Efficient Algorithms for Coastal Geographic Problems

The increasing performance of computers has made it possible to solve algorithmically problems for which manual and possibly inaccurate methods have been previously used. Nevertheless, one must still pay attention to the performance of an algorithm if huge datasets are used or if the problem iscomputationally difficult. Two geographic problems are studied in the articles included in this thesis. In the first problem the goal is to determine distances from points, called study points, to shorelines in predefined directions. Together with other in-formation, mainly related to wind, these distances can be used to estimate wave exposure at different areas. In the second problem the input consists of a set of sites where water quality observations have been made and of the results of the measurements at the different sites. The goal is to select a subset of the observational sites in such a manner that water quality is still measured in a sufficient accuracy when monitoring at the other sites is stopped to reduce economic cost. Most of the thesis concentrates on the first problem, known as the fetch length problem. The main challenge is that the two-dimensional map is represented as a set of polygons with millions of vertices in total and the distances may also be computed for millions of study points in several directions. Efficient algorithms are developed for the problem, one of them approximate and the others exact except for rounding errors. The solutions also differ in that three of them are targeted for serial operation or for a small number of CPU cores whereas one, together with its further developments, is suitable also for parallel machines such as GPUs.

Declines of Aerial Insectivores in North America Follow a Geographic Gradient

North American birds that feed on aerial insects are experiencing widespread population declines. An analysis of the North American Breeding Bird Survey trend estimates for 1966 to 2006 suggests that declines in this guild are significantly stronger than in passerines in general. The pattern of decline also shows a striking geographical gradient, with aerial insectivore declines becoming more prevalent towards the northeast of North America. Declines are also more acute in species that migrate long distances compared to those that migrate short distances. The declines become manifest, almost without exception, in the mid 1980s. The taxonomic breadth of these downward trends suggests that declines in aerial insectivore populations are linked to changes in populations of flying insects, and these changes might be indicative of underlying ecosystem changes.

International entry modes in Brazil and the CAGE distances effects

The international entry mode choices have a relevant importance for the impact they have on successful internationalization strategies. Many theories have been developed to describe which entry mode may be better than another according to the particular situation. The CAGE Distances Framework developed by Ghemawat to identify which dimensions companies should look when develop an internationalization strategy, may be useful to identify also how those dimensions impact on the international entry mode decision. The aim of this thesis is to study which kind of relationship exists between Cultural, Administrative, Geographic and Economic Distances and international entry mode choice. It analyzes a sample of companies that have been entered in Brazil through a logistic regression. According to this analysis, a negative and significant relation between Cultural Distance and need of control exists, a positive one exists between Administrative and Geographic, while no significant relationship has been found with the Economic dimension. Those findings are conceivably explainable through the theories found by scholars, but a deeper analysis that may take into account the specificity of every country is highly recommended, like the one developed with Brazil in this thesis.

Geometric morphometrics of the wing as a tool for assigning genetic lineages and geographic origin to Melipona beecheii (Hymenoptera: Meliponini)

The stingless bee Melipona beecheii presents great variability and is considered a complex of species. In order to better understand this species complex, we need to evaluate its diversity and develop methods that allow geographic traceability of the populations. Here we present a fast, efficient, and inexpensive means to accomplish this using geometric morphometrics of wings. We collected samples from Mexico, Guatemala, El Salvador, Nicaragua, and Costa Rica and we were able to correctly assign 87.1% of the colonies to their sampling sites and 92.4% to their haplotype. We propose that geometric morphometrics of the wing could be used as a first step analysis leaving the more expensive molecular analysis only to doubtful cases.

Geographic Information Systems (GIS) in Assessing Dental Health

The present study investigated the distribution profile of dental caries and its association with areas of social deprivation at the individual and contextual level. The cluster sample consisted of 1,002 12-year-old schoolchildren from Piracicaba, SP, Brazil. The DMFT Index was used for dental caries and the Care Index was used to determine access to dental services. On the individual level, variables were associated with a better oral status. On the contextual level, areas were not associated with oral status. However, maps enabled determining that the central districts have better social and oral conditions than the deprived outlying districts.

Precision of distances and ordering of microsatellite markers in consensus linkage maps of chromosomes 1, 3 and 4 from two reciprocal chicken populations using bootstrap sampling

Some factors complicate comparisons between linkage maps from different studies. This problem can be resolved if measures of precision, such as confidence intervals and frequency distributions, are associated with markers. We examined the precision of distances and ordering of microsatellite markers in the consensus linkage maps of chromosomes 1, 3 and 4 from two F 2 reciprocal Brazilian chicken populations, using bootstrap sampling. Single and consensus maps were constructed. The consensus map was compared with the International Consensus Linkage Map and with the whole genome sequence. Some loci showed segregation distortion and missing data, but this did not affect the analyses negatively. Several inversions and position shifts were detected, based on 95% confidence intervals and frequency distributions of loci. Some discrepancies in distances between loci and in ordering were due to chance, whereas others could be attributed to other effects, including reciprocal crosses, sampling error of the founder animals from the two populations, F(2) population structure, number of and distance between microsatellite markers, number of informative meioses, loci segregation patterns, and sex. In the Brazilian consensus GGA1, locus LEI1038 was in a position closer to the true genome sequence than in the International Consensus Map, whereas for GGA3 and GGA4, no such differences were found. Extending these analyses to the remaining chromosomes should facilitate comparisons and the integration of several available genetic maps, allowing meta-analyses for map construction and quantitative trait loci (QTL) mapping. The precision of the estimates of QTL positions and their effects would be increased with such information.

Allopatric speciation in ticks: genetic and reproductive divergence between geographic strains of Rhipicephalus (Boophilus) microplus

Background: The cattle tick, Rhipicephalus (Boophilus) microplus, economically impact cattle industry in tropical and subtropical regions of the world. The morphological and genetic differences among R. microplus strains have been documented in the literature, suggesting that biogeographical and ecological separation may have resulted in boophilid ticks from America/Africa and those from Australia being different species. To test the hypothesis of the presence of different boophilid species, herein we performed a series of experiments to characterize the reproductive performance of crosses between R. microplus from Australia, Africa and America and the genetic diversity of strains from Australia, Asia, Africa and America. Results: The results showed that the crosses between Australian and Argentinean or Mozambican strains of boophilid ticks are infertile while crosses between Argentinean and Mozambican strains are fertile. These results showed that tick strains from Africa (Mozambique) and America (Argentina) are the same species, while ticks from Australia may actually represent a separate species. The genetic analysis of mitochondrial 12S and 16S rDNA and microsatellite loci were not conclusive when taken separately, but provided evidence that Australian tick strains were genetically different from Asian, African and American strains. Conclusion: The results reported herein support the hypothesis that at least two different species share the name R. microplus. These species could be redefined as R. microplus (Canestrini, 1887) (for American and African strains) and probably the old R. australis Fuller, 1899 (for Australian strains), which needs to be redescribed. However, experiments with a larger number of tick strains from different geographic locations are needed to corroborate these results.

Molecular and geographic analyses of vampire bat-transmitted cattle rabies in central Brazil

Background: Vampire bats are important rabies virus vectors, causing critical problems in both the livestock industry and public health sector in Latin America. In order to assess the epidemiological characteristics of vampire bat-transmitted rabies, the authors conducted phylogenetic and geographical analyses using sequence data of a large number of cattle rabies isolates collected from a wide geographical area in Brazil. Methods: Partial nucleoprotein genes of rabies viruses isolated from 666 cattle and 18 vampire bats between 1987 and 2006 were sequenced and used for phylogenetic analysis. The genetic variants were plotted on topographical maps of Brazil. Results: In this study, 593 samples consisting of 24 genetic variants were analyzed. Regional localization of variants was observed, with the distribution of several variants found to be delimited by mountain ranges which served as geographic boundaries. The geographical distributions of vampire-bat and cattle isolates that were classified as the identical phylogenetic group were found to overlap with high certainty. Most of the samples analyzed in this study were isolated from adjacent areas linked by rivers. Conclusion: This study revealed the existence of several dozen regional variants associated with vampire bats in Brazil, with the distribution patterns of these variants found to be affected by mountain ranges and rivers. These results suggest that epidemiological characteristics of vampire bat-related rabies appear to be associated with the topographical and geographical characteristics of areas where cattle are maintained, and the factors affecting vampire bat ecology.

Genetic Variation among Major Human Geographic Groups Supports a Peculiar Evolutionary Trend in PAX9

A total of 172 persons from nine South Amerindian, three African and one Eskimo populations were studied in relation to the Paired box gene 9 (PAX9) exon 3 (138 base pairs) as well as its 5' and 3' flanking intronic segments (232 bp and 220 bp, respectively) and integrated with the information available for the same genetic region from individuals of different geographical origins. Nine mutations were scored in exon 3 and six in its flanking regions; four of them are new South American tribe-specific singletons. Exon3 nucleotide diversity is several orders of magnitude higher than its intronic regions. Additionally, a set of variants in the PAX9 and 101 other genes related with dentition can define at least some dental morphological differences between Sub-Saharan Africans and non-Africans, probably associated with adaptations after the modern human exodus from Africa. Exon 3 of PAX9 could be a good molecular example of how evolvability works.

Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies

Background: The ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized. Results: We examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for similar to 40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance. Conclusion: These findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.

THREE-DIMENSIONAL PHOTOIONIZATION STRUCTURE AND DISTANCES OF PLANETARY NEBULAE. IV. NGC 40

Continuing our series of papers on the three-dimensional (3D) structure and accurate distances of planetary nebulae (PNe), we present here the results obtained for PN NGC 40. Using data from different sources and wavelengths, we construct 3D photoionization models and derive the physical quantities of the ionizing source and nebular gas. The procedure, discussed in detail in the previous papers, consists of the use of 3D photoionization codes constrained by observational data to derive the 3D nebular structure, physical and chemical characteristics, and ionizing star parameters of the objects by simultaneously fitting the integrated line intensities, the density map, the temperature map, and the observed morphologies in different emission lines. For this particular case we combined hydrodynamical simulations with the photoionization scheme in order to obtain self-consistent distributions of density and velocity of the nebular material. Combining the velocity field with the emission-line cubes we also obtained the synthetic position-velocity plots that are compared to the observations. Finally, using theoretical evolutionary tracks of intermediate-and low-mass stars, we derive the mass and age of the central star of NGC 40 as (0.567 +/- 0.06) M(circle dot) and (5810 +/- 600) yr, respectively. The distance obtained from the fitting procedure was (1150 +/- 120) pc.

The genus Rhagomys (Thomas 1917) (Rodentia, Cricetidae, Sigmodontinae) in South America: morphological considerations, geographic distribution and zoogeographic comments

American Museum of Natural History

Geographic variation of sex pheromone and mitochondrial DNA in Diatraea saccharalis (Fab., 1794) (Lepidoptera: Crambidae)

(9Z,11E)-hexadecadienal and (Z11)-hexadecenal, the main sex pheromone components of the sugarcane borer, Diatraea saccharalis, were identified and quantified from four Brazilian and one Colombian populations using GC-EAD, GC-MS and GC analyses. Three different ratios were observed, 9:1,6:1, and 3:1. The pheromone concentration for the major component, (9Z,11E)-hexadecadienal, varied from 6.8 ng/gland to 21.9 ng/gland and from 1.7 ng/gland to 6.5 to the minor component, (Z11)-hexadecenal. The 25 D. saccharalis cytochrome oxidase II sequences that were analyzed showed low intra-specific variation and represented only 11 haplotypes, with the most frequent being the one represented by specimens from Sao Paulo, Parana, and Pernambuco states. Specimens from Colombia showed the highest genetic divergence from the others haplotypes studied. Data on the genetic variability among specimens, more than their geographic proximity, were in agreement with data obtained from analyses of the pheromone extracts. Our data demonstrate a variation in pheromone composition and a covariation in haplotypes of the D. saccharalis populations studied. (C) 2010 Elsevier Ltd. All rights reserved.

The Effects of Host, Geographic Origin, and Gender on the Thermal Requirements of Diaphorina citri (Hemiptera: Psyllidae)

Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is the vector of the bacteria that causes citrus greening and is considered one of the world`s most important citrus diseases. We examined how host, geographic region, and gender affect the thermal requirements of D. citri. The insects were reared in climatic chambers at constant temperatures of 18, 20, 22, 25, 28, 30, and 32 1 degrees C, 70 +/- 10% RH, and a 14 h photophase. Host plants for D. citri included orange (Citrus sinensis [Rutaceae]) varieties Pera and Natal, the rootstock, Rungpur lime (C. limonia [Rutaceae]) and the natural host, Orange jessamine (Murraya paniculata [Rutaceae]). To study the influence of geographic origin on thermal requirements, we studied D. citri populations from Piracicaba, SP (warmer region) and Itapetininga, SP (cooler region). The duration and survival of the development stages and the duration of the total development (egg-adult) did not differ significantly on the different hosts, but it did vary with temperature. Nymphs of D. citri created on the different hosts have the same thermal requirements. The thermal requirements for this species collected from the two climate regions were identical; males and females also had the same thermal requirements.

Snake venomics and antivenomics of Crotalus durissus subspecies from Brazil: Assessment of geographic variation and its implication on snakebite management

We report the comparative proteomic and antivenomic characterization of the venoms of subspecies cascavella and collilineatus of the Brazilian tropical rattlesnake Crotalus durissus. The venom proteomes of C. d. collilineatus and C. d. cascavella comprise proteins in the range of 4-115 kDa belonging to 9 and 8 toxin families, respectively. Collilineatus and cascavella venoms contain 20-25 main toxins belonging to the following protein families: disintegrin, PLA(2), serine proteinase, cysteine-rich secretory protein (CRISP), vascular endothelial growth factor-like (VEGF), L-amino acid oxidase, C-type lectin-like, and snake venom metalloproteinase (SVMP). As judged by reverse-phase HPLC and mass spectrometry, cascavella and collilineatus share about 90% of their venom proteome. However, the relative occurrence of the toxin families departs among the two C. durissus subspecies venoms. The most notable difference is the presence of the myotoxin crotamine in some C. d. collilineatus specimens (averaging 20.8% of the total proteins of pooled venom), which is absent in the venom of C. d. cascavella. On the other hand, the neurotoxic PLA2 crotoxin represents the most abundant protein in both C. durissus venoms, comprising 67.4% of the toxin proteome in C. d. collilineatus and 72.5% in C. d. cascavella. Myotoxic PLA(2)s are also present in the two venoms albeit in different relative concentrations (18.1% in C. d. cascavella vs. 4.6% in C. d. collilineatus). The venom composition accounts for the clinical manifestations caused by C. durissus envenomations: systemic neurotoxicity and myalgic symptoms and coagulation disturbances, frequently accompanied by myoglobinuria and acute renal failure. The overall compositions of C. d. subspecies cascavella and collilineatus venoms closely resemble that of C. d. terrificus, supporting the view that these taxa can be considered geographical variations of the same species. Pooled venom from adult C.d. cascavella and neonate C.d. terrificus lack crotamine, whereas this skeletal muscle cell membrane depolarizing inducing myotoxin accounts for similar to 20% of the total toxins of venom pooled from C.d. collilineatus and C.d. terrificus from Southern Brazil. The possible relevance of the observed venom variability among the tropical rattlesnake subspecies was assessed by antivenomics using anti-crotalic antivenoms produced at Instituto Butantan and Instituto Vital Brazil. The results revealed that both antivenoms exhibit impaired immunoreactivity towards crotamine and display restricted (similar to 60%) recognition of PLA(2) molecules (crotoxin and D49-myotoxins) from C. d. cascavella and C. d. terrificus venoms. This poor reactivity of the antivenoms may be due to a combination of factors: on the one hand, an inappropriate choice of the mixture of venoms for immunization and, on the other hand, the documented low immunogenicity of PLA(2) molecules. C. durissus causes most of the lethal snakebite accidents in Brazil. The implication of the geographic variation of venom composition for the treatment of bites by different C. durissus subspecies populations is discussed. (C) 2010 Elsevier B.V. All rights reserved.