A resource-frugal probabilistic dictionary and applications in (meta)genomics

Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing techniques, one must rely on extremely scalable methods and solutions. Indexing billions of objects is a task considered too expensive while being a fundamental need in this field. In this paper we propose a straightforward indexing structure that scales to billions of element and we propose two direct applications in genomics and metagenomics. We show that our proposal solves problem instances for which no other known solution scales-up. We believe that many tools and applications could benefit from either the fundamental data structure we provide or from the applications developed from this structure.Comment: Submitted to PSC 201

Restoring the Past: The Knitting Mills of Logan, Utah Circa 1904

Logan, Utah. 1904. I was not there. Nor could I have been. A trim, clean-shaven businessman crosses dirt-packet Main Street in the cold sunlight of early morning. It\u27s Monday, a new day, a new week for his knitting mill. He is tall and angular, wearing a brown suit and a round bowler hat. There\u27s a look of determination in his eyes, a fixed state at unseen hurdles ahead. He must be to work early. The girls will be arriving soon. He must check the knitting machines, run over the inventory, count out cash for the register, and prepare for another day of running the most successful knitting mill in Northern Utah. Assistant manager is an important job. He is... He is..

Les arboviroses tropicales émergentes en France (dengue et chikungunya) : étude du rôle du pharmacien d'officine dans la lutte anti-vectorielle (Thèse d'exercice de Pharmacie)

En 2005, l’épidémie de chikungunya qui a sévi sur l’île de la Réunion a marqué les esprits. Depuis, avec l’arrivée d’un moustique pouvant être le vecteur de cette maladie en France ; Aedes albopictus, la problématique s’est élargie. Venu initialement d’Italie, ce moustique se propage en effet le long du littoral méditerranéen français et peut véhiculer les virus de la dengue et du chikungunya pour les transmettre à l’homme. Pour éviter l’émergence de ces arboviroses, il faut donc lutter contre le moustique tigre sous deux aspects : l’aspect de la nuisance mais aussi et surtout, l’aspect de sa capacité et de sa compétence vectorielle. Les différents messages de la lutte anti-vectorielle peuvent apparaître ambigus et leur utilité est parfois remise en question. Ainsi, le pharmacien est un acteur de santé incontournable, sollicité par les populations des régions endémiques pour disposer de plus d’informations et savoir comment se protéger contre Aedes albopictus. Une étude a donc été réalisée pour réaliser un état des lieux des connaissances des pharmaciens d’officine dans ce domaine, dans la ville de Marseille. Or, les enseignements tirés de cette enquête ont été la mise en évidence des lacunes pouvant porter préjudice à la bonne information et donc éducation communautaire. Un plan d’actions est donc proposé pour améliorer la prise en charge

Navigating in a sea of repeats in RNA-seq without drowning

The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which transposable elements are one of the main examples. Most transcriptome assemblers are based on de Bruijn graphs and have no clear and explicit model for repeats in RNA-seq data, relying instead on heuristics to deal with them. The results of this work are twofold. First, we introduce a formal model for repre- senting high copy number repeats in RNA-seq data and exploit its properties for inferring a combinatorial characteristic of repeat-associated subgraphs. We show that the problem of identifying in a de Bruijn graph a subgraph with this charac- teristic is NP-complete. In a second step, we show that in the specific case of a local assembly of alternative splicing (AS) events, we can implicitly avoid such subgraphs. In particular, we designed and implemented an algorithm to efficiently identify AS events that are not included in repeated regions. Finally, we validate our results using synthetic data. We also give an indication of the usefulness of our method on real data

Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching

The exponential increase in publicly available sequencing data and genomic resources necessitates the development of highly efficient methods for data processing and analysis. Locality-sensitive hashing techniques have successfully transformed large datasets into smaller, more manageable sketches while maintaining comparability using metrics such as Jaccard and containment indices. However, fixed-size sketches encounter difficulties when applied to divergent datasets. Scalable sketching methods, such as Sourmash, provide valuable solutions but still lack resource-efficient, tailored indexing. Our objective is to create lighter sketches with comparable results while enhancing efficiency. We introduce the concept of Fractional Hitting Sets, a generalization of Universal Hitting Sets, which uniformly cover a specified fraction of the k-mer space. In theory and practice, we demonstrate the feasibility of achieving such coverage with simple but highly efficient schemes. By encoding the covered k-mers as super-k-mers, we provide a space-efficient exact representation that also enables optimized comparisons. Our novel tool, SuperSampler, implements this scheme, and experimental results with real bacterial collections closely match our theoretical findings. In comparison to Sourmash, SuperSampler achieves similar outcomes while utilizing an order of magnitude less space and memory and operating several times faster. This highlights the potential of our approach in addressing the challenges presented by the ever-expanding landscape of genomic data

Influence Of The Ti/Al Substitution On Ba/La Cationic Order In The Ba6-x-yLa8+2/3x+yTi18-yAlyO54 Solid Solution

The study of the Ba/La order in the Ba6-x-yLa8+2/3x+yTi18-y AlyO54 solid-solution was performed by X-ray diffraction on powders and single-crystals. The crystal structure of these phases belongs to the tetragonal tungsten bronze type, build on the basis of (3x3) TiO6 octahedron more than (2X2) (space group Pnma, a≈22.4Å, b≈7.7Å, c≈12.2Å). Two structural models were built, corresponding to two different orders within the structure. The model I, of formula [Ba4] A2 [Ba2-z La2x/3+y+q  q’ ]A1'[La8-q' q] A1Ti18-y AlyO54, corresponds to a model associated to infinite perovskite rows parallels to Oy axis, build on the basis of (3X3) TiO6 octahedron. The model II, with formula [Ba6-z z-2] A2 [La8+2x/3+y 2-(2x/3)-y] A1’A1Ti18-yAlyO54, can be described on the basis of three perovskite octahedron layers parallels to xOz plane.The study of the Ba/La order in the Ba6-x-yLa8+2/3x+yTi18-y AlyO54 solid-solution was performed by X-ray diffraction on powders and single-crystals. The crystal structure of these phases belongs to the tetragonal tungsten bronze type, build on the basis of (3x3) TiO6 octahedron more than (2X2) (space group Pnma, a≈22.4Å, b≈7.7Å, c≈12.2Å). Two structural models were built, corresponding to two different orders within the structure. The model I, of formula [Ba4] A2 [Ba2-z La2x/3+y+q  q’ ]A1'[La8-q' q] A1Ti18-y AlyO54, corresponds to a model associated to infinite perovskite rows parallels to Oy axis, build on the basis of (3X3) TiO6 octahedron. The model II, with formula [Ba6-z z-2] A2 [La8+2x/3+y 2-(2x/3)-y] A1’A1Ti18-yAlyO54, can be described on the basis of three perovskite octahedron layers parallels to xOz plane

Citizen Brown, Race for Profit : race et citoyenneté aux xxe et xxie siècles. Présentations d’ouvrages

Organisées tous les deux ans, les rencontres de la Society of American City and Regional Planning History (SACRPH) rassemblent sur plusieurs jours près de deux cents spécialistes de l’aménagement urbain états-unien et international. Pour leur dix-huitième édition, elles se sont tenues dans le quartier de Crystal City d’Arlington, dans la banlieue de Washington, DC (et dont on pourra retrouver une présentation vidéo d’introduction ici, et le programme complet des interventions ici). Des acteu..

Avaliação de indicadores de desempenho na análise de importância de segmentos de uma rede viária

A identificação dos segmentos críticos da rede viária é um conhecimento básico que todo planejador de transportes deve ter sobre a rede viária. É inevitável a ocorrência de incidentes e eventos de redução da capacidade nos elementos da rede. O efeito de acidentes e obstruções em segmentos críticos da rede ocasionam impactos que prejudicam o desempenho da rede. Este estudo foi desenvolvido com o apoio do modelo de alocação de tráfego do software VISUM (versão 2015) e propõe um método para determinar a importância de cada segmento da rede viária, a identificação de segmentos críticos da rede e a avaliação de sua obstrução de forma estática e dinâmica. Para isso, são utilizados diversos indicadores de desempenho da rede viária. O método foi aplicado na região do Litoral Norte do Rio Grande do Sul, utilizando os dados de tráfego fornecidos pela CONCEPA TRIUNFO, DAER e DNIT. A determinação da importância de cada segmento decorreu da avaliação do impacto na rede causado pela obstrução do próprio segmento. Através do método proposto neste estudo foi possível identificar o segmento crítico da rede viária estudada e, de forma qualitativa, verificar a extensão da obstrução desse segmento nas análises estática e dinâmica Verificou-se que o indicador diferença do total de tempo despendido na rede é o indicador que mais apresenta crescimento com o incremento da demanda, não apresenta alterações de priorização dos segmentos frente a variações de intensidade e sentido da demanda. Os resultados deste estudo mostraram que o segmento crítico da rede pertence a BR-101 entre os municípios de Osório e Terra de Areia. O método de hierarquização proposto independe do sentido e da intensidade da demanda, e está sujeito a mais de uma métrica para avaliar o segmento crítico. Estes resultados podem subsidiar o planejamento de transportes, identificando trechos críticos da rede viária que necessitam de mais atenção dos gestores e apontando medidas de operação no caso de eventos disruptivos nos trechos críticos.Identifying the most important link of the network is essential knowledge that the transport planners should have over the network. Incidents and events of capacity reduction in network elements are inevitable. The effect of accidents and obstructions on critical network links causes impacts that hamper network performance. This study was developed with support of VISUM (version 2015) traffic assignment model software with proposes a method to determinate each network link importance level, to identify the critical link and to measure the critical link blockage impact on network. For this, several road network performance indicators are used. The method was applied in the North Coast region of Rio Grande do Sul, using traffic data provided by CONCEPA TRIUNFO, DAER and DNIT. The link level importance in define from the own link impact due its obstruction. The proposed method identified the most critical link of the studied network and verified the qualitative impact of its obstruction extent in the static and dynamic assignment analyses It was verified that the measure total spent time difference in the network is the most sensible measure that growth with a demand increase, this measure does not present changes the link importance rank against variations of intensity and direction of demand flow changes. The results of this study show that the critical link of the network belongs to the BR-101 highway between the municipalities of Osório and Terra de Areia. The proposed hierarchical method developed with several metrics measures fond the critical link in an independent demand direction and intensity analysis. The findings may support transport planners to identify the most critical arc of a network. To better implement resources of road management and repairs. Also identify where the operation measures may be implanted in face a disruptive event on a critical link