Histological analysis of effects of 24% EDTA gel for nonsurgical treatment of periodontal tissues

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (F ROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13-0.91 and 0.12-0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

Simple and clean determination of tetracyclines by flow injection analysis

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Development, validation, and application of a method for the GC-MS analysis of fipronil and three of its degradation products in samples of water, soil, and sediment

A method for the identification and quantification of pesticide residues in water, soil, and sediment samples has been developed, validated, and applied for the analysis of real samples. The specificity was determined by the retention time and the confirmation and quantification of analyte ions. Linearity was demonstrated over the concentration range of 20 to 120 µg L(-1), and the correlation coefficients varied between 0.979 and 0.996, depending on the analytes. The recovery rates for all analytes in the studied matrix were between 86% and 112%. The intermediate precision and repeatability were determined at three concentration levels (40, 80, and 120 µg L(-1)), with the relative standard deviation for the intermediate precision between 1% and 5.3% and the repeatability varying between 2% and 13.4% for individual analytes. The limits of detection and quantification for fipronil, fipronil sulfide, fipronil-sulfone, and fipronil-desulfinyl were 6.2, 3.0, 6.6, and 4.0 ng L(-1) and 20.4, 9.0, 21.6, and 13.0 ng L(-1), respectively. The method developed was used in water, soil, and sediment samples containing 2.1 mg L(-1) and 1.2% and 5.3% of carbon, respectively. The recovery of pesticides in the environmental matrices varied from 88.26 to 109.63% for the lowest fortification level (40 and 100 µg kg(-1)), from 91.17 to 110.18% for the intermediate level (80 and 200 µg kg(-1)), and from 89.09 to 109.82% for the highest fortification level (120 and 300 µg kg(-1)). The relative standard deviation for the recovery of pesticides was under 15%.

Immunohistochemical, tomographic, and histological study on onlay bone graft remodeling. Part III: allografts

Objective In the last decades aroused the interest for bone tissue bank as an alternative to autogenous grafting, avoiding donor sites morbidity, surgical time, and costs reduction. The purpose of the study was to compare allografts (ALg) with autografts (AUg) using histology, immunochemistry, and tomographic analysis. Material and methods Fifty-six New Zealand White rabbits were submitted to surgical procedures. Twenty animals were donors and 36 were actually submitted to onlay grafting with ALg (experimental group) and AUg (control group) randomly placed bilaterally in the mandible. Six animals of each group were sacrificed at 3, 5, 7, 10, 20, and 60 postoperative days. Immunolabeling was accomplished with osteoprotegerin (OPG); receptor activator of nuclear factor-k ligand (RANKL); alkaline phosphatase (ALP); osteopontin (OPN); vascular endothelial growth factor (VEGF); tartrate-resistant acid phosphatase (TRAP); collagen type I (COL I); and osteocalcin (OC). Density and volume of the grafts was evaluated on tomography obtained at the surgery and sacrifice. Results The ALg and AUg exhibited similar patterns of density and volume throughout the experiments. The intra-group data showed statistical differences at days 7 and 60 in comparison with other time points (P = 0.001), in both groups. A slight graft expansion from fixation until day 20 (P = 0.532) was observed in the AUg group and then resorbed significantly at the day 60 (P = 0.015). ALg volume remained stable until day 7 and decreased at day 10 (P = 0.045). The light microscopy analysis showed more efficient incorporation of AUg onto the recipient bed if compared with the ALg group. The immunohistochemical labeling picked: at days 10 and 20 with OPG in the AUg group and at day 7 with TRAP in the ALg group (P = 0.001 and P = 0.002, respectively). Conclusions ALg and AUg were not differing in patterns of volume and density during entire experiment. Histological data exhibit more efficient AUg incorporation into recipient bed compared with the ALg group. Immunohistochemistry outcomes demonstrated similar pattern for both ALg and AUg groups, except for an increasing resorption activity in the ALg group mediated by TRAP and in the AUg group by higher OPG labeling. However, this latter observation does not seem to influence clinical outcomes.

Television violence and young adults in Brazil: a content analysis of the popular telenovella, Malhação = Violência na televisão brasileira e jovens : uma análise de conteúdo da telenovela popular, Malahção

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Production, characterization and structural analysis of proteins from Corynebacterium pseudotuberculosis and snake venoms

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Review of Applied Spatial Data Analysis with R by R. S. Bivand, E. J. Pebesma, and V. Gomez-Rubio

Most authors struggle to pick a title that adequately conveys all of the material covered in a book. When I first saw Applied Spatial Data Analysis with R, I expected a review of spatial statistical models and their applications in packages (libraries) from the CRAN site of R. The authors’ title is not misleading, but I was very pleasantly surprised by how deep the word “applied” is here. The first half of the book essentially covers how R handles spatial data. To some statisticians this may be boring. Do you want, or need, to know the difference between S3 and S4 classes, how spatial objects in R are organized, and how various methods work on the spatial objects? A few years ago I would have said “no,” especially to the “want” part. Just let me slap my EXCEL spreadsheet into R and run some spatial functions on it. Unfortunately, the world is not so simple, and ultimately we want to minimize effort to get all of our spatial analyses accomplished. The first half of this book certainly convinced me that some extra effort in organizing my data into certain spatial class structures makes the analysis easier and less subject to mistakes. I also admit that I found it very interesting and I learned a lot.

Trophic structure on the West Antarctic Peninsula shelf: Detritivory and benthic inertia revealed by delta(13)C and delta(15)N analysis

Summer bloom-derived phytodetritus settles rapidly to the seafloor on the West Antarctic Peninsula (WAP) continental shelf, where it appears to degrade relatively slowly, forming a sediment ""food bank"" for benthic detritivores. We used stable carbon and nitrogen isotopes to examine sources and sinks of particulate organic material (POM) reaching the WAP shelf benthos (550-625 m depths), and to explore trophic linkages among the most abundant benthic megafauna. We measured delta(13)C and delta(15)N values in major megafaunal taxa (n = 26) and potential food sources, including suspended and sinking POM, ice algae, sediment organic carbon, phytodetritus, and macrofaunal polychaetes. The range in delta(13)C values (> 14 parts per thousand) of suspended POM was considerably broader than in sedimentary POC, where little temporal variability in stable isotope signatures was observed. While benthic megafauna also exhibited a broad range of VC values, organic carbon entering the benthic food web appeared to be derived primarily from phytoplankton production, with little input from ice algae. One group of organisms, primarily deposit-feeders, appeared to rely on fresh phytodetritus recovered from the sediments, and sediment organic material that had been reworked by sediment microbes. A second group of animals, including many mobile invertebrate and fish predators, appeared to utilize epibenthic or pelagic food resources such as zooplankton. One surface-deposit-feeding holothurian (Protelpidia murrayi) exhibited seasonal variability in stable isotope values of body tissue, while other surface- and subsurface-deposit-feeders showed no evidence of seasonal variability in food source or trophic position. Detritus from phytoplankton blooms appears to be the primary source of organic material for the detritivorous benthos; however, seasonal variability in the supply of this material is not mirrored in the sediments, and only to a minor degree in the benthic fauna. This pattern suggests substantial inertia in benthic-pelagic coupling, whereby the sediment ecosystem integrates long-term variability in production processes in the water column above. Published by Elsevier Ltd.

Color texture analysis based on fractal descriptors

Color texture classification is an important step in image segmentation and recognition. The color information is especially important in textures of natural scenes, such as leaves surfaces, terrains models, etc. In this paper, we propose a novel approach based on the fractal dimension for color texture analysis. The proposed approach investigates the complexity in R, G and B color channels to characterize a texture sample. We also propose to study all channels in combination, taking into consideration the correlations between them. Both these approaches use the volumetric version of the Bouligand-Minkowski Fractal Dimension method. The results show a advantage of the proposed method over other color texture analysis methods. (C) 2011 Elsevier Ltd. All rights reserved.

Paleoenvironmental reconstruction of a Late Quaternary lagoon system in southern Brazil (Jaguaruna region, Santa Catarina state) based on multi-proxy analysis

This paper provides a paleoenvironmental reconstruction of a Late Quaternary lagoon system in the Jaguaruna region of Santa Catarina state, southern Brazil. Integrated results of bulk sedimentary organic matter characterization (delta C-13, delta N-15 and C/N), microfossil (pollen and diatom) and grain-size analysis from three shallow cores (similar to 2.5m depth) allowed us to propose an evolving paleogeographic scenario in this coastal region for the last ca. 5500 cal a BP. The lagoonal system in this area was more extensive during the mid-Holocene than today, with a gradual and continuous lagoon-sea disconnection until the present. We add to the debate regarding relative sea-level (RSL) variations for the Brazilian coast during the Holocene and discuss the importance of sedimentary dynamics for interpreting changes in coastal ecosystems. The multi-proxy analysis suggests that changes in coastal ecosystems could be directly related to local sedimentary processes, which are not necessarily linked to RSL fluctuations and/or to climatic variations. Copyright (c) 2011 John Wiley & Sons, Ltd.

A mixed model QTL analysis for sugarcane multiple-harvest-location trial data

Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.

Fuzzy linguistic model for bioelectrical impedance vector analysis

Backgrounds Ea aims: The boundaries between the categories of body composition provided by vectorial analysis of bioimpedance are not well defined. In this paper, fuzzy sets theory was used for modeling such uncertainty. Methods: An Italian database with 179 cases 18-70 years was divided randomly into developing (n = 20) and testing samples (n = 159). From the 159 registries of the testing sample, 99 contributed with unequivocal diagnosis. Resistance/height and reactance/height were the input variables in the model. Output variables were the seven categories of body composition of vectorial analysis. For each case the linguistic model estimated the membership degree of each impedance category. To compare such results to the previously established diagnoses Kappa statistics was used. This demanded singling out one among the output set of seven categories of membership degrees. This procedure (defuzzification rule) established that the category with the highest membership degree should be the most likely category for the case. Results: The fuzzy model showed a good fit to the development sample. Excellent agreement was achieved between the defuzzified impedance diagnoses and the clinical diagnoses in the testing sample (Kappa = 0.85, p < 0.001). Conclusions: fuzzy linguistic model was found in good agreement with clinical diagnoses. If the whole model output is considered, information on to which extent each BIVA category is present does better advise clinical practice with an enlarged nosological framework and diverse therapeutic strategies. (C) 2012 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

The reduced modulus in the analysis of sharp instrumented indentation tests

In the analysis of instrumented indentation data, it is common practice to incorporate the combined moduli of the indenter (E-i) and the specimen (E) in the so-called reduced modulus (E-r) to account for indenter deformation. Although indenter systems with rigid or elastic tips are considered as equivalent if E-r is the same, the validity of this practice has been questioned over the years. The present work uses systematic finite element simulations to examine the role of the elastic deformation of the indenter tip in instrumented indentation measurements and the validity of the concept of the reduced modulus in conical and pyramidal (Berkovich) indentations. It is found that the apical angle increases as a result of the indenter deformation, which influences in the analysis of the results. Based upon the inaccuracies introduced by the reduced modulus approximation in the analysis of the unloading segment of instrumented indentation applied load (P)-penetration depth (delta) curves, a detailed examination is then conducted on the role of indenter deformation upon the dimensionless functions describing the loading stages of such curves. Consequences of the present results in the extraction of the uniaxial stress-strain characteristics of the indented material through such dimensional analyses are finally illustrated. It is found that large overestimations in the assessment of the strain hardening behavior result by neglecting tip compliance. Guidelines are given in the paper to reduce such overestimations.

Numerical analysis of different methods to calculate residual stresses in thin films based on instrumented indentation data

In this work, different methods to estimate the value of thin film residual stresses using instrumented indentation data were analyzed. This study considered procedures proposed in the literature, as well as a modification on one of these methods and a new approach based on the effect of residual stress on the value of hardness calculated via the Oliver and Pharr method. The analysis of these methods was centered on an axisymmetric two-dimensional finite element model, which was developed to simulate instrumented indentation testing of thin ceramic films deposited onto hard steel substrates. Simulations were conducted varying the level of film residual stress, film strain hardening exponent, film yield strength, and film Poisson's ratio. Different ratios of maximum penetration depth h(max) over film thickness t were also considered, including h/t = 0.04, for which the contribution of the substrate in the mechanical response of the system is not significant. Residual stresses were then calculated following the procedures mentioned above and compared with the values used as input in the numerical simulations. In general, results indicate the difference that each method provides with respect to the input values depends on the conditions studied. The method by Suresh and Giannakopoulos consistently overestimated the values when stresses were compressive. The method provided by Wang et al. has shown less dependence on h/t than the others.