and L. Mitchell, "Solver Composition Across the PDE/Linear Algebra Barrier," SIAM J. Sci. Comput., vol. 40, no. 1, pp. C76–C98, 2017, doi: 10.1137/17M1133208. [3] H. C. Elman, D. J. Silvester, and A. J. Wathen, Finite elements and fast iterative solvers: with applications in incompressible fluid dynamics. 2014, doi: 10.1093/acprof:oso/9780199678792.001.0001. Acknowledgements The present work is supported by the National Research Fund, Luxembourg in the frame of the Industrial Fellowship project RIFLE (13754363). The experiments presented in this work were carried out using the HPC facilities of the University of Luxembourg. [less ▲]

Detailed reference viewed: 68 (8 UL)
See detailDynamic context logic
Aucher, Guillaume UL; Grossi, Davide; Herzig, Andreas et al

in Logic, Rationality, and Interaction (2009)

Building on a simple modal logic of context, the paper presents a dynamic logic characterizing operations of contraction and expansion on theories. We investigate the mathematical properties of the logic ... [more ▼]

Building on a simple modal logic of context, the paper presents a dynamic logic characterizing operations of contraction and expansion on theories. We investigate the mathematical properties of the logic, and show how it can capture some aspects of the dynamics of normative systems once they are viewed as logical theories. [less ▲]

Detailed reference viewed: 30 (0 UL)
See detailDynamic context logic and its application to norm change
Aucher, Guillaume UL; Grossi, Davide; Herzig, Andreas et al

in Proceedings of Dagstuhl Seminar (2009, November 03), 09121

Building on a simple modal logic of context, the paper presents a dynamic logic characterizing operations of contraction and expansion on theories. We investigate the mathematical properties of the logic ... [more ▼]

Building on a simple modal logic of context, the paper presents a dynamic logic characterizing operations of contraction and expansion on theories. We investigate the mathematical properties of the logic, and use it to develop an axiomatic and semantic analysis of norm change in normative systems. The proposed analysis advances the state of the art by providing a formal semantics of norm-change which, at the same time, takes into account several different aspects of the phenomenon, such as permission and obligation dynamics, as well as the dynamics of classificatory rules. [less ▲]

Detailed reference viewed: 43 (1 UL)
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See detailDynamic controllers for column synchronization of rotation matrices: a QR-factorization approach
Thunberg, Johan UL; Markdahl, Johan UL; Goncalves, Jorge UL

in Automatica (2018), 93

In the multi-agent systems setting, this paper addresses continuous-time distributed synchronization of columns of rotation matrices. More precisely, k specific columns shall be synchronized and only the ... [more ▼]

In the multi-agent systems setting, this paper addresses continuous-time distributed synchronization of columns of rotation matrices. More precisely, k specific columns shall be synchronized and only the corresponding k columns of the relative rotations between the agents are assumed to be available for the control design. When one specific column is considered, the problem is equivalent to synchronization on the (d-1)-dimensional unit sphere and when all the columns are considered, the problem is equivalent to synchronization on SO(d). We design dynamic control laws for these synchronization problems. The control laws are based on the introduction of auxiliary variables in combination with a QR-factorization approach. The benefit of this QR-factorization approach is that we can decouple the dynamics for the $k$ columns from the remaining d-k ones. Under the control scheme, the closed loop system achieves almost global convergence to synchronization for quasi-strong interaction graph topologies. [less ▲]

Detailed reference viewed: 162 (2 UL)
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See detailDynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation.
He, Feng UL; Buer, Jan; Zeng, An-Ping et al

in Genome Biology (2007), 8(9), 181

BACKGROUND: The regulation of genes in multicellular organisms is generally achieved through the combinatorial activity of different transcription factors. However, the quantitative mechanisms of how a ... [more ▼]

BACKGROUND: The regulation of genes in multicellular organisms is generally achieved through the combinatorial activity of different transcription factors. However, the quantitative mechanisms of how a combination of transcription factors controls the expression of their target genes remain unknown. RESULTS: By using the information on the yeast transcription network and high-resolution time-series data, the combinatorial expression profiles of regulators that best correlate with the expression of their target genes are identified. We demonstrate that a number of factors, particularly time-shifts among the different regulators as well as conversion efficiencies of transcription factor mRNAs into functional binding regulators, play a key role in the quantification of target gene expression. By quantifying and integrating these factors, we have found a highly significant correlation between the combinatorial time-series expression profile of regulators and their target gene expression in 67.1% of the 161 known yeast three-regulator motifs and in 32.9% of 544 two-regulator motifs. For network motifs involved in the cell cycle, these percentages are much higher. Furthermore, the results have been verified with a high consistency in a second independent set of time-series data. Additional support comes from the finding that a high percentage of motifs again show a significant correlation in time-series data from stress-response studies. CONCLUSION: Our data strongly support the concept that dynamic cumulative regulation is a major principle of quantitative transcriptional control. The proposed concept might also apply to other organisms and could be relevant for a wide range of biotechnological applications in which quantitative gene regulation plays a role. [less ▲]

Detailed reference viewed: 121 (4 UL)
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See detailDynamic damage identification using linear and nonlinear testing methods on a two-span prestressed concrete bridge
Mahowald, Jean UL; Maas, Stefan UL; Scherbaum, Frank UL et al

in Proceedings of the Third International Symposium on Life-Cycle Civil Engineering, IALCCE’12 (2012)

Detailed reference viewed: 136 (37 UL)
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See detailDynamic Dependence and Diversification in Corporate Credit
Jin, Xisong UL

Scientific Conference (2015)

Detailed reference viewed: 57 (0 UL)
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See detailDynamic Dependence in Corporate Credit
Jin, Xisong UL; Christoffersen, Peter; Jacobs, Kris et al

E-print/Working paper (2013)

Detailed reference viewed: 100 (0 UL)
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See detailDynamic encounters between asylum applicants and the multilingual society of Luxembourg - linguistic repertoires built with truncated competences?
Kalocsanyiova, Erika UL

Scientific Conference (2016, October 05)

Our contribution aims at investigating the communication challenges brought by a rather abrupt and recent change in Luxembourg’s refugee intake patterns, reflected in the increased number and shifted ... [more ▼]

Our contribution aims at investigating the communication challenges brought by a rather abrupt and recent change in Luxembourg’s refugee intake patterns, reflected in the increased number and shifted geographic origin of international protection applicants. We have adopted a border studies approach to explore the new linguistic and social reality, which emerges through continuous interactions between the diverse, mobile and multilingual society of Luxembourg, on one hand, and on the other hand, the linguistic and cultural repertoires that recently arrived asylum seekers – mostly Syrians, Iraqis and Afghanis – bring to this context. We argue that theoretical and applied knowledge generated by previous research on multilingualism in cross-border regions is transferable to this new field of inquiry. [less ▲]

Detailed reference viewed: 58 (5 UL)
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See detailDynamic facial expression generation on hilbert hypersphere with conditional wasserstein generative adversarial nets
Otberdout, Naima; Daoudi, Mohamed; Kacem, Anis UL et al

in IEEE Transactions on Pattern Analysis and Machine Intelligence (2020)

In this work, we propose a novel approach for generating videos of the six basic facial expressions given a neutral face image. We propose to exploit the face geometry by modeling the facial landmarks ... [more ▼]

In this work, we propose a novel approach for generating videos of the six basic facial expressions given a neutral face image. We propose to exploit the face geometry by modeling the facial landmarks motion as curves encoded as points on a hypersphere. By proposing a conditional version of manifold-valued Wasserstein generative adversarial network (GAN) for motion generation on the hypersphere, we learn the distribution of facial expression dynamics of different classes, from which we synthesize new facial expression motions. The resulting motions can be transformed to sequences of landmarks and then to images sequences by editing the texture information using another conditional Generative Adversarial Network. To the best of our knowledge, this is the first work that explores manifold-valued representations with GAN to address the problem of dynamic facial expression generation. We evaluate our proposed approach both quantitatively and qualitatively on two public datasets; Oulu-CASIA and MUG Facial Expression. Our experimental results demonstrate the effectiveness of our approach in generating realistic videos with continuous motion, realistic appearance and identity preservation. We also show the efficiency of our framework for dynamic facial expression generation, dynamic facial expression transfer and data augmentation for training improved emotion recognition models. [less ▲]

Detailed reference viewed: 84 (6 UL)
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See detailThe dynamic genetic repertoire of microbial communities
Wilmes, Paul UL; Simmons, Sheri; Denef, Vincent J. et al

in FEMS Microbiology Reviews (2009), 33(1), 109-132

Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as ... [more ▼]

Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. In the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. A major unresolved question is how much of the observed variation is due to neutral vs. adaptive processes. Limited experimental data hint that some of this fine-scale variation may be in part functionally relevant, whereas sequence-based and modeling analyses suggest that much of it may be neutral. While methods for interpreting population genomic data are still in their infancy, we discuss current interpretations of existing datasets in the light of evolutionary processes and models. Finally, we highlight the importance of virus-host dynamics in generating and shaping within-population diversity. [less ▲]

Detailed reference viewed: 153 (1 UL)
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See detailDynamic Hedging and Extreme Asset Co-movements
Stefanova, Denitsa UL; Elkamhi, Redouane

E-print/Working paper (2014)

Detailed reference viewed: 136 (6 UL)
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See detailDynamic Hedging and Extreme Asset Co-movements
Stefanova, Denitsa UL; Elkamhi, Redouane

in Review of Financial Studies (2015), 28(3), 743-790

Detailed reference viewed: 88 (2 UL)
See detailThe dynamic implications of liberalizing global migration
Machado Carneiro, Joël UL

Scientific Conference (2015, August 26)

Detailed reference viewed: 48 (1 UL)
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See detailDynamic insights on transcription initiation and RNA processing during bacterial adaptation
Lacoux, Caroline; Fouquier d'Hérouël, Aymeric UL; Wessner- Le Bohec, Françoise et al

in RNA (2020)

Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental ... [more ▼]

Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled σE system in E. coli was coupled to our previously-described tagRNA-seq method to yield process kinetics information. Changes in transcription initiation frequencies (TIF) and RNA processing frequencies (PF) were followed using 5’ RNA tags. Changes in TIF showed a binary increased/decreased pattern that alternated between transcriptionally activated and repressed promoters, providing the bacterial population with transcriptional oscillation. PF variation fell into three categories of cleavage activity; i) constant and independent of RNA levels, ii) increased once RNA has accumulated, and iii) positively correlated to changes in TIF. This work provides a comprehensive and dynamic view of major events leading to transcriptomic reshaping during bacterial adaptation. It unveils an interplay between transcription initiation and the activity of specific RNA cleavage sites. This study utilized a well-known genetic system to analyze fundamental processes, and can serve as blueprint for comprehensive studies that exploit the RNA metabolism to decipher and understand bacterial gene expression control. [less ▲]

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See detailDynamic interplay of language policy, beliefs and pedagogy in a nursery class in Luxembourg
Kirsch, Claudine UL

Scientific Conference (2017, July 24)

Detailed reference viewed: 48 (1 UL)
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See detailDynamic interplay of language policy, beliefs and pedagogy in a nursery class in Luxembourg
Kirsch, Claudine UL

in Language and Education (2018), 32(5), 444-461

This presentation focuses on the relationship between the language policy, language ideologies and language practices in a nursery class in trilingual Luxembourg. Individual multilingualism is an ... [more ▼]

This presentation focuses on the relationship between the language policy, language ideologies and language practices in a nursery class in trilingual Luxembourg. Individual multilingualism is an educational goal in Luxembourg, a small country in central Europe, and, thus, children learn Luxembourgish from the compulsory nursery school, become literate in German in Year 1 and learn oral and written French from Year 2 and Year 3, respectively. Currently, 62.4% of the children do not speak Luxembourgish on school entry (MENJE 2016). Many speak Portuguese, French or a language of the Balkans. As a result, educational policies focus on the teaching of Luxembourgish from preschool, sometimes at the expense of other languages. Gretsch and Kirsch (2015) developed the app iTEO in order to promote innovative teaching methods that capitalize on the children’s diverse language resources and that promote a dynamic view of bilingualism. This ipad app, which allows for the recording and editing of oral speech, was designed with social-constructivist theories and Bakhtin’s theory of dialogism in mind. This case-study presents the ways in which a preschool teacher’s ideological beliefs influence a child’s language use over a period of two years leading to the child’s understanding of the legitimacy of translanguaging. The focus lies on the interplay between the educational policy focusing on the teaching of Luxembourgish, the teacher’s language ideologies rooted in her multilingual identity and in societal multilingualism, and the child’s experiences of separating languages at home (Kirsch, 2014). The data stem from a qualitative, longitudinal study using a multi-method approach. The study shows that dialogue between teachers, parents, children, policy-makers and researchers can contribute to shifting ideologies and to opening up dynamic languaging spaces. [less ▲]

Detailed reference viewed: 224 (31 UL)