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See detailDMFSGD: A Decentralized Matrix Factorization Algorithm for Network Distance Prediction
Liao, Yongjun ULg; Du, Wei; Geurts, Pierre ULg et al

Report (2012)

The knowledge of end-to-end network distances is essential to many Internet applications. As active probing of all pairwise distances is infeasible in large-scale networks, a natural idea is to measure a ... [more ▼]

The knowledge of end-to-end network distances is essential to many Internet applications. As active probing of all pairwise distances is infeasible in large-scale networks, a natural idea is to measure a few pairs and to predict the other ones without actually measuring them. This paper formulates the distance prediction problem as matrix completion where unknown entries of an incomplete matrix of pairwise distances are to be predicted. The problem is solvable because strong correlations among network distances exist and cause the constructed distance matrix to be low rank. The new formulation circumvents the well-known drawbacks of existing approaches based on Euclidean embedding. A new algorithm, so-called Decentralized Matrix Factorization by Stochastic Gradient Descent (DMFSGD), is proposed to solve the network distance prediction problem. By letting network nodes exchange messages with each other, the algorithm is fully decentralized and only requires each node to collect and to process local measurements, with neither explicit matrix constructions nor special nodes such as landmarks and central servers. In addition, we compared comprehensively matrix factorization and Euclidean embedding to demonstrate the suitability of the former on network distance prediction. We further studied the incorporation of a robust loss function and of non-negativity constraints. Extensive experiments on various publicly-available datasets of network delays show not only the scalability and the accuracy of our approach but also its usability in real Internet applications. [less ▲]

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See detailThe DmpA aminopeptidase from Ochrobactrum anthropi LMG7991 is the prototype of a new terminal nucleophile hydrolase family.
Fanuel, L; Goffin, Colette ULg; Cheggour, A et al

in Biochemical Journal (1999), 341(Pt 1), 147-55

The DmpA (d-aminopeptidase A) protein produced by Ochrobactrum anthropi hydrolyses p-nitroanilide derivatives of glycine and d-alanine more efficiently than that of l-alanine. When regular peptides are ... [more ▼]

The DmpA (d-aminopeptidase A) protein produced by Ochrobactrum anthropi hydrolyses p-nitroanilide derivatives of glycine and d-alanine more efficiently than that of l-alanine. When regular peptides are utilized as substrates, the enzyme behaves as an aminopeptidase with a preference for N-terminal residues in an l configuration, thus exemplifying an interesting case of stereospecificity reversal. The best-hydrolysed substrate is l-Ala-Gly-Gly, but tetra- and penta-peptides are also efficiently hydrolysed. The gene encodes a 375-residue precursor, but the active enzyme contains two polypeptides corresponding to residues 2-249 (alpha-subunit) and 250-375 (beta-subunit) of the precursor. Residues 249 and 250 are a Gly and a Ser respectively, and various substitutions performed by site-directed mutagenesis result in the production of an uncleaved and inactive protein. The N-terminal Ser residue of the beta-subunit is followed by a hydrophobic peptide, which is predicted to form a beta-strand structure. All these properties strongly suggest that DmpA is an N-terminal amidohydrolase. An exploration of the databases highlights the presence of a number of open reading frames encoding related proteins in various bacterial genomes. Thus DmpA is very probably the prototype of an original family of N-terminal hydrolases. [less ▲]

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See detailDMPO for quantitative measurements of singlet oxygen production?
Damoiseau, X.; Heyne, B.; Hoebeke, Maryse ULg

Conference (2002)

Detailed reference viewed: 29 (4 ULg)
See detailA DMS platform for monitoring and analysing large distribution networks
Rousseaux, Patricia ULg; Quoilin, Isabelle; Van Cutsem, Thierry ULg et al

in Proceedings of the 15th International Conference on Electricity Distribution (1999)

Detailed reference viewed: 24 (0 ULg)
See detailDMSP cell quota and the conversion into DMS by key Southern North Sea spring diatoms (Skeletonema costatum and Chaetoceros socialis) and Phaeocystis globosa
Speeckaert, Gaëlle ULg; Lancelot, Christiane; Borges, Alberto ULg et al

Poster (2014, May)

DMSP cell quota and the conversion into DMS by key Southern North Sea spring diatoms (Skeletonema costatum and Chaetoceros socialis) and Phaeocystis globosa

Detailed reference viewed: 32 (1 ULg)
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See detailThe DNA 3'-phosphatase and 5'-hydroxyl kinase of rat liver chromatin
Habraken, Yvette ULg; Verly, Walter

in FEBS Letters (1983), 160(1,2), 46-50

Detailed reference viewed: 15 (5 ULg)
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See detailDNA and RNA distribution in the nucleus of trypanosomatids: a cytochemical and immunocytochemical study
Motta, M C M; De Souza, W; Thiry, Marc ULg

in Memorias do Instituto Oswaldo Cruz (1999), 94

Detailed reference viewed: 12 (2 ULg)
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See detailDNA bending by the silencer protein NeP1 is modulated by TR and RXR.
Arnold, R.; Burcin, M.; Kaiser, Bruno ULg et al

in Nucleic Acids Research (1996), 24(14), 2640-7

NeP1 binds to the F1 silencer element of the chicken lysozyme gene and, in the presence of TR, v-ERBA or RAR, synergistically represses transcriptional activity. This repression involves a silencing ... [more ▼]

NeP1 binds to the F1 silencer element of the chicken lysozyme gene and, in the presence of TR, v-ERBA or RAR, synergistically represses transcriptional activity. This repression involves a silencing mechanism acting independently of the relative promoter position. Here we show that NeP1 alone can induce a significant directed bend on DNA. The chicken homologue of human NeP1, CTCF, shows identical binding and bending properties. In contrast, the isolated DNA binding domain of CTCF efficiently binds DNA, but fails to confer bending. Similarly, the TR-RXR hetero- or homodimer, binding adjacent to NeP1 at the F2 sequence, do not show significant DNA bending. The binding of the T3 ligand to TR changes neither the magnitude nor the direction of the NeP1 induced bend. However, when all factors are bound simultaneously as a quaternary complex, the TR-RXR heterodimer changes the location of the bend center, the flexure angle and the bending direction. [less ▲]

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See detailDNA binding activity of transcription factors in bronchial cells of horses with recurrent airway obstruction.
Couetil, Laurent L; Art, Tatiana ULg; De Moffarts, Brieuc et al

in Veterinary Immunology and Immunopathology (2006), 113(1-2), 11-20

Horses with recurrent airway obstruction (RAO) present many similarities with human asthmatics including airway inflammation, hyperresponsiveness, reversible obstruction, and increased NF-kappaB ... [more ▼]

Horses with recurrent airway obstruction (RAO) present many similarities with human asthmatics including airway inflammation, hyperresponsiveness, reversible obstruction, and increased NF-kappaB expression. Studies in experimental asthma models have shown that transcriptions factors such as activator protein-1 (AP-1), GATA-3, cyclic AMP response element binding protein (CREB) and CAAT/enhancer binding protein (C/EBP) may also play an important role in airway inflammation. The purpose of this study was to measure DNA binding activity of these transcription factors in the airways of horses with RAO and to compare it to pulmonary function and bronchoalveolar lavage fluid (BALF) cytology. Seven horses with RAO and six control animals were studied during a moldy hay challenge and after 2 months at pasture. Pulmonary function, BALF cytology and transcription factors' activities in bronchial brushings were measured during hay and pasture exposures. During moldy hay challenge, RAO-affected horses developed severe airway obstruction and inflammation and a significantly higher airway AP-1 binding activity than in controls. After 2 months on pasture, pulmonary function and airway AP-1 binding activity were not different between RAO and control horses. The DNA binding activity of CREB in airways of RAO-affected horses increased significantly after 2 months at pasture and became higher than in controls. A significant positive correlation was detected between AP-1 binding activity and indicators of airway obstruction and inflammation. Airway GATA-3, CEBP and CREB binding activities were negatively correlated with indices of airway obstruction. However, contrarily to CREB binding activity, GATA-3 and CEBP binding activities were not different between RAO and control horses and were unaffected by changes in environment. These data support the view that AP-1 and CREB play a role in modulating airway inflammation in horses with RAO [less ▲]

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See detailDNA Computing Circuits Using Libraries of DNAzyme Subunits
Elbaz, J.; Lioubashevskia, O.; Remacle, Françoise ULg et al

in Nature Nanotechnology (2010), 5

Detailed reference viewed: 51 (1 ULg)
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See detailDNA Damage and Thyroid Cancer
Neelature Sriramareddy, Sathyanarayana ULg; Staumont, Bernard ULg; Willems, Luc ULg

in GIGADay-2014 (2014)

Detailed reference viewed: 12 (2 ULg)
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See detailDNA fingerprinting in domestic animals using four different minisatellite probes.
Georges, Michel ULg; Lequarré, Anne-Sophie ULg; Castelli, M. et al

in CytoGenetics & Cell Genetics (1988), 47(3), 127-31

Four probes known to allow DNA fingerprinting in the human (M13, Jeffreys' core sequence, the human alpha globin hypervariable region [HVR], and a mouse probe related to the Drosophila Per gene) were ... [more ▼]

Four probes known to allow DNA fingerprinting in the human (M13, Jeffreys' core sequence, the human alpha globin hypervariable region [HVR], and a mouse probe related to the Drosophila Per gene) were checked for their ability to reveal "genetic bar codes" in cattle, horses, pigs, dogs, chickens, and a European cyprinid fish, the barbel (Barbus barbus L.). Individual-specific patterns were obtained in cattle using M13, Jeffreys' core sequence, and the alpha globin HVR, in horses, dogs, and pigs using M13, Jeffreys' core sequence, and the Per probe, and in chicken and fish using the four different probes. Although we observed a considerable heterogeneity in the extent of interindividual variation, depending on the particular probe-species combination, the fingerprints are polymorphic enough to be used efficiently in animal identification, paternity testing, and as a source of genetic markers for linkage analysis. These markers should substantially accelerate the mapping of genes affecting economically important traits. [less ▲]

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See detailDNA Fingerprinting in Man Using a Mouse Probe Related to Part of the Drosophila 'Per' Gene
Georges, Michel ULg; Cochaux, P.; Lequarré, Anne-Sophie ULg et al

in Nucleic Acids Research (1987), 15(17), 7193

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See detailDNA fingerprinting using Diversilab system for genotyping characterization of Microsporum audouinii and Trichophyton violaceum
SACHELI, Rosalie ULg; DIMO, Lauryl; GRAIDE, Hélène ULg et al

in Mycoses (2013, October 01), 56(Supplement S3), 99

Objectives: To investigate the epidemiological determinants responsible for the high number of anthropophilic dermatophytes received by the National Reference Center for Mycosis of Liege (NRCL) during the ... [more ▼]

Objectives: To investigate the epidemiological determinants responsible for the high number of anthropophilic dermatophytes received by the National Reference Center for Mycosis of Liege (NRCL) during the year 2012. To perform a genotypic characterization by the Diversilab® system focusing on the two main isolated species, Microsporum audouinii and Trichophyton violaceum. To present a preliminary study preceding the national survey launched in 2013. Methods: A total of 51 strains of M. audouinii (50 clinical + 1 reference (ref.) strains) and 15 strains of T. violaceum (14 clinical + 1 ref. strain) originating from different locations through Belgium were included in the study. The fungal strains were first cultivated on Malt agar, then sub-cultured in Sabouraud liquid medium (Fluka). The grown mycelium was processed for DNA extraction following recommendations of the manufacturer (Ultra Clean® DNA Microbial isolation kit, MoBio laboratories). Genotypic analysis was performed using the DiversiLab® system (BioMérieux) for DNA fingerprinting and analysis. Results: Regarding M. audouinii, four different genotypic groups of strains were separated. Group 1 includes 11 strains and is only found in the Liège surroundings. Group 2 includes only one strain with little differences compared to group 1 and collected from the Liège area. These two groups may be related to each other. Group 3 contains 36 strains and the reference strain. This genotype is distributed in different Belgium locations. The last group, group 4, contains only 3 isolates sharing low similarities in comparison with the 3 other groups. Concerning T. violaceum, 6 different genotypic groups with a mixed geographical distribution were determined. Group 1 includes 8 clinical isolates and the ref. strain. The other five isolates are all different and seem not to be related to each other. Conclusion: The automated typing DiversiLab® system proved to be an easy and efficient method to investigate the molecular epidemiology of dermatophytes infections. Preliminary results of the study show that, through Belgium, several groups of isolates co-exist for M. audouinii and T. violaceum providing evidence of genetic heterogeneity. This variation can be related to acquired mutations due to environmental adaptation. Further investigations are necessary to better understand the impact of this genotypic variation. [less ▲]

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See detailDNA immunisation. New histochemical and morphometric data.
Ehirchiou, D.; Zorzi, Willy ULg; Biemans, R. et al

in European Journal of Histochemistry (2002), 46(3), 215-22

Splenic germinal center reactions were measured during primary response to a plasmidic DNA intramuscular injection. Cardiotoxin-pretreated Balb/c mice were immunized with DNA plasmids encodmg or not the ... [more ▼]

Splenic germinal center reactions were measured during primary response to a plasmidic DNA intramuscular injection. Cardiotoxin-pretreated Balb/c mice were immunized with DNA plasmids encodmg or not the SAG1 protein, a membrane antigen of Toxoplasma gondii. Specific anti-SAG1 antibodies were detected on days 16 and 36 after injection of coding plasmids. The results of ELISAs showed that the SAG1-specific antibodies are of the IgG2a class. Morphometric analyses were done on serial immunostained cryosections of spleen and draining or non-draining lymph nodes. This new approach made it possible to evaluate the chronological changes induced by DNA immunisation in the germinal centres (in number and in size). Significant increases in the number of germinal centres were measured in the spleen and only in draining lymph nodes after plasmid injection, the measured changes of the germinal centers appeared to result from the adjuvant stimulatory effect of the plasmidic DNA since both the coding and the noncoding plasmid DNA induced them. No measurable changes were recorded in the T-dependent zone of lymph organs. [less ▲]

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See detailDNA immunization with plasmids encoding fusion and nucleocapsid proteins of bovine respiratory syncytial virus induces a strong cell-mediated immunity and protects calves against challenge.
Boxus, Mathieu ULg; Tignon, Marylene; Roels, Stefan et al

in Journal of Virology (2007), 81(13), 6879-89

Respiratory syncytial viruses (RSV) are one of the most important respiratory pathogens of humans and cattle, and there is currently no safe and effective vaccine prophylaxis. In this study, we designed ... [more ▼]

Respiratory syncytial viruses (RSV) are one of the most important respiratory pathogens of humans and cattle, and there is currently no safe and effective vaccine prophylaxis. In this study, we designed two codon-optimized plasmids encoding the bovine RSV fusion (F) and nucleocapsid (N) proteins and assessed their immunogenicity in young calves. Two administrations of both plasmids elicited low antibody levels but primed a strong cell-mediated immunity characterized by lymphoproliferative response and gamma interferon production in vitro and in vivo. Interestingly, this strong cellular response drastically reduced viral replication, clinical signs, and pulmonary lesions after a highly virulent challenge. Moreover, calves that were further vaccinated with a killed-virus vaccine developed high levels of neutralizing antibody and were fully protected following challenge. These results indicate that DNA vaccination could be a promising alternative to the classical vaccines against RSV in cattle and could therefore open perspectives for vaccinating young infants. [less ▲]

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See detailDNA in chromatin: from genome-wide sequence analysis to the modelling of replication in mammals
Arbeodo, Alain; d'Aubenton-Carafa, Y.; Audit, B. et al

in Advances in Chemical Physics (2006), 135

Understanding how chromatin is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. In that context ... [more ▼]

Understanding how chromatin is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. In that context the role of the DNA sequence itself in these condensation- decondensation processes is still debated. In this chapter, we explore large-scale nucleotide compositional fluctuations along the human genome through the optics of the wavelet transform microscope. Analysis of the GC content and of the TA and GC skews re- veals the existence of rhythms with characteristic fundamental frequencies that enlighten a remarkable cooperative organization of gene location and orientation. We describe a multi-scale methodology that allows us to predict 1012 replication origins in the 22 hu- man autosomal chromosomes. We present a model of replication with well-positioned replication origins and random termination sites that accounts for the highly relaxational nature of the oscillations observed in the skew profiles. We emphasize these putative replication initiation zones as regions where the chromatin fiber is likely to be more open so that DNA be more easily accessible. We show that, in the crowded environment of the cell nucleus, the presence of these intrinsic decondensed structural defects actually pre- disposes the fiber to spontaneously form multi-looped rosette-like structures that provide an attractive description of genome organization into replication foci that are observed in interphase mammalian nuclei as stable autonomous chromatin domains favoring com- partmentalized DNA replication and gene expression. New experimental perspectives are discussed. [less ▲]

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