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.

Automatic Network Fingerprinting through Single-Node Motifs

Complex networks have been characterised by their specific connectivity patterns (network motifs), but their building blocks can also be identified and described by node-motifs-a combination of local network features. One technique to identify single node-motifs has been presented by Costa et al. (L. D. F. Costa, F. A. Rodrigues, C. C. Hilgetag, and M. Kaiser, Europhys. Lett., 87, 1, 2009). Here, we first suggest improvements to the method including how its parameters can be determined automatically. Such automatic routines make high-throughput studies of many networks feasible. Second, the new routines are validated in different network-series. Third, we provide an example of how the method can be used to analyse network time-series. In conclusion, we provide a robust method for systematically discovering and classifying characteristic nodes of a network. In contrast to classical motif analysis, our approach can identify individual components (here: nodes) that are specific to a network. Such special nodes, as hubs before, might be found to play critical roles in real-world networks.

Universal and nonuniversal contributions to block-block entanglement in many-fermion systems

We calculate the entanglement entropy of blocks of size x embedded in a larger system of size L, by means of a combination of analytical and numerical techniques. The complete entanglement entropy in this case is a sum of three terms. One is a universal x- and L-dependent term, first predicted by Calabrese and Cardy, the second is a nonuniversal term arising from the thermodynamic limit, and the third is a finite size correction. We give an explicit expression for the second, nonuniversal, term for the one-dimensional Hubbard model, and numerically assess the importance of all three contributions by comparing to the entropy obtained from fully numerical diagonalization of the many-body Hamiltonian. We find that finite-size corrections are very small. The universal Calabrese-Cardy term is equally small for small blocks, but becomes larger for x > 1. In all investigated situations, however, the by far dominating contribution is the nonuniversal term stemming from the thermodynamic limit.

On the k-restricted structure ratio in planar and outerplanar graphs

A planar k-restricted structure is a simple graph whose blocks are planar and each has at most k vertices. Planar k-restricted structures are used by approximation algorithms for Maximum Weight Planar Subgraph, which motivates this work. The planar k-restricted ratio is the infimum, over simple planar graphs H, of the ratio of the number of edges in a maximum k-restricted structure subgraph of H to the number edges of H. We prove that, as k tends to infinity, the planar k-restricted ratio tends to 1/2. The same result holds for the weighted version. Our results are based on analyzing the analogous ratios for outerplanar and weighted outerplanar graphs. Here both ratios tend to 1 as k goes to infinity, and we provide good estimates of the rates of convergence, showing that they differ in the weighted from the unweighted case.

LEARNING A COMPLEX MOTOR SKILL FROM VIDEO AND POINT-LIGHT DEMONSTRATIONS

The aim of this Study was to compare the learning process of a highly complex ballet skill following demonstrations of point light and video models 16 participants divided into point light and video groups (ns = 8) performed 160 trials of a pirouette equally distributed in blocks of 20 trials alternating periods of demonstration and practice with a retention test a day later Measures of head and trunk oscillation coordination d1 parity from the model and movement time difference showed similarities between video and point light groups ballet experts evaluations indicated superiority of performance in the video over the point light group Results are discussed in terms of the task requirements of dissociation between head and trunk rotations focusing on the hypothesis of sufficiency and higher relevance of information contained in biological motion models applied to learning of complex motor skills

Economic viability of doses and split-applications of nitrogen fertilization in corn crop in a eutrophic Red Latosol

Nitrogen is the nutrient that is most absorbed by the corn crop, with the most complex management, and has the highest share on the cost of corn production. The objective of this work was to evaluate the economic viability of different rates and split-applications of nitrogen fertilization, as such as urea, in the corn crop in a eutrophic Red Latosol (Oxisol). The study was carried out in the Experimental Station of the Regional Pole of the Sao Paulo Northwest Agribusiness Development (APTA), in Votuporanga, State of Sao Paulo, Brazil. The experimental design was randomized complete blocks with nine treatments and four replications, consisting of five N rates: 0, 55, 95, 135 and 175 kg ha(-1), 15 kg ha-l applied in the seeding and the remainder in top dressing: 40 and 80 kg ha(-1) N at forty days after seeding (DAS), or 1/2 + 1/2 at 20 and 40 DAS; 120 kg ha-1 N split in 1/2 + 1/2 or 1/3 + 1/3 + 1/3 at 20, 40 or 60 DAS; 160 kg ha(-1) N split in 1/4 + 3/8 + 3/8 or 114 + 1/4 + 1/4 + 1/4 at 20, 40, 60 and 80 DAS. The application of 135 kg ha-l of N split in three times provided the best benefit/cost ratio. The non-application of N provided the lowest economic return, proving to be unviable.

Contribuition of nitrogen from biological nitrogen fixation, nitrogen fertilizer and soil nitrogen on the growth of the common bean and cowpea

Biological nitrogen fixation (BNF) constitutes a valuable source of this nutrient for the common bean Phaseolus vulgaris L and cowpea Vigna unguiculata (L.) Walp., being its avaibility affected by mineral N in the soil solution. The objectives of this work were to evaluate the effects of nitrogen rate, as urea, on symbiotic fixation of N(2) in common bean and cowpea plants, using the isotopic technique, and quantifying the relative contributions of N sources symbiotic N(2) fixation, soil native nitrogen and urea N on the growth of the common bean and cowpea. Non nodulating soybean plants were used as standard. The research was carried out in greenhouse, using pots with 5 kg of soil from a Typic Haplustox (Dystrophic Red Yellow Latosol). The experimental design was completely randomized blocks, with 30 treatments and three replications, arranged in 5x3x2 factorial outline. The treatments consisted of five N rates: 2, 15, 30, 45 and 60 mg N kg(-1) soil; three sampling times: 23, 40 and 76 days after sowing (DAS) and two crops: common bean and cowpea. The BNF decreased with increase N rates, varying from 81.5% to 55.6% for cowpea, and from 71.9% to 55.1% for common bean. The symbiotic N(2) fixation in cowpea can substitute totally the nitrogen fertilization. The nitrogen absorption from soil is not affected by nitrogen fertilizer rate. The N recovery from fertilizer at 76 DAS was of 60.7% by common bean, and 57.1% by cowpea. The symbiotic association in common bean needs the application of a starting dose (40 kg N ha(-1)) for economically acceptable yields.

Seed phytate and protein content in beans depending on the application of basalt powder

Seed phytate and protein content in beans depending on the application of basalt powder. The content of phytate in the grains is correlated with the supply of phosphorus to the plant, but there is a lack of knowledge as to possible effect of slower availability of nutrients in the soil. The objectives of this study were to assess the effect of rock powder, alone or combined with cattle manure, on the productivity, levels of phosphorus, protein and phytate content in beans. The experiment was carried out in a randomized blocks design, with four replications. The treatments were control (limestone, granite and natural phosphate); conventional fertilization; powder basalt (2.5, 5.0, 10.0 and 20.0 ton. ha(-1)); cattle manure, and doses of powder basalt with cattle manure. In the treatment with conventional fertilizer, the total phosphorus content in grain was higher than the control, but the application of powder of basalt did not show a difference significant. Increase in the doses of basalt powder increased the phosphorus content, but phytate content remained constant. Basalt powder proved to be an alternative to maintain low levels of phosphorus in the form of phytate in the grains.

Fractionation of Zn, Cd and Pb in a Tropical Soil After Nine-Year Sewage Sludge Applications

A long-term field experiment was carried out in the experiment farm of the Sao Paulo State University, Brazil, to evaluate the phytoavailability of Zn, Cd and Pb in a Typic Eutrorthox soil treated with sewage sludge for nine consecutive years, using the sequential extraction and organic matter fractionation methods. During 2005-2006, maize (Zea mays L.) was used as test plants and the experimental design was in randomized complete blocks with four treatments and five replicates. The treatments consisted of four sewage sludge rates (in a dry basis): 0.0 (control, with mineral fertilization), 45.0, 90.0 and 127.5 t ha(-1), annually for nine years. Before maize sowing, the sewage sludge was manually applied to the soil and incorporated at 10 cm depth. Soil samples (0-20 cm layer) for Zn, Cd and Pb analysis were collected 60 days after sowing. The successive applications of sewage sludge to the soil did not affect heavy metal (Cd and Pb) fractions in the soil, with exception of Zn fractions. The Zn, Cd and Pb distributions in the soil were strongly associated with humin and residual fractions, which are characterized by stable chemical bonds. Zinc, Cd and Pb in the soil showed low phytoavailability after nine-year successive applications of sewage sludge to the soil.

Barium uptake by maize plants as affected by sewage sludge in a long-term field study

Along-term experiment was carried out under field conditions in Jaboticabal, SP, Brazil, with the objective of evaluating the concentration of Ba in soil and in maize plants grown in a soil treated with sewage sludge for nine consecutive years. During 2005/2006, maize was used as test plants and the experimental design was in randomized complete blocks with four treatments and five replicates. Treatments consisted of: 0.0, 45.0, 90.0 and 127.5 t ha(-1) sewage sludge (dry basis). Sewage sludge application increased soil Ba concentration. Barium accumulated in the parts of maize plants were generally affected by the successive applications of sewage sludge to the soil. However, the concentration of Ba in maize grain did not exceed the critical levels of Ba for human consumption. Sewage sludge applied to soil for a long time did not affect dry matter and grain production, nevertheless had the similar effect of mineral fertilization. Published by Elsevier B.V.

A comparison between the concentration of mast cells in squamous cell carcinomas of the skin and oral cavity

FUNDAMENTS: The lethality of squamous cell carcinomas (SCC) of the skin is considered low. SCC in the mouth is usually associated with poor prognosis. Current evidence suggests that mast cells in the normal tissue contribute to the tumorigenesis of SCC, probably by promoting angiogenesis. OBJECTIVE: The aim of this study was to compare the concentration of mast cells in SCC of the mouth and skin and evaluate whether there is a correlation with the degree of differentiation of these tumors. MATERIAL AND METHODS: Thirty cases of SCC of the skin and 34 of the mouth were investigated. Toluidine blue staining was used to identify mast cells in blocks containing the central portion of the neoplasm. RESULTS: A concentration of between 0 and 10 mast cells was found in one single case of SCC of the skin and there were no cases of SCC of the mouth with concentrations of mast cells in the tumor >201. In the majority of cases of SCC of the mouth (47%; n=16), mast cell concentration was between 0 and 10, with a concentration >51 mast cells in 80% of cases of SCC of the skin. All the cases of SCC of the mouth with a concentration of mast cells between 100 and 200 and 80% of those with a concentration of 51-99 were located on the lip. The concentration of mast cells was unrelated to the degree of differentiation of the tumor. CONCLUSION: The concentration of mast cells is lower in SCC of the mouth except when the tumor is located on the lip. This may reflect a lower need for cell activation in the microenvironment to improve vascularization in oral cancer.

Effects of goal difficulty and temporality in motor skill acquisition using the Bachman ladder

The effects of different types of goal setting on motor skill learning were investigated. 100 individuals (64 men, 36 women) without experience in the performance of the Bachman ladder task participated. Participants were randomly assigned to one of five goal groups: (a) generic, (b) long-term, difficult, (c) long-term, easy; (d) short- and long-term, difficult, and (e) short- and long-term, easy. In the acquisition phase, participants performed 200 trials, and in the transfer and retention phases, each performed 50 trials. The dependent variable was the number of steps achieved in blocks of 10 trials. The results showed that the groups had similar performances in both the transfer and retention phases. Setting of generic, difficult, easy, long- and short-term, and self-setting goals all enabled similar effects on motor learning.

Modeling associations between genetic markers using Bayesian networks

Motivation: Understanding the patterns of association between polymorphisms at different loci in a population ( linkage disequilibrium, LD) is of fundamental importance in various genetic studies. Many coefficients were proposed for measuring the degree of LD, but they provide only a static view of the current LD structure. Generative models (GMs) were proposed to go beyond these measures, giving not only a description of the actual LD structure but also a tool to help understanding the process that generated such structure. GMs based in coalescent theory have been the most appealing because they link LD to evolutionary factors. Nevertheless, the inference and parameter estimation of such models is still computationally challenging. Results: We present a more practical method to build GM that describe LD. The method is based on learning weighted Bayesian network structures from haplotype data, extracting equivalence structure classes and using them to model LD. The results obtained in public data from the HapMap database showed that the method is a promising tool for modeling LD. The associations represented by the learned models are correlated with the traditional measure of LD D`. The method was able to represent LD blocks found by standard tools. The granularity of the association blocks and the readability of the models can be controlled in the method. The results suggest that the causality information gained by our method can be useful to tell about the conservability of the genetic markers and to guide the selection of subset of representative markers.

On the compressive strength prediction for concrete masonry prisms

The results of a combined experimental program and numerical modeling program to evaluate the behavior of ungrouted hollow concrete blocks prisms under uniaxial compression are addressed. In the numerical program, three distinct approaches have been considered using a continuum model with a smeared approach, namely plane-stress, plane-strain and three-dimensional conditions. The response of the numerical simulations is compared with experimental data of masonry prisms using concrete blocks specifically designed for this purpose. The elastic and inelastic parameters were acquired from laboratory tests on concrete and mortar samples that constitute the blocks and the bed joint of the prisms. The results from the numerical simulations are discussed with respect to the ability to reproduce the global response of the experimental tests, and with respect to the failure behavior obtained. Good agreement between experimental and numerical results was found for the peak load and for the failure mode using the three-dimensional model, on four different sets of block/mortar types. Less good agreement was found for plain stress and plain strain models.

Proposal of a test specimen to evaluate the shear strength of vertical interfaces of running bond masonry walls

There is no normalized test to assess the shear strength of vertical interfaces of interconnected masonry walls. The approach used to evaluate this strength is normally indirect and often unreliable. The aim of this study is to propose a new test specimen to eliminate this deficiency. The main features of the proposed specimen are failure caused by shear stress on the vertical interface and a small number of units (blocks). The paper presents a numerical analysis based on the finite element method, with the purpose of showing the theoretical performance of the designed specimen, in terms of its geometry, boundary conditions, and loading scheme, and describes an experimental program using the specimen built with full- and third-scale clay blocks. The main conclusions are that the proposed specimen is easy to build and is appropriate to evaluate the sheaf strength of vertical interfaces of masonry walls.