Provenance: The Bridge Between Experiments and Data

Current scientific applications are often structured as workflows and rely on workflow systems to compile abstract experiment designs into enactable workflows that utilise the best available resources. The automation of this step and of the workflow enactment, hides the details of how results have been produced. Knowing how compilation and enactment occurred allows results to be reconnected with the experiment design. We investigate how provenance helps scientists to connect their results with the actual execution that took place, their original experiment and its inputs and parameters.

Performance of an operating high energy physics data grid: DOSAR-Grid

The DO experiment at Fermilab's Tevatron will record several petabytes of data over the next five years in pursuing the goals of understanding nature and searching for the origin of mass. Computing resources required to analyze these data far exceed capabilities of any one institution. Moreover, the widely scattered geographical distribution of DO collaborators poses further serious difficulties for optimal use of human and computing resources. These difficulties will exacerbate in future high energy physics experiments, like the LHC. The computing grid has long been recognized as a solution to these problems. This technology is being made a more immediate reality to end users in DO by developing a grid in the DO Southern Analysis Region (DOSAR), DOSAR-Grid, using a available resources within it and a home-grown local task manager, McFarm. We will present the architecture in which the DOSAR-Grid is implemented, the use of technology and the functionality of the grid, and the experience from operating the grid in simulation, reprocessing and data analyses for a currently running HEP experiment.

The GHEP-EMPOP collaboration on mtDNA population data-A new resource for forensic casework

Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian and South American subcontinents, we here report the results of a collaborative study involving nine laboratories from the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and EMPOP. The individual laboratories contributed population data that were generated throughout the past 10 years, but in the majority of cases have not been made available to the scientific community. A total of 1019 haplotypes from Iberia (Basque Country, 2 general Spanish populations, 2 North and 1 Central Portugal populations), and Latin America (3 populations from São Paulo) were collected, reviewed and harmonized according to defined EMPOP criteria. The majority of data ambiguities that were found during the reviewing process (41 in total) were transcription errors confirming that the documentation process is still the most error-prone stage in reporting mtDNA population data, especially when performed manually. This GHEP-EMPOP collaboration has significantly improved the quality of the individual mtDNA datasets and adds mtDNA population data as valuable resource to the EMPOP database (www.empop.org). (C) 2010 Elsevier B.V. All rights reserved.

Constraints on electroweak contact interactions from LEP and tevatron data

A complete set of dimension-six effective contact interactions involving Higgs, gauge bosons and quarks is studied. Limits on the coefficients of these new operators are obtained from the experimental values of the Z and W gauge bosons widths.

End-to-end validation of EPS / MetOp GOME-2 trace gas data

Within the next decade, the improved version 2 of Global Ozone Monitoring Experiment (GOME-2), a ultraviolet-visible spectrometer dedicated to the observation of key atmospheric trace species from space, will be launched successively on board three EUMETSAT Polar System (EPS) MetOp satellites. Starting with the launch of MetOp-1 scheduled for summer 2006, the GOME-2 series will extend till 2020 the global monitoring of atmospheric composition pioneered with ERS-2 GOME-1 since 1995 and enhanced with Envisat SCIAMACHY since 2002 and EOS-Aura OMI since 2004. For more than a decade, an international pool of scientific teams active in ground-and space-based ultraviolet-visible remote sensing have contributed to the successful post-launch validation of trace gas data products and the associated maturation of retrieval algorithms for the latter satellites, ensuring that geophysical data products are/become reliable and accurate enough for intended research and applications. Building on this experience, this consortium plans now to develop and carry out appropriate validation of a list of GOME-2 trace gas column data of both tropospheric and stratospheric relevance: nitrogen dioxide (NO 2), ozone (O 3), bromine monoxide (BrO), chlorine dioxide (OClO), formaldehyde (HCHO), and sulphur dioxide (SO 2). The proposed investigation will combine four complementary approaches resulting in an end-to-end validation of expected column data products.

The Brazilian Seismographic Integrated Systems (BRASIS): Infrastructure and data management

In geophysics and seismology, raw data need to be processed to generate useful information that can be turned into knowledge by researchers. The number of sensors that are acquiring raw data is increasing rapidly. Without good data management systems, more time can be spent in querying and preparing datasets for analyses than in acquiring raw data. Also, a lot of good quality data acquired at great effort can be lost forever if they are not correctly stored. Local and international cooperation will probably be reduced, and a lot of data will never become scientific knowledge. For this reason, the Seismological Laboratory of the Institute of Astronomy, Geophysics and Atmospheric Sciences at the University of São Paulo (IAG-USP) has concentrated fully on its data management system. This report describes the efforts of the IAG-USP to set up a seismology data management system to facilitate local and international cooperation. © 2011 by the Istituto Nazionale di Geofisica e Vulcanologia. All rights reserved.

3D geovisualisation techniques applied in spatial data mining

The increase in the number of spatial data collected has motivated the development of geovisualisation techniques, aiming to provide an important resource to support the extraction of knowledge and decision making. One of these techniques are 3D graphs, which provides a dynamic and flexible increase of the results analysis obtained by the spatial data mining algorithms, principally when there are incidences of georeferenced objects in a same local. This work presented as an original contribution the potentialisation of visual resources in a computational environment of spatial data mining and, afterwards, the efficiency of these techniques is demonstrated with the use of a real database. The application has shown to be very interesting in interpreting obtained results, such as patterns that occurred in a same locality and to provide support for activities which could be done as from the visualisation of results. © 2013 Springer-Verlag.

Sustainable development in the BRICS countries: an efficiency analysis by data envelopment

There is much concern about the social and environmental impacts caused by the economic growth of nations. Thus, to evaluate the socio-economic performance of nations, economists have increasingly addressed matters related to social welfare and the environment. It is within the scope of this context that this work discusses the performance of countries in the BRICS group regarding sustainable development. The objective of this study regards evaluating the efficiency of these countries in transforming productive resources and technological innovation into sustainable development. The proposed objective was achieved by using econometric tools as well as the data envelopment analysis method to then create economic, environmental, and social efficiency rankings for the BRICS countries, which enabled to carry out comparative analyses on the sustainable development of those countries. The results of such assessments can be of interest for more specific scientific explorations.

Scientific collaboration network among Brazilian universities: an analysis in Dentistry area

This paper analyses the scientific collaboration network formed by the Brazilian universities that investigate in dentistry area. The constructed network is based on the published documents in the Scopus (Elsevier) database covering a period of 10 (ten) years. It is used social network analysis as the best methodological approach to visualize the capacity for collaboration, dissemination and transmission of new knowledge among universities. Cohesion and density of the collaboration network is analyzed, as well as the centrality of the universities as key-actors and the occurrence of subgroups within the network. Data were analyzed using the software UCINET and NetDraw. The number of documents published by each university was used as an indicator of its scientific production.

Scientific use of the finite element method in Orthodontics

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Visualisation and reconstruction in dentistry

Visualisation in the field of dentistry has nor, thus far, reached the same development as other medical fields. Potential applications of visualisation techniques in this area, however, are many, ranging from educational displays to training for delicate procedures. This paper reports on the investigation of techniques for handling three-dimensional models of teeth, aiming at investigation of dental structures. An algorithm was implemented for this purpose, which reconstructs three-dimensional teeth models from two-dimensional contour slices. Results employing various data sets are presented, including the output of VRML models for exploration.

The briefing in paleodesign: selection and arrangement of data for the reconstruction of Paleovertebrates

Representing visually the external appearance of an extinct animal requires, for a reasonably reliable and expressive reconstitution, a good compilation and arrangement of the scientific conclusions on the fossil findings. It is proposed in this work an initial model of a briefing to be applied in a paleodesign process of a paleovertebrate. Briefing can be understood as a gathering of all necessary data to perform a project. We point out what must be known about the relevant structures in order to access all the data and the importance of such information. It is expected that the present briefing suggested might be faced with flexibility, serving as a facilitating interface of the relation between paleoartists and paleontologists.

Saving the Vaquita: Immediate Action, Not More Data

The recent likely extinction of the baiji (Chinese river dolphin [Lipotes vexillifer]) (Turvey et al. 2007) makes the vaquita (Gulf of California porpoise [Phocoena sinus]) the most endangered cetacean. The vaquita has the smallest range of any porpoise, dolphin, or whale and, like the baiji, has long been threatened primarily by accidental deaths in fishing gear (bycatch) (Rojas-Bracho et al. 2006). Despite repeated recommendations from scientific bodies and conservation organizations, no effective actions have been taken to remove nets from the vaquita’s environment. Here, we address three questions that are important to vaquita conservation: (1) How many vaquitas remain? (2) How much time is left to find a solution to the bycatch problem? and (3) Are further abundance surveys or bycatch estimates needed to justify the immediate removal of all entangling nets from the range of the vaquita? Our answers are, in short: (1) there are about 150 vaquitas left, (2) there are at most 2 years within which to find a solution, and (3) further abundance surveys or bycatch estimates are not needed. The answers to the first two questions make clear that action is needed now, whereas the answer to the last question removes the excuse of uncertainty as a delay tactic. Herein we explain our reasoning.

Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa Scientific

The Cedar River alluvial aquifer is the primary source of municipal water in the Cedar Rapids, Iowa, area. Since 1992, the U.S. Geological Survey, in cooperation with the City of Cedar Rapids, has investigated the hydrogeology and water quality of the Cedar River alluvial aquifer. This report describes a detailed analysis of the ground-water flow system in the alluvial aquifer, particularly near well field areas. The ground-water flow system in the Cedar Rapids area consists of two main components, the unconsolidated Quaternary deposits and the underlying carbonate bedrock that has a variable fracture density. Quaternary deposits consist of eolian sand, loess, alluvium, and glacial till. Devonian and Silurian bedrock aquifers overlie the Maquoketa Shale (Formation) of Ordovician age, a regional confining unit. Ground-water and surface-water data were collected during the study to better define the hydrogeology of the Cedar River alluvial aquifer and Devonian and Silurian aquifers. Stream stage and discharge, ground-water levels, and estimates of aquifer hydraulic properties were used to develop a conceptual ground-water flow model and to construct and calibrate a model of the flow system. This model was used to quantify the movement of water between the various components of the alluvial aquifer flow system and provide an improved understanding of the hydrology of the alluvial aquifer.

Influence of landscape evolution on the distribution of floristic patterns in northern Amazonia revealed by delta 13C data

The Amazonian lowlands include large patches of open vegetation which contrast sharply with the rainforest, and the origin of these patches has been debated. This study focuses on a large area of open vegetation in northern Brazil, where d13C and, in some instances, C/N analyses of the organic matter preserved in late Quaternary sediments were used to achieve floristic reconstructions over time. The main goal was to determine when the modern open vegetation started to develop in this area. The variability in d13C data derived from nine cores ranges from -32.2 to -19.6 parts per thousand, but with nearly 60% of data above -26.5 parts per thousand. The most enriched values were detected only in ecotone and open vegetated areas. The development of open vegetation communities was asynchronous, varying between estimated ages of 6400 and 3000 cal a BP. This suggests that the origin of the studied patches of open vegetation might be linked to sedimentary dynamics of a late Quaternary megafan system. As sedimentation ended, this vegetation type became established over the megafan surface. In addition, the data presented here show that the presence of C4 plants must be used carefully as a proxy to interpret dry paleoclimatic episodes in Amazonian areas. Copyright (c) 2012 John Wiley & Sons, Ltd.