Compression guidée par automate et noyaux rationnels

Due to the expansion of datas, compression algorithms are now crucial algorithms. We address here the problem of finding an optimal compression algorithm with respect to a given Markovian source. To this purpose, we extend the classical Huffman algorithm. The kernels are popular methods to measure the similarity between words for classication and learning. We generalize the definition of rational kernels in order to apply kernels to the comparison of languages. We study this generalization for factor and subsequence kerneland prove that these kernels are defined for parameters chosen in an appropriate interval. We give different methods to build weighted transducers which compute these kernelsEn raison de l'expansion des données, les algorithmes de compression sont désormais cruciaux. Nous abordons ici le problème de trouver des algorithmes de compression optimaux par rapport à une source de Markov donnée. A cet effet, nous étendons l'algorithme de Huffman classique. Pour se faire premièrement on applique Huffman localement à chaque état de la source Markovienne, en donnant le résultat de l'efficacité obtenue pour cet algorithme. Mais pour bien approfondir et optimiser quasiment l'efficacité de l'algorithme, on donne un autre algorithme qui est toujours appliqué localement à chaque états de la source Markovienne, mais cette fois ci en codant les facteurs partant de ces états de la source Markovienne de sorte à ce que la probabilité du facteur soit une puissance de 1/2 (sachant que l'algorithme de Huffman est optimal si et seulement si tous les symboles à coder ont une probabilité puissance de 1/2). En perspective de ce chapitre on donne un autre algorithme (restreint à la compression de l'étoile) pour coder une expression à multiplicité, en attendant dans l'avenir à coder une expression complèt

Picometer resolution profilometer for hollow-core fiber surface roughness characterization

We build a picometer-sensitivity optical surface-profiler based on polarization-interferometry. The profilometer is design to measure surface roughness profiles of HCPCF. Two HCPCF categories with different fabrication processes were characterized. We observe that for HCPCFs fabricated the new process exhibit a reduction of rms core-surface roughness rms by a factor of close to 3 relative to the surface capillary wave thermodynamic limit, and thus explaining the record loss achieved in the VIS-UV range achieved with these fibers

Pre-treatment and extraction techniques for recovery of added value compounds from wastes throughout the agri-food chain

The enormous quantity of food wastes discarded annually force to look for alternatives for this interesting feedstock. Thus, food bio-waste valorisation is one of the imperatives of the nowadays society. This review is the most comprehensive overview of currently existing technologies and processes in this field. It tackles classical and innovative physical, physico-chemical and chemical methods of food waste pre-treatment and extraction for recovery of added value compounds and detection by modern technologies and are an outcome of the COST Action EUBIS, TD1203 Food Waste Valorisation for Sustainable Chemicals, Materials and Fuels

Investigating the function of cis-regulatory elements for Runx1

Detection of nucleotide sequence variations in patients of some diseases, provides strong evidence as to which genes and regulatory elements play a critical role in vivo. Acute Myeloid Leukaemia (AML) is a fast acting blood cancer acquired in the myeloid lineage. It can be caused by a number of genetic mutations or chromosome translocations, many of which are prognostically informative. However, because the molecular events that lead to the development and pathology of this leukaemia have thus far not been completely defined, difficulties arise in providing prognoses to AML patients without well-known mutations. Although AML subtypes are highly variable, the outlook is poor, with the majority of patients dying from the disease. The developmental transcription factor RUNX1/AML1 is a well-known leukaemia-associated gene. Runx1 is an important regulator of haematopoiesis in vertebrates; it is crucial for early myeloid differentiation, and plays a vital role in adult blood development. Disruptions to the RUNX1 gene are frequently associated with AML. Despite the well-established role of RUNX1 in haematopoiesis and disease contribution, the cis-regulatory mechanisms that modulate RUNX1 require further elucidation. In cases where no mutation is found in the coding sequence, there may instead be mutations in regulatory sequence, for example conserved non protein-coding DNA elements (CNEs) that affect gene function. Several research groups have identified an intronic Runx1 enhancer in mice, Runx1 +24 mouse conserved non-coding element (mCNE). The discovery of +24 mCNE as a haemogenic endothelial cell-specific enhancer in mouse and zebrafish embryos provided an insight into a mechanism for the tissue-specific transcriptional regulation of Runx1. Ng et al., (2010) then used comparative genomics to identify ten further putative Runx1 cis-regulatory elements. In light of the identified +24 enhancer, this project set out to investigate the functions other mCNEs detected by Ng et al., (2010). From the ten putative mCNEs described by Ng et al., (2010), five were selected for further investigation, with +24 acting as a positive control (-368, -101, +58.5, +110, +110.5-2 mCNEs). To investigate the putative cis-regulatory role of previously identified mCNEs in vivo, reporter constructs were used in zebrafish embryos, as well as human and mice cell lines. These reporter constructs provided evidence that the selected mCNEs do not act as ‘insulators’, which block transcription. However, potential enhancer activity was observed in the zebrafish assays from four of the mCNEs (-368, -101, +110, +24). Cell-specific enhancer assays indicated that one of the mCNEs, +110, might act as a heart specific enhancer, while another (-368 mCNE) could represent a blood specific enhancer. Cell culture reporter assays confirmed the enhancer activity of the +24 and +110 mCNEs. Further studies are required to validate functional roles of the other mCNEs and their interaction with Runx1. This study has provided novel evidence that +110 mCNE may act as a heart specific enhancer of Runx1, and showed that none of the mCNEs act as insulators. Preliminary data from zebrafish in this project suggests that further analysis of the mCNEs will provide insight into the elaborate orchestration of Runx1 regulation, as well as elucidate the genetic roles of RUNX1 and cis-regulatory elements in AML development

Compression guided by automata and rational kernels

En raison de l'expansion des données, les algorithmes de compression sont désormais cruciaux. Nous abordons ici le problème de trouver des algorithmes de compression optimaux par rapport à une source de Markov donnée. A cet effet, nous étendons l'algorithme de Huffman classique. Pour se faire premièrement on applique Huffman localement à chaque état de la source Markovienne, en donnant le résultat de l'efficacité obtenue pour cet algorithme. Mais pour bien approfondir et optimiser quasiment l'efficacité de l'algorithme, on donne un autre algorithme qui est toujours appliqué localement à chaque états de la source Markovienne, mais cette fois ci en codant les facteurs partant de ces états de la source Markovienne de sorte à ce que la probabilité du facteur soit une puissance de 1/2 (sachant que l'algorithme de Huffman est optimal si et seulement si tous les symboles à coder ont une probabilité puissance de 1/2). En perspective de ce chapitre on donne un autre algorithme (restreint à la compression de l'étoile) pour coder une expression à multiplicité, en attendant dans l'avenir à coder une expression complèteDue to the expansion of datas, compression algorithms are now crucial algorithms. We address here the problem of finding an optimal compression algorithm with respect to a given Markovian source. To this purpose, we extend the classical Huffman algorithm. The kernels are popular methods to measure the similarity between words for classication and learning. We generalize the definition of rational kernels in order to apply kernels to the comparison of languages. We study this generalization for factor and subsequence kerneland prove that these kernels are defined for parameters chosen in an appropriate interval. We give different methods to build weighted transducers which compute these kernel

Investigating the function of cis-regulatory elements for Runx1

Detection of nucleotide sequence variations in patients of some diseases, provides strong evidence as to which genes and regulatory elements play a critical role in vivo. Acute Myeloid Leukaemia (AML) is a fast acting blood cancer acquired in the myeloid lineage. It can be caused by a number of genetic mutations or chromosome translocations, many of which are prognostically informative. However, because the molecular events that lead to the development and pathology of this leukaemia have thus far not been completely defined, difficulties arise in providing prognoses to AML patients without well-known mutations. Although AML subtypes are highly variable, the outlook is poor, with the majority of patients dying from the disease. The developmental transcription factor RUNX1/AML1 is a well-known leukaemia-associated gene. Runx1 is an important regulator of haematopoiesis in vertebrates; it is crucial for early myeloid differentiation, and plays a vital role in adult blood development. Disruptions to the RUNX1 gene are frequently associated with AML. Despite the well-established role of RUNX1 in haematopoiesis and disease contribution, the cis-regulatory mechanisms that modulate RUNX1 require further elucidation. In cases where no mutation is found in the coding sequence, there may instead be mutations in regulatory sequence, for example conserved non protein-coding DNA elements (CNEs) that affect gene function. Several research groups have identified an intronic Runx1 enhancer in mice, Runx1 +24 mouse conserved non-coding element (mCNE). The discovery of +24 mCNE as a haemogenic endothelial cell-specific enhancer in mouse and zebrafish embryos provided an insight into a mechanism for the tissue-specific transcriptional regulation of Runx1. Ng et al., (2010) then used comparative genomics to identify ten further putative Runx1 cis-regulatory elements. In light of the identified +24 enhancer, this project set out to investigate the functions other mCNEs detected by Ng et al., (2010). From the ten putative mCNEs described by Ng et al., (2010), five were selected for further investigation, with +24 acting as a positive control (-368, -101, +58.5, +110, +110.5-2 mCNEs). To investigate the putative cis-regulatory role of previously identified mCNEs in vivo, reporter constructs were used in zebrafish embryos, as well as human and mice cell lines. These reporter constructs provided evidence that the selected mCNEs do not act as ‘insulators’, which block transcription. However, potential enhancer activity was observed in the zebrafish assays from four of the mCNEs (-368, -101, +110, +24). Cell-specific enhancer assays indicated that one of the mCNEs, +110, might act as a heart specific enhancer, while another (-368 mCNE) could represent a blood specific enhancer. Cell culture reporter assays confirmed the enhancer activity of the +24 and +110 mCNEs. Further studies are required to validate functional roles of the other mCNEs and their interaction with Runx1. This study has provided novel evidence that +110 mCNE may act as a heart specific enhancer of Runx1, and showed that none of the mCNEs act as insulators. Preliminary data from zebrafish in this project suggests that further analysis of the mCNEs will provide insight into the elaborate orchestration of Runx1 regulation, as well as elucidate the genetic roles of RUNX1 and cis-regulatory elements in AML development

Factor and Subsequence Kernels and Signatures of Rational Languages

International audienceThe kernels are popular methods to measure the similarity between words for classification and learning. We generalize the definition of rational kernels in order to apply kernels to the comparison of languages. We study this generalization for factor and subsequence kernels and prove that these kernels are defined for parameters chosen in an appropriate interval. We give different methods to build weighted transducers which compute these kernels

Transcriptional Regulation of RUNX1: An Informatics Analysis

The RUNX1/AML1 gene encodes a developmental transcription factor that is an important regulator of haematopoiesis in vertebrates. Genetic disruptions to the RUNX1 gene are frequently associated with acute myeloid leukaemia. Gene regulatory elements (REs), such as enhancers located in non-coding DNA, are likely to be important for Runx1 transcription. Non-coding elements that modulate Runx1 expression have been investigated over several decades, but how and when these REs function remains poorly understood. Here we used bioinformatic methods and functional data to characterise the regulatory landscape of vertebrate Runx1. We identified REs that are conserved between human and mouse, many of which produce enhancer RNAs in diverse tissues. Genome-wide association studies detected single nucleotide polymorphisms in REs, some of which correlate with gene expression quantitative trait loci in tissues in which the RE is active. Our analyses also suggest that REs can be variant in haematological malignancies. In summary, our analysis identifies features of the RUNX1 regulatory landscape that are likely to be important for the regulation of this gene in normal and malignant haematopoiesis