An ExpSpace Tableau-based Algorithm for SHOIQ

In this work, we propose an ExpSpace tableau-based algorithm for deciding consistency of a knowledge base in the description logic SHOIQ. The construction of this algorithm is founded on the standard tableau-based method for SHOIQ and the technique used for designing a NExpTime algorithm for the two-variable fragment of first-order logic with counting quantifiers C^2.Cer article propose un algorithme ExpSpace basé sur tableaux pour vérifier la cohérence d'une base de connaissances en SHOIQ

Enhancement of pure titanium localized corrosion resistance by anodic oxidation

The corrosion behavior of commercially pure titanium (UNS R50400) was investigated in presence of aggressive, bromides containing, species; reported to cause severer localized corrosion compared to chlorides. To enhance localized corrosion resistance of the metal, several surface treatments were performed. Samples anodized at potentials between 10 V and 200 V were characterized in term of oxide thickness and morphology and tested with potentiodynamic analyses in NH4Br. This treatment was found to greatly enhance corrosion resistance of titanium but it suffers localized removal of the oxide due to wrong handling of the part before their installation. For this reason, another treatment, suitable for in-situ surface recovering was developed through chemical oxidation in NaOH 10 M

Genoma Humano. Aspectos estructurales

Guillermo Lamolle: Laboratorio de Organización y Evolución del Genoma, Unidad de Genómica Evolutiva, Facultad de Ciencias, Montevideo, Uruguay.-- Héctor Musto: Laboratorio de Organización y Evolución del Genoma, Unidad de Genómica Evolutiva, Facultad de Ciencias, Montevideo, Uruguay.-- Contacto: [email protected] genoma humano, como el de todos los mamíferos y aves, es un mosaico de isocoros, los que son regiones muy largas de ADN (>> 100 kb) que son homogéneas en cuanto a su composición de bases. Los isocoros pueden ser divididos en un pequeño número de familias que cubren un amplio rango de niveles de GC (GC es la relación molar de guanina+citosina en el ADN). En el genoma humano encontramos cinco familias, que (yendo de valores bajos a altos de GC) son L1, L2, H1, H2 y H3. Este tipo de organización tiene importantes consecuencias funcionales, tales como la diferente concentración de genes, su regulación, niveles de transcripción, tasas de recombinación, tiempo de replicación, etc. Además, la existencia de los isocoros lleva a las llamadas “correlaciones composicionales”, lo que signifi ca que en la medida en que diferentes secuencias están localizadas en diferentes isocoros, todas sus regiones (exones y sus tres posiciones de los codones, intrones, etc.) cambian su contenido en GC, y como consecuencia, cambian tanto el uso de aminoácidos como de codones sinónimos en cada familia de isocoros. Finalmente, discutimos el origen de estas estructuras en un marco evolutivo.The human genome, as the genome of all mammals and birds, are mosaic of isochores, which are very long streches (>> 100 kb) of DNA that are homogeneous in base composition. Isochores can be divided in a small number of families that cover a broad range of GC levels (GC is the molar ratio of guanine+cytosine in DNA). In the human genome, we fi nd fi ve families, which are (going from GC-poor to GC- rich) L1, L2, H1, H2 and H3. This organization has important consequences, as is the case of the concentration of genes, their regulation, transcription levels, rate of recombination, time of repli cation, etc. Furthermore, the existence of isochores has as a consequence the so called “compositional correlations”, which means that as long as sequences are placed in diff erent families of isochores, all of their regions (exons and their three codon positions, introns, etc.) change their GC content, and as a consequence, both codon and amino acids usage change in each isochore family. Finally, we discuss the origin of isochores within an evolutioary framework.O genoma humano, como todos os mamíferos e aves, é um mosaico de isocóricas, que são muito longas regiões de ADN (>>100 kb) que são homogéneos na sua composição de base. Isóquos podem ser divididos em um pequeno número de famílias que cobrem uma ampla gama de níveis de GC (GC é a razão molar de guanina + citosina no DNA). No genoma humano, encontramos cinco famílias, que (variando de valores baixos a altos de GC) são L1, L2, H1, H2 e H3. Este tipo de organização tem importantes conseqüências funcionais, como a diferente concentração de genes, sua regulação, níveis de transcrição, taxas de recombinação, tempo de replicação, etc. Além disso, a existência de isocóri cas portada chamado “correlações de composição”, o que signifi ca que, na medida em que diferentes sequências estão localizados em diferentes isocóricas, todas as regiões (exs e três posições de codões, intrs, etc.) mudam seu conteúdo em GC e, como consequência, alteram tanto o uso de aminoácidos quanto de códons sinônimos em cada família de isócoros. Finalmente, discutimos a origem dessas estruturas em uma estrutura evolucionária

The short-sequence design of DNA and its involvement in the 3-D structure of the genome

Recent investigations have shown that isochores are characterized by a 3-D structure which is primarily responsible for the topology of chromatin domains. More precisely, an analysis of human chromosome 21 demonstrated that low-heterogeneity, GC-poor isochores are characterized by the presence of oligo-Adenines that are intrinsically stiff, curved and unfavorable for nucleosome binding. This leads to a structure of the corresponding chromatin domains, the Lamina Associated Domains, or LADs, which is well suited for interaction with the lamina. In contrast, the high-heterogeneity GC-rich isochores are in the form of compositional peaks and valleys characterized by increasing gradients of oligo-Guanines in the peaks and oligo-Adenines in the valleys that lead to increasing nucleosome depletions in the corresponding chromatin domains, the Topological Associating Domains, or TADs. These results encouraged us to investigate in detail the di- and tri-nucleotide profiles of 100 Kb segments of chromosome 21, as well as those of the di- to octa-Adenines and di- to octa-Guanines in some representative regions of the chromosome. The results obtained show that the 3-D structures of isochores and chromatin domains depend not only upon oligo-Adenines and oligo-Guanines but also, to a lower but definite extent, upon the majority of di- and tri-nucleotides. This conclusion has strong implications for the biological role of non-coding sequences

Compositional analysis of flatworm genomes shows strong codon usage biases across all classes

In the present work, we performed a comparative genome-wide analysis of 22 species representative of the main clades and lifestyles of the phylum Platyhelminthes. We selected a set of 700 orthologous genes conserved in all species, measuring changes in GC content, codon, and amino acid usage in orthologous positions. Values of 3rd codon position GC spanned over a wide range, allowing to discriminate two distinctive clusters within freshwater turbellarians, Cestodes and Trematodes respectively. Furthermore, a hierarchical clustering of codon usage data differs remarkably from the phylogenetic tree. Additionally, we detected a synonymous codon usage bias that was more dramatic in extreme GC-poor or GC-rich genomes, i.e., GC-poor Schistosomes preferred to use AT-rich terminated synonymous codons, while GC-rich M. lignano showed the opposite behavior. Interestingly, these biases impacted the amino acidic usage, with preferred amino acids encoded by codons following the GC content trend. These are associated with non-synonymous substitutions at orthologous positions. The detailed analysis of the synonymous and non-synonymous changes provides evidence for a two-hit mechanism where both mutation and selection forces drive the diverse coding strategies of flatworms

Enhancing Big Data Warehousing and Analytics for Spatio-Temporal Massive Data

The increasing amount of data generated by earth observation missions like Copernicus, NASA Earth Data, and climate stations is overwhelming. Every day, terabytes of data are collected from these resources for different environment applications. Thus, this massive amount of data should be effectively managed and processed to support decision-makers. In this paper, we propose an information system-based on a low latency spatio-temporal data warehouse which aims to improve drought monitoring analytics and to support the decision-making process. The proposed framework consists of 4 main modules: (1) data collection, (2) data preprocessing, (3) data loading and storage, and (4) the visualization and interpretation module. The used data are multi-source and heterogeneous collected from various sources like remote sensing sensors, biophysical sensors, and climate sensors. Hence, this allows us to study drought in different dimensions. Experiments were carried out on a real case of drought monitoring in China between 2000 and 2020