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.

Geographical distribution and associated environments characterisation of catuba (Trichilia catigua A. Juss. - Meliaceae) in Paraná State - Brazil

Trichilia catigua A. Juss. - Meliaceae has been traditionally used as a tonic and digestive medicine. Some Brazilian pharmaceutical firms use this species to produce phytopharmaceuticals and alcoholic beverages. The aim of this work is to determine its geographical distribution and characterise the environments where catuaba is found in the state of Paraná, in order to support the domestication strategy for the agricultural production of this species. Based on the literature, botanical collections and field observations it was established, that five species of the genus occurring in Paraná, which were identified as T casaretti, T catigua, T claussenii, T elegans, T pallida and another supposed to be T pattens. Trichilia catigua occurs within a wide but defined strip in the state. By evaluating data of climate; soil types; natural vegetation formations; mean, maximum and minimum temperatures; relative humidity; rainfall; altitudes and evapotranspiration the strip may be localised above latitude 25° in the central and Eastern regions of the state and above latitude 26° in South-western Parana. In general, T catigua was found to occur on fertile, organic-matter-rich soils and predominantly under forest canopies.

Oral cancer mortality trends in Brazilian geographical regions from 1996-2001

The purpose of this study was to analyse the oral cancer mortality trends in Brazil by geographic region, age and sex, from 1996 to 2001. The Brazilian Ministry of Health database DATASUS and the Brazilian Institute of Geography and Statistics were used as the source of data. Oral cancer mortality rates per 100,000 population were estimated. Statistical analyses comprised estimates of oral cancer mortality rates, grouped according to the study variables, in 1996, 1997, 1998, 1999, 2000 and 2001; also, the three-year periods 1996-1998 and 1999-2001 were analysed, allowing the oral cancer mortality trends between these two periods to be calculated. For comparison, in each geographical region, the ratio between two death rates (related to period or sex) was calculated. In the period 1996-2001, a total of 25,972 deaths due to oral cancer were reported, giving a mortality rate of 2.67. The rates for the periods 1996-1998 and 1999-2001 were 2.53 and 2.73, respectively, showing a slight increase in the rate. There was a predominance of oral cancer in males with a male/female ratio of approximately 4. All regions exhibited an increase in mortality rates, with the exception of the Southeast region. From 1996 to 2001, the average mortality rates were 3.55 and 3.58 for the Southeast and South regions, and 1.94, 1.41, and 0.86 for the Mid-West, Northeast, and North regions, respectively. Over the age of 40, oral cancer mortality rates were seen to increase rapidly with age. Oral cancer mortality increased in all regions, except in the Southeast, and was considerably higher among males and older individuals.

Evaluation of tropospheric and ionospheric effects on the geographic localization of data collection platforms

The Brazilian National Institute for Space Research (INPE) is operating the Brazilian Environmental Data Collection System that currently amounts to a user community of around 100 organizations and more than 700 data collection platforms installed in Brazil. This system uses the SCD-1, SCD-2, and CBERS-2 low Earth orbit satellites to accomplish the data collection services. The main system applications are hydrology, meteorology, oceanography, water quality, and others. One of the functionalities offered by this system is the geographic localization of the data collection platforms by using Doppler shifts and a batch estimator based on least-squares technique. There is a growing demand to improve the quality of the geographical location of data collection platforms for animal tracking. This work presents an evaluation of the ionospheric and tropospheric effects on the Brazilian Environmental Data Collection System transmitter geographic location. Some models of the ionosphere and troposphere are presented to simulate their impacts and to evaluate performance of the platform location algorithm. The results of the Doppler shift measurements, using the SCD-2 satellite and the data collection platform (DCP) located in Cuiabá town, are presented and discussed.

Electronic data interchange in port management: the experience of the port of Barcelona

Every port is unique. Although all ports exist for the same basic purpose (to act as an interface in the transfer from one mode of transport to another), no two are ever organized in the same way.Ports may be classified according to: Physical conditions: location (geographical position, man-made or natural harbour, estuary location, difficult weather conditions, tides, etc.) and size (large, small or medium-sized). Use: commercial (general cargo, bulk solids, bulk liquids, oil, break bulk, mixed), passenger, sport and leisure, fishing, mixed, etc. Ownership: private, municipal, regional or State-owned. The Port Authority's role in management of the port: Overall control, i.e. the Port Authority plans, sets up and operates the whole range of services. Facilitator, i.e. the Port Authority plans and sets up the infrastructure and the superstructure, but services are provided by private companies. Landlord, i.e. the Port Authority allows private companies to be responsible for the superstructure and provide port services. Different combinations of port types will therefore give rise to different kinds of organization and different information flows, which means that the associated information systems may differ significantly from port to port. Since this paper relates to the port of Barcelona, with its own specific characteristics, the contents may not always be applicable to other ports.

Geographical variation in the reproduction and sexual dimorphism of the Boddaert's tropical racer, Mastigodryas boddaerti (Serpentes: Colubridae)

We obtained data on time of sexual maturity, dimorphism, fecundity and on the reproductive cycle of Mastigodryas boddaerti (Sentzen, 1796) through the examination of 321 preserved specimens, of which 221 were collected in the Brazilian Amazon region and 100 in the Cerrado savannas of Central Brazil. The degree of sexual size dimorphism (snout-vent length, SVL) was significantly greater in the specimens from the Cerrado in comparison with those from the Amazon. Females had a significantly larger number of ventral scales, on average, whereas males had more sub-caudal scales. However, there was no intersexual difference in tail length or head width, although the heads of the males were significantly longer, which may reflect dietary differences. Breeding females from the Amazon region contained between one and six eggs (N = 12, mean = 3.0), whereas two females from the Cerrado had four to six eggs (N = 10, mean = 5.0). No relationship was found between the SVL of the Amazonian females and the number of eggs or vitellogenic follicles they contained (Cerrado females were not analyzed here due to small sample size). Males are smaller than their female counterpart when they reach sexual maturity. Even though females from the Amazon reproduce throughout the year, females from the Cerrado breed seasonality.

Interaction between GIS and hydrologic model: a preliminary approach using ArcHydro Framework Data Model

In different regions of Brazil, population growth and economic development can degrade water quality, compromising watershed health and human supply. Because of its ability to combine spatial and temporal data in the same environment and to create water resources management (WRM) models, the Geographical Information System (GIS) is a powerful tool for managing water resources, preventing floods and estimating water supply. This paper discusses the integration between GIS and hydrological models and presents a case study relating to the upper section of the Paraíba do Sul Basin (Sao Paulo State portion), situated in the Southeast of Brazil. The case study presented in this paper has a database suitable for the basin's dimensions, including digitized topographic maps at a 50,000 scale. From an ArcGIS®/ArcHydro Framework Data Model, a geometric network was created to produce different raster products. This first grid derived from the digital elevation model grid (DEM) is the flow direction map followed by flow accumulation, stream and catchment maps. The next steps in this research are to include the different multipurpose reservoirs situated along the Paraíba do Sul River and to incorporate rainfall time series data in ArcHydro to build a hydrologic data model within a GIS environment in order to produce a comprehensive spatial-temporal model.

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.

Cryptic species in Iphisa elegans Gray, 1851 (Squamata: Gymnophthalmidae) revealed by hemipenial morphology and molecular data

Iphisa elegans Gray, 1851 is a ground-dwelling lizard widespread over Amazonia that displays a broadly conserved external morphology over its range. This wide geographical distribution and conservation of body form contrasts with the expected poor dispersal ability of the species, the tumultuous past of Amazonia, and the previously documented prevalence of cryptic species in widespread terrestrial organisms in this region. Here we investigate this homogeneity by examining hemipenial morphology and conducting phylogenetic analyses of mitochondrial (CYTB) and nuclear (C-MOS) DNA sequence data from 49 individuals sampled across Amazonia. We detected remarkable variation in hemipenial morphology within this species, with multiple cases of sympatric occurrence of distinct hemipenial morphotypes. Phylogenetic analyses revealed highly divergent lineages corroborating the patterns suggested by the hemipenial morphotypes, including co-occurrence of different lineages. The degrees of genetic and morphological distinctness, as well as instances of sympatry among mtDNA lineages/morphotypes without nuDNA allele sharing, suggest that I. elegans is a complex of cryptic species. An extensive and integrative taxonomic revision of the I. elegans complex throughout its wide geographical range is needed. (c) 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166, 361376.

Engineering geological data in support of municipal land use planning-a case study in Analandia, southeast Brazil

This paper presents a method for transforming the information of an engineering geological map into useful information for non-specialists involved in land-use planning. The method consists of classifying the engineering geological units in terms of land use capability and identifying the legal and the geologic restrictions that apply in the study area. Both informations are then superimposed over the land use and a conflict areas map is created. The analysis of these data leads to the identification of existing and forthcoming land use conflicts and enables the proposal of planning measures on a regional and local scale. The map for the regional planning was compiled at a 1:50,000 scale and encompasses the whole municipal land area where uses are mainly rural. The map for the local planning was compiled at a 1:10,000 scale and encompasses the urban area. Most of the classification and operations on maps used spatial analyst tools available in the Geographical Information System. The regional studies showed that the greater part of Analandia's territory presents appropriate land uses. The local-scale studies indicate that the majority of the densely occupied urban areas are in suitable land. Although the situation is in general positive, municipal policies should address the identified and expected land use conflicts, so that it can be further improved.

Haplotype frequencies based on eight polymorphic sites at the 3' untranslated region of the HLA-G gene in individuals from two different geographical regions of Brazil

The Brazilian population represents an admixture of native Amerindians, Portuguese settlers and Africans who were brought as slaves during the colonization period that began in the 16th century and was followed by waves of immigrations of Europeans and Asians in the 20th century. The contribution of these different ethnic groups to the constitution of Brazilian populations from different geographic regions is variable and, in addition to environmental factors, might act by determining different allele profiles among Brazilian populations from different regions. We studied polymorphic sites at the 3' untranslated region of the HLA-G gene in individuals from a Northeastern Brazilian region and compared them to our previously published data about a Southeastern Brazilian region, located at a distance of 2589 km. Our results showed that most polymorphic sites present a similar distribution in both populations, except for the lower frequency of the +3003C allele in the Northeastern population compared to the Southeastern population. Although differences in genotypic distribution were only significant for the +3003 locus (P = 0.0201), the diversity of haplotypes was distinct for each population. These results are important for casecontrol studies on the association of human leucocyte antigen-G polymorphism with disease and also in terms of the genetic structure of two distinct Brazilian populations.

Geographical distribution of American cutaneous leishmaniasis and its phlebotomine vectors (Diptera: Psychodidae) in the state of São Paulo, Brazil

Abstract Background American cutaneous leishmaniasis (ACL) is a re-emerging disease in the state of São Paulo, Brazil. It is important to understand both the vector and disease distribution to help design control strategies. As an initial step in applying geographic information systems (GIS) and remote sensing (RS) tools to map disease-risk, the objectives of the present work were to: (i) produce a single database of species distributions of the sand fly vectors in the state of São Paulo, (ii) create combined distributional maps of both the incidence of ACL and its sand fly vectors, and (iii) thereby provide individual municipalities with a source of reference material for work carried out in their area. Results A database containing 910 individual records of sand fly occurrence in the state of São Paulo, from 37 different sources, was compiled. These records date from between 1943 to 2009, and describe the presence of at least one of the six incriminated or suspected sand fly vector species in 183/645 (28.4%) municipalities. For the remaining 462 (71.6%) municipalities, we were unable to locate records of any of the six incriminated or suspected sand fly vector species (Nyssomyia intermedia, N. neivai, N. whitmani, Pintomyia fischeri, P. pessoai and Migonemyia migonei). The distribution of each of the six incriminated or suspected vector species of ACL in the state of São Paulo were individually mapped and overlaid on the incidence of ACL for the period 1993 to 1995 and 1998 to 2007. Overall, the maps reveal that the six sand fly vector species analyzed have unique and heterogeneous, although often overlapping, distributions. Several sand fly species - Nyssomyia intermedia and N. neivai - are highly localized, while the other sand fly species - N. whitmani, M. migonei, P. fischeri and P. pessoai - are much more broadly distributed. ACL has been reported in 160/183 (87.4%) of the municipalities with records for at least one of the six incriminated or suspected sand fly vector species, while there are no records of any of these sand fly species in 318/478 (66.5%) municipalities with ACL. Conclusions The maps produced in this work provide basic data on the distribution of the six incriminated or suspected sand fly vectors of ACL in the state of São Paulo, and highlight the complex and geographically heterogeneous pattern of ACL transmission in the region. Further studies are required to clarify the role of each of the six suspected sand fly vector species in different regions of the state of São Paulo, especially in the majority of municipalities where ACL is present but sand fly vectors have not yet been identified.

A Dark Matter Search with AMANDA : Limits on the Muon Flux from Neutralino Annihilations at the Centre of the Earth with 1997-99 Data

The nature of the dark matter in the Universe is one of the greatest mysteries in modern astronomy. The neutralino is a nonbaryonic dark matter candidate in minimal supersymmetric extensions to the standard model of particle physics. If the dark matter halo of our galaxy is made up of neutralinos some would become gravitationally trapped inside massive bodies like the Earth. Their pair-wise annihilation produces neutrinos that can be detected by neutrino experiments looking in the direction of the centre of the Earth. The AMANDA neutrino telescope, currently the largest in the world, consists of an array of light detectors buried deep in the Antarctic glacier at the geographical South Pole. The extremely transparent ice acts as a Cherenkov medium for muons passing the array and using the timing information of detected photons it is possible to reconstruct the muon direction. A search has been performed for nearly vertically upgoing neutrino induced muons with AMANDA-B10 data taken over the three year period 1997-99. No excess above the atmospheric neutrino background expectation was found. Upper limits at the 90 % confidence level has been set on the annihilation rate of neutralinos at the centre of the Earth and on the muon flux induced by neutrinos created by the annihilation products.

Opportunistic Data Gathering and Dissemination in Urban Scenarios

In the era of the Internet of Everything, a user with a handheld or wearable device equipped with sensing capability has become a producer as well as a consumer of information and services. The more powerful these devices get, the more likely it is that they will generate and share content locally, leading to the presence of distributed information sources and the diminishing role of centralized servers. As of current practice, we rely on infrastructure acting as an intermediary, providing access to the data. However, infrastructure-based connectivity might not always be available or the best alternative. Moreover, it is often the case where the data and the processes acting upon them are of local scopus. Answers to a query about a nearby object, an information source, a process, an experience, an ability, etc. could be answered locally without reliance on infrastructure-based platforms. The data might have temporal validity limited to or bounded to a geographical area and/or the social context where the user is immersed in. In this envisioned scenario users could interact locally without the need for a central authority, hence, the claim of an infrastructure-less, provider-less platform. The data is owned by the users and consulted locally as opposed to the current approach of making them available globally and stay on forever. From a technical viewpoint, this network resembles a Delay/Disruption Tolerant Network where consumers and producers might be spatially and temporally decoupled exchanging information with each other in an adhoc fashion. To this end, we propose some novel data gathering and dissemination strategies for use in urban-wide environments which do not rely on strict infrastructure mediation. While preserving the general aspects of our study and without loss of generality, we focus our attention toward practical applicative scenarios which help us capture the characteristics of opportunistic communication networks.

Genetic and morphological variation and differentiation of Raja clavata populations in the European seas: marker development and preliminary data

In this study the population structure and connectivity of the Mediterranean and Atlantic Raja clavata (L., 1758) were investigated by analyzing the genetic variation of six population samples (N = 144) at seven nuclear microsatellite loci. The genetic dataset was generated by selecting population samples available in the tissue databases of the GenoDREAM laboratory (University of Bologna) and of the Department of Life Sciences and Environment (University of Cagliari), all collected during past scientific surveys (MEDITS, GRUND) from different geographical locations in the Mediterranean basin and North-east Atlantic sea, as North Sea, Sardinian coasts, Tuscany coasts and Cyprus Island. This thesis deals with to estimate the genetic diversity and differentiation among 6 geographical samples, in particular, to assess the presence of any barrier (geographic, hydrogeological or biological) to gene flow evaluating both the genetic diversity (nucleotide diversity, observed and expected heterozygosity, Hardy- Weinberg equilibrium analysis) and population differentiation (Fst estimates, population structure analysis). In addition to molecular analysis, quantitative representation and statistical analysis of morphological individuals shape are performed using geometric morphometrics methods and statistical tests. Geometric coordinates call landmarks are fixed in 158 individuals belonging to two population samples of Raja clavata and in population samples of closely related species, Raja straeleni (cryptic sibling) and Raja asterias, to assess significant morphological differences at multiple taxonomic levels. The results obtained from the analysis of the microsatellite dataset suggested a geographic and genetic separation between populations from Central-Western and Eastern Mediterranean basins. Furthermore, the analysis also showed that there was no separation between geographic samples from North Atlantic Ocean and central-Western Mediterranean, grouping them to a panmictic population. The Landmark-based geometric morphometry method results showed significant differences of body shape able to discriminate taxa at tested levels (from species to populations).