Parallel distributed computing using Python

This work presents two software components aimed to relieve the costs of accessing high-performance parallel computing resources within a Python programming environment: MPI for Python and PETSc for Python.MPI for Python is a general-purpose Python package that provides bindings for the Message Passing Interface (MPI) standard using any back-end MPI implementation. Its facilities allow parallel Python programs to easily exploit multiple processors using the message passing paradigm. PETSc for Python provides access to the Portable, Extensible Toolkit for Scientific Computation (PETSc) libraries. Its facilities allow sequential and parallel Python applications to exploit state of the art algorithms and data structures readily available in PETSc for the solution of large-scale problems in science and engineering.MPI for Python and PETSc for Python are fully integrated to PETSc-FEM, an MPI and PETSc based parallel, multiphysics, finite elements code developed at CIMEC laboratory. This software infrastructure supports research activities related to simulation of fluid flows with applications ranging from the design of microfluidic devices for biochemical analysis to modeling of large-scale stream/aquifer interactions.     

Structural controls on Quaternary deepwater sedimentation, mud diapirism, and hydrocarbon distribution within the actively evolving Columbus foreland basin, eastern offshore Trinidad

Eastward migration of the Caribbean plate relative to the South American plate has caused lithospheric loading along the northern margin of South America, which is recorded by an 1100-km-long foreland basin which is oldest in the west (Maracaibo basin, 65-55 Ma) and youngest in the east (Columbus basin, eastern offshore Trinidad, 15-0 Ma). The Orinoco River has been the primary source of sediment for the basin since early Miocene. We have integrated approximately 775 km of deep-penetration 2D seismic lines acquired in the area of eastern offshore Trinidad as part of the 2004 “Broadband Ocean-Land Investigations of Venezuela and the Antilles arc Region” (BOLIVAR) project, 8000 km² of shallow industry 3D seismic data, and published industry well data from offshore eastern Trinidad. Active mud diapirism in the Columbus basin is widespread and is related to overthrusting and tectono-sedimentary loading of upper Miocene-lower Pliocene age mud. Analysis of the shallow 3D seismic data reveals the presence of extensive gravity-flow depositional elements on the Columbus basin slope and the deepwater area. These stacked gravity-flow deposits are characterized by mass-transport deposits at the base, turbidite frontal-splay deposits, leveed-channel deposits, and capped by fine-grained condensed-section deposits. Exploration targets in the deepwater area are located towards the center of the Columbus basin, where northeast-trending fault-propagation folds are important Plio-Pleistocene trap-forming elements. Deep basin wells drilled in recent years have proven that turbidites were transported into the deepwater Columbus basin during the Plio-Pleistocene. Analysis of these well results suggests that a deeper oil charge is present within the deepwater Columbus basin area. The primary uncertainty for this variable hydrocarbon system is whether fault or diapiric pathways connect or divert the petroleum charge at depth with shallower reservoir rocks.     

Contextual factors influencing sustainable fisheries in Mexico

Sustainable fisheries take into consideration that managed fisheries ecosystems shift over time in response to evolving environmental as well as market and political factors. These contextual forces are especially valuable in understanding developing countries such as Mexico, where the unconsolidated fisheries administration faces productive marine ecosystems but unsustainable fisheries. To recognize the issues that have inhibited the consolidation of a regulatory system for sustainable fisheries, a contextual factor analysis was applied to the co-development of two current policies in the Mexican fishery regime: fisheries and environmental policies. Six historical phases have been identified in which there are few long periods of stability and frequent short periods of radical change that alternate between stable and adverse contextual situations. These short and contrasting contextual situations cause a kind of tug-of-war in Mexican fisheries policy-making. On the one hand, domestic economic, scientific, and technological forces seem to slowly lead toward the consolidation of sustainable fisheries; on the other hand, domestic policies drift from one position to another at other timing than the international fisheries and environmental policies. Although recent crises seem to highlight new periods of radical change in Mexico, they also provide an opportunity to adopt new structural plans to consolidate domestic forces as a basis for long-term strategies.     

Interplay of S and As in Mekong Delta sediments during redox oscillations

The cumulative effects of periodic redox cycling on the mobility of As,Fe,and S from alluvial sediment to groundwater were investigated in bioreactor experiments.Two particular sediments from the alluvial floodplain of the Mekong Delta River were investigated:Matrix A(14 m deep)had a higher pyrite concentration than matrix B(7 m deep)sediments.Gypsum was present in matrix B but absent in matrix A.In the reactors,the sediment suspensions were supplemented with As(Ⅲ)and SO_4~(2-),and were subjected to three full-redox cycles entailing phases of nitrogen/CO_2,compressed air sparging,and cellobiose addition.Major differences in As concentration and speciation were observed upon redox cycling.Evidences support the fact that initial sediment composition is the main factor controlling arsenic release and its speciation during the redox cycles.Indeed,a high pyrite content associated with a low SO_4~(2-)content resulted in an increase in dissolved As concentrations,mainly in the form of As(Ⅲ),after anoxic half-cycles;whereas a decrease in As concentrations mainly in the form of As(Ⅴ),was instead observed after oxic half-cycles.In addition,oxic conditions were found to be responsible for pyrite and arsenian pyrite oxidation,increasing the As pool available for mobilization.The same processes seem to occur in sediment with the presence of gypsum,but,in this case,dissolved As were sequestered by biotic or abiotic redox reactions occurring in the Fe—S system,and by specific physico-chemical condition(e.g.pH).The contrasting results obtained for two sediments sampled from the same core show that many complexes and entangled factors are at work,and further refinement is needed to explain the spatial and temporal variability of As release to groundwater of the Mekong River Delta(Vietnam).     

Presence of Hippidion at two sites of western Argentina: Diet composition and contribution to the study of the extinction of Pleistocene megafauna

The composition of Hippidion diet, and possible changes that could relate to its extinction, were evaluated in the Argentinean-Chilean Central Andes, a Neotropical environment characterized by arid to semiarid conditions (Andean hot and cold deserts). Microhistological analyses were made on feces of Hippidion found at Los Morrillos (31°43′S–68°42′W, 3000 m a.s.l.) and Gruta del Indio (34°35′S, 68°22′W, 660 m a.s.l.). At Gruta del Indio the diet of Hippidion was based mainly on woody species. At Los Morrillos, it was based on herbaceous species.This flexibility in diet composition could be a relative adaptive advantage allowing a longer permanence of this species in comparison to others recorded in the region (such as Megatheriumand Mylodon). Nevertheless, this advantage was not enough to guarantee its survival during the Holocene. Extinction could have been affected by diverse agents, such as growing aridification of the area, increasing competition with other species (mainly Lama guanicoe), and human presence, along with a relatively low population density (as expected from the limited presence of Hippidion at the archaeological and palaeontological sites of South America. At Gruta del Indio significant changes in the diet of Hippidion corresponding to different intervals of the period 31,000–9000 ¹⁴C BP are not evident. Given this evidence for similar diets for Hippidion throughout the late Quaternary, other factors need to be considered to explain the extinction of this horse.     

An Analysis of Polar Coronal Hole Evolution: Relations to Other Solar Phenomena and Heliospheric Consequences

We use observations of the green corona low-brightness regions to construct a time series of a polar coronal hole area from 1939 to 1996, covering 5 solar cycles. We then perform a power-spectral analysis of the monthly data time series. Several persistent significant periodicities appear in the spectra, which are related with those found in solar magnetic flux emergence, geomagnetic storm sudden commencements and cosmic-ray flux at Earth. Of particular importance are the peak at around 1.6–1.8 yr recently found in cosmic-ray intensity fluctuations, and the peak at around 1 yr, also identified in coronal hole magnetic flux variations. Additional interesting features are the peaks close to 5 yr, 3 yr and the possible peak at around 30 yr, that were also found in other solar and interplanetary phenomena. Our results stress the physical connection between the solar magnetic flux emergence and the interplanetary medium dynamics, in particular the importance of coronal hole evolution in the structuring of the heliosphere.     

shinyNORRRM: A Cross-Platform Software to Calculate the CIPW Norm

In this paper, a novelty-free software to assess an efficient CIPW Norm (± 0.006 wt.% in differences between input and output data) is presented. The package is available in the official repository for user-contributed R packages (CRAN: Comprehensive R Archive Network). The software is able to handle big data sets and considers minor and trace element compositions. The algorithm can calculate odd minerals in igneous rocks, such as cancrinite and calcite, adjust the Fe⁺³/Fe⁺² ratio in different standard approaches, and recalculate the compositions of the rocks in an anhydrous basis (100 ± 0.003 wt.% volatile-free adjusted). Furthermore, the package calculates several petrological parameters, and the graphical outputs are displayed following IUGS scheme standards. The prime aspect of shinyNORRRM is the symbiosis of native R functions with the R package’s shiny (Web Application Framework for R) to run the norm in a user-friendly interface. shinyNORRRM can be executed in any operating system and requires no previous programming knowledge, thus promising to be the universal computational program in this matter. The output data are printed in the standard comma-separated values (*.csv) format, which is highly compatible with general spreadsheet editors. In this work, the algorithm of our program is validated using already compiled whole-rock geochemical databases.

     

Biochemical alterations in juvenile carp (Cyprinus carpio) exposed to zinc: glutathione reductase as a target

The aim of this study was to investigate biochemical changes in juvenile carp (Cyprinus carpio) exposed to zinc chloride (10, 30 and 100 microM) for a period of 48 h. Zinc exposure caused a concentration-dependent reduction in glutathione reductase (GR) activity in gills, liver and brain. Gill glutathione S-transferase (GST) was reduced when animals were exposed to the highest concentration of 100 microM zinc. The phosphorylation of p38(MAPK) increased in the brain of fish exposed to zinc 100 microM, while phosphorylation of the extracellular signal-regulated protein kinase 1/2 (ERK1/2) and c-Jun N-terminal protein kinase 1/2 (JNK1/2) remained unchanged. Expression of proteins HSP60 and HSP70 were not affected by zinc exposure. Considering the significant concentration-dependent inhibition of GR in all tissues analyzed, this enzyme could be a potential biomarker of exposure to zinc, which has to be confirmed.     

Morphological variation and reproductive biology of Polaskia chende (Cactaceae) under domestication in Central Mexico

The columnar cactus Polaskia chende, endemic to Central Mexico, occurs in the wild and in silviculturally managed populations where artificial selection for better edible fruits operates by sparing and favouring desirable phenotypes during vegetation clearance. Wild and managed populations were compared in morphology and reproductive biology to analyse if human selection has influenced phenotypic divergence, if it has modified breeding systems and if reproductive isolation exists between them. Fruits from managed populations were larger (6·36±0·17 cm³), heavier (19·62±1·32), sweeter (9·07±0·25 °Brix), and with thinner peel (2·09±0·13 mm) than those from wild populations (5·77±0·18 cm³, 15·73±0·85 g, 8·23±0·31 °Brix, and 2·58±0·14 mm, respectively). Both population types bloom synchronically, show diurnal anthesis, with bees as the most likely pollinators, and have breeding system predominantly self-incompatible. Spatial and temporal barriers to pollen exchange between wild and managed populations are unlikely, and morphological differences would be related with an ongoing process of artificial selection.     

Assessing land use/cover changes: a nationwide multidate spatial database for Mexico

A nationwide multidate GIS database was generated in order to carry out the quantification and spatial characterization of land use/cover changes (LUCC) in Mexico. Existing cartography on land use/cover at a 1:250,000 scale was revised to select compatible inputs regarding the scale, the classification scheme and the mapping method. Digital maps from three different dates (the late 1970s, 1993 and 2000) were revised, evaluated, corrected and integrated into a GIS database. In order to improve the reliability of the database, an attempt was made to assess the accuracy of the digitalisation procedure and to detect and correct unlikely changes due to thematic errors in the maps. Digital maps were overlaid in order to generate LUCC maps, transition matrices and to calculate rates of conversion. Based upon this database, rates of deforestation between 1976 and 2000 were evaluated as 0.25 and 0.76% per year for temperate and tropical forests, respectively.