Parallel Image Processing Using a Pure Topological Framework

Image processing is a fundamental operation in many real time applications, where lots of parallelism can be extracted. Segmenting the image into different connected components is the most known operations, but there are many others like extracting the region adjacency graph (RAG) of these regions, or searching for features points, being invariant to rotations, scales, brilliant changes, etc. Most of these algorithms part from the basis of Tracing-type approaches or scan/raster methods. This fact necessarily implies a data dependence between the processing of one pixel and the previous one, which prevents using a pure parallel approach. In terms of time complexity, this means that linear order O(N) (N being the number of pixels) cannot be cut down. In this paper, we describe a novel approach based on the building of a pure Topological framework, which allows to implement fully parallel algorithms. Concerning topological analysis, a first stage is computed in parallel for every pixel, thus conveying the local neighboring conditions. Then, they are extended in a second parallel stage to the necessary global relations (e.g. to join all the pixels of a connected component). This combinatorial optimization process can be seen as the compression of the whole image to just one pixel. Using this final representation, every region can be related with the rest, which yields to pure topological construction of other image operations. Besides, complex data structures can be avoided: all the processing can be done using matrixes (with the same indexation as the original image) and element-wise operations. The time complexity order of our topological approach for a m×n pixel image is near O(log(m+n)), under the assumption that a processing element exists for each pixel. Results for a multicore processor show very good scalability until the memory bandwidth bottleneck is reached, both for bigger images and for much optimized implementations. The inherent parallelism of our approach points to the direction that even better results will be obtained in other less classical computing architectures.1Ministerio de Economía y Competitividad (España) TEC2012-37868-C04-02AEI/FEDER (UE) MTM2016-81030-PVPPI of the University of Sevill

The mRNA degradation factor Xrn1 regulates transcription elongation in parallel to Ccr4

Co-transcriptional imprinting of mRNA by Rpb4 and Rpb7 subunits of RNA polymerase II (RNAPII) and by the Ccr4–Not complex conditions its posttranscriptional fate. In turn, mRNA degradation factors like Xrn1 are able to influence RNAPII-dependent transcription, making a feedback loop that contributes to mRNA homeostasis. In this work, we have used repressible yeast GAL genes to perform accurate measurements of transcription and mRNA degradation in a set of mutants. This genetic analysis uncovered a link from mRNA decay to transcription elongation. We combined this experimental approach with computational multi-agent modelling and tested different possibilities of Xrn1 and Ccr4 action in gene transcription. This double strategy brought us to conclude that both Xrn1-decaysome and Ccr4–Not regulate RNAPII elongation, and that they do it in parallel. We validated this conclusion measuring TFIIS genome-wide recruitment to elongating RNAPII. We found that xrn1Δ and ccr4Δ exhibited very different patterns of TFIIS versus RNAPII occupancy, which confirmed their distinct role in controlling transcription elongation. We also found that the relative influence of Xrn1 and Ccr4 is different in the genes encoding ribosomal proteins as compared to the rest of the genome

Vertical mass impact and features of Saharan dust intrusions derived from ground-based remote sensing in synergy with airborne in-situ measurements

A study of the vertical mass impact of Saharan dust intrusions is presented in this work. Simultaneous ground-based remote-sensing and airborne in-situ measurements performed during the AMISOC-TNF campaign over the Tenerife area (Canary Islands) in summertime from 01 July to 11 August 2013 were used for that purpose. A particular dusty (DD) case, associated to a progressively arriving dust intrusion lasting for two days on 31 July (weak incidence) and 01 August (strong incidence), is especially investigated. AERONET AOD and AEx values were ranging, respectively, from 0.2 to 1.4 and 0.35 to 0.05 along these two days. Vertical particle size distributions within fine and coarse modes (0.16e2.8 mm range) were obtained from aircraft aerosol spectrometer measurements. Extinction profiles and Lidar Ratio (LR) values were derived from MPLNET/Micro Pulse Lidar observations. MAXDOAS measurements were also used to retrieve the height-resolved aerosol extinction for evaluation purposes in comparison to Lidarderived profiles.This work is supported by the Spanish Ministerio de Economía y Competitividad (MINECO) under grants CGL2011-24891 and CGL2014-55230-R

Mecánica de fluidos computacional: tipos de mallas y calidad del mallado

En este artículo vamos a presentar los principales tipos de mallas utilizados en problemas de mecánica de fluidos computacional mediante la aproximación de volúmenes finitos. Se describen las mallas estructuradas y no estructuradas, mallas por bloques, mallas móviles y deformables, mallas quimera o los tipos de celdas utilizados. Además, vamos a dar algunas pinceladas sobre cómo se puede asegurar la calidad de las mismas, incluyendo una descripción de los métodos estándar para definir el índice de convergencia de una malla.García-Cuevas González, LM.; Gil Megías, A.; Navarro García, R.; Quintero Igeño, PM. (2020). Mecánica de fluidos computacional: tipos de mallas y calidad del mallado. http://hdl.handle.net/10251/146219DE

Mecánica de fluidos computacional: reconstrucción de la solución para el cálculo de flujos y métodos multigrid

En este artículo vamos a presentar cómo se puede reconstruir la solución para calcular los flujos entre celdas en el método de volúmenes finitos para la resolución de problemas de mecánica de fluidos computacional. Además, introduciremos los métodos multigrid, con sus ventajas para la resolución de grandes sistemas de ecuaciones linealizados como los encontrados en los problemas de mecánica de fluidos computacional.García-Cuevas González, LM.; Gil Megías, A.; Navarro García, R.; Quintero Igeño, PM. (2020). Mecánica de fluidos computacional: reconstrucción de la solución para el cálculo de flujos y métodos multigrid. http://hdl.handle.net/10251/146096DE

Shear-wave velocity structure from MASW and SPAC methods. The case of Adra town, SE Spain

The damage distribution in the town of Adra (south-eastern Spain) during the 1993 and 1994 Adra earthquakes, magnitude Mw 5.0 and maximum intensity degree of VII (European Macroseismic Scale), was mainly concentrated in the southeast sector, where low-diagenetic (soft) sediments outcrop. As new urbanizations are planned in that sector, a soil classification based on the shallow shear-wave velocity (Vs) structure is needed. For the purpose of earthquake disaster mitigation, the Spatial Autocorrelation (SPAC) and the Multichannel Analysis of Surface Waves (MASW) methods were used to propose integrated 2D Vs models for the seismic response characterization of shallow geology. Joint inversion of H/V spectral ratios of ambient noise, interpreted under the Diffuse Field Approach, and dispersion curves derived from the SPAC method allowed to obtain more constrained models. Both, SPAC and MASW methods provided similar results for the surveyed geological formations. From these models, a classification of the geological formations has been carried out in terms of Vs30 values and Eurocode 8 (EC8, 1998) classes. Lower Vs30 values in the 180-360 m/s range were found in the southeastern sector of the town, where soft sediments outcrop and some building damage was reported from the 1993-1994 earthquakes. The highest Vs30 values above 800 m/s appear at the northern sector, where the hardest rocks outcrop and no building damage was reported. The combination of the well-suited Vs database prepared for different geological formations with the 1:5,000 scale geological mapping was a step to obtain a detailed soil microzonation map of Adra. It gives a new predictive insight into the building damage distribution, which will contribute to the appropriate urban planning of the future growth of the town

The yeast prefoldin-like URI-orthologue Bud27 associates with the RSC nucleosome remodeler and modulates transcription

Bud27, the yeast orthologue of human URI/RMP, is a member of the prefoldin-like family of ATPindependent molecular chaperones. It has recently been shown to mediate the assembly of the three RNA polymerases in an Rpb5-dependent manner. In this work, we present evidence of Bud27 modulating RNA pol II transcription elongation. We show that Bud27 associates with RNA pol II phosphorylated forms (CTD-Ser5P and CTD-Ser2P), and that its absence affects RNA pol II occupancy of transcribed genes. We also reveal that Bud27 associatesin vivo with the Sth1 component of the chromatin remodeling complex RSC and mediates its association with RNA pol II. Our data suggest that Bud27, in addition of contributing to Rpb5 folding within the RNA polymerases, also participates in the correct assembly of other chromatin-associated protein complexes, such as RSC, thereby modulating their activit

Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration

mRNA homoeostasis is favoured by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques in Saccharomyces cerevisiae. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5ʹ exhibited significant alterations that were compatible with decreased elongation rates in the absence of Xrn1. Nucleosome mapping detected altered chromatin configuration in the gene bodies. We also detected accumulation of RNA pol II shortly upstream of polyadenylation sites by CRAC, although not by BioGRO-seq, suggesting higher frequency of backtracking before pre-mRNA cleavage. This phenomenon was particularly linked to genes with poorly positioned nucleosomes at this position. Accumulation of RNA pol II at 3ʹ was also detected in other mRNA decay mutants. According to these and other pieces of evidence, Xrn1 seems to influence transcription elongation at least in two ways: by directly favouring elongation rates and by a more general mechanism that connects mRNA decay to late elongation.This work has been supported by grants from the Ministerio de Economía, Industria y Competitividad – Agencia Estatal de Investigación, and European Union funds (FEDER) [BFU2016-77728-C3-1-P to S. C.],[BFU2016-77728-C3-3-P to J.E.P-O & P.A], [BFU2016-77728-C3-2-P to F.N.] and RED2018‐102467‐T to J.E.P-O, F.N. and S.C.; by FPI grants from the Spanish Government to V.B and A.C-B; by the Regional Andalusian Government [BIO271 and US-1256285 to S. C.], [BIO258 and FEDER-UJA 1260360 to F.N.] and from the Regional Valencian Government [AICO/2019/088 to J.E.P-O]. Funding for open access charge: [BFU2016-77728-C3-1-P]

Renovación urbana de los espacios comunitarios Polanquito - La Mezquitera

ITESO, A.C

The association of the RSC remodeler complex with chromatin is influenced by the prefoldin-like Bud27 and determines nucleosome positioning and polyadenylation sites usage in Saccharomyces cerevisiae

The tripartite interaction between the chromatin remodeler complex RSC, RNA polymerase subunit Rpb5 and prefoldin-like Bud27 is necessary for proper RNA pol II elongation. Indeed lack of Bud27 alters this association and affects transcription elongation. This work investigates the consequences of lack of Bud27 on the chromatin association of RSC and RNA pol II, and on nucleosome positioning. Our results demonstrate that RSC binds chromatin in gene bodies and lack of Bud27 alters this association, mainly around polyA sites. This alteration impacts chromatin organization and leads to the accumulation of RNA pol II molecules around polyA sites, likely due to pausing or arrest. Our data suggest that RSC is necessary to maintain chromatin organization around those sites, and any alteration of this organization results in the widespread use of alternative polyA sites. Finally, we also find a similar molecular phenotype that occurs upon TOR inhibition with rapamycin, which suggests that alternative polyadenylation observed upon TOR inhibition is likely Bud27-dependent.Peer reviewe