Integration of gis technology, remote sensing and multivariate analysis in the delimitation of physiographic units for pedological mapping

Este trabalho foi conduzido com o propósito de estabelecer-se um levantamento pedológico semidetalhado no Município de Ivatuba-PR, usando a associação entre técnicas e equipamentos que pudessem levar a delimitação de unidades físiográfícas cujos limites e subdivisões não se restringissem apenas ao critério do foto intérprete. Para tanto, foi avaliada uma matriz de dados obtida através do cruzamento, por meio de um Sistema de Informações Geográficas (SIG), entre uma grade regular com células de 300 x 300 metros e um mapa base de drenagem da área de estudos, bandas 3, 4, 5 e 7 do TM-LANDSAT e um mapa de declividades da área gerado em SIG. As variáveis coletadas dentro de cada célula da grade regular foram: canais longo, médio e curto das ordens 1ª à 7ª, declividade ponderada e o nível de cinza das bandas, resultando na produção de uma matriz com 1167 indivíduos com vinte e sete variáveis, cujos dados foram expostos à analise de agrupamentos. A análise propiciou a produção de dendrogramas que foram analisados, permitindo a representação pelas células da grade regular, com a finalidade de criação de pictogramas em que a separação de grupos de indivíduos servissem de "guias" que, sobrepostos às imagens orbitais HRV-SPOT devidamente tratadas e manipuladas, pudessem orientar a discriminação de unidades fisiográfícas através da interpretação destas sobre o monitor colorido do sistema SITIM. Foram delimitados 62 polígonos que configuraram a presença de nove unidades fisiográficas que geraram um mapa de solos semidetalhado do município. Em relação à possibilidade de mapeamento das unidades fisiográficas sobre o monitor colorido, os resultados apresentados demonstraram que, através da utilização dos guias, tais unidades podem ser delimitadas com grande redução da subjetividade do foto intérprete. Os polígonos semelhantes, delimitados pela metodologia utilizada, apresentaram solos homogêneos dentro de sua classe taxonómica. Já os polígonos diferentes apresentaram solos com características diferenciadoras entre si.This study was based on an association of techniques and equipment that could lead to the delimitation of physiographic units not merely restricted to the photointerpreter's criteria. A data matrix was evaluated which was obtained from the crossing, by means of Geographic Information System (GIS), of a regular grid with cells 300 x 300 meters and a drainage base map of the study area and bands 3, 4, 5 and 7 from TM-LANDSAT and a slope map generated in a GIS. The variables collected in each cell of the regular grid were: long, medium and short channels from the first to the seventh order, weighted slope and the grey levels (DNs) in bands, resulting in a matrix with 1167 individuals with 27 variables, whose data were subjected to cluster analysis. This analysis provided dendrograms which enabled the separation of groups of individuals represented by cells from the regular grid, aiming at creating pictograms to serve as "guides". These guides overlaid upon properly treated and handled orbital HRV-SPOT images oriented the discrimination of physiographic units on the color monitor of the image processing system. Among the variables used, those referring to drainage network were best for cluster analysis of regular grid cells. The variables relief and grey levels of TM-LANDSAT image also presented satisfactory results with the methodology applied

Virus-like Particle (VLP) Vaccines for Cancer Immunotherapy

Cancer vaccines are increasingly being studied as a possible strategy to prevent and treat cancers. While several prophylactic vaccines for virus-caused cancers are approved and efficiently used worldwide, the development of therapeutic cancer vaccines needs to be further implemented. Virus-like particles (VLPs) are self-assembled protein structures that mimic native viruses or bacteriophages but lack the replicative material. VLP platforms are designed to display single or multiple antigens with a high-density pattern, which can trigger both cellular and humoral responses. The aim of this review is to provide a comprehensive overview of preventive VLP-based vaccines currently approved worldwide against HBV and HPV infections or under evaluation to prevent virus-caused cancers. Furthermore, preclinical and early clinical data on prophylactic and therapeutic VLP-based cancer vaccines were summarized with a focus on HER-2-positive breast cancer

Modeling the competition between lung metastases and the immune system using agents

<p>Abstract</p> <p>Background</p> <p>The Triplex cell vaccine is a cancer cellular vaccine that can prevent almost completely the mammary tumor onset in HER-2/neu transgenic mice. In a translational perspective, the activity of the Triplex vaccine was also investigated against lung metastases showing that the vaccine is an effective treatment also for the cure of metastases. A future human application of the Triplex vaccine should take into account several aspects of biological behavior of the involved entities to improve the efficacy of therapeutic treatment and to try to predict, for example, the outcomes of longer experiments in order to move faster towards clinical phase I trials. To help to address this problem, MetastaSim, a hybrid Agent Based - ODE model for the simulation of the vaccine-elicited immune system response against lung metastases in mice is presented. The model is used as in silico wet-lab. As a first application MetastaSim is used to find protocols capable of maximizing the total number of prevented metastases, minimizing the number of vaccine administrations.</p> <p>Results</p> <p>The model shows that it is possible to obtain "in silico" a 45% reduction in the number of vaccinations. The analysis of the results further suggests that any optimal protocol for preventing lung metastases formation should be composed by an initial massive vaccine dosage followed by few vaccine recalls.</p> <p>Conclusions</p> <p>Such a reduction may represent an important result from the point of view of translational medicine to humans, since a downsizing of the number of vaccinations is usually advisable in order to minimize undesirable effects. The suggested vaccination strategy also represents a notable outcome. Even if this strategy is commonly used for many infectious diseases such as tetanus and hepatitis-B, it can be in fact considered as a relevant result in the field of cancer-vaccines immunotherapy. These results can be then used and verified in future "in vivo" experiments, and their outcome can be used to further improve and refine the model.</p

Hormone replacement treatment and breast cancer risk: a cooperative Italian study.

The relationship between hormone replacement treatment (HRT) and breast cancer risk was analysed using data from a case-control study conducted between June 1991 and February 1994 in six Italian centres on 2569 patients aged below 75 with histologically confirmed breast cancer and 2588 controls admitted to hospital for a wide spectrum of acute, non-neoplastic, non hormone-related diseases. Ever HRT use was reported by 7.5% of cases and 7.5% of controls, corresponding to a multivariate odds ratio (OR) of 1.2 [95% confidence interval (CI), 0.9-1.5]. The risk increased with increasing duration of use: the ORs were 1.0 for use lasting less than 1 year, 1.3 for 1-4 years and 1.5 for 5 years or more. There was no clear pattern of risk with reference to time since starting use, but the OR was significantly elevated (OR = 2.0, 95% CI 1.3-2.9) for women who had stopped HRT within the last 10 years. No association was observed in those who had stopped HRT more than 10 years ago (OR = 1.0). The increased OR for women who had stopped HRT within the last 10 years was consistent across strata of identified covariates, and was significantly related to duration of use. This study confirms the absence of a strong association between HRT and breast cancer risk, although the risk estimate was above unity for women who had used HRT for 5 years or longer. However, the risk was significantly elevated in the short to medium term after use, particularly for long-term use. This short-term increased risk is consistent with an effect of HRT on one of the later stages of the process of breast carcinogenesis. The flattening of risk with increasing time since stopping, and hence the absence of a long-term cumulative excess in breast cancer risk after stopping HRT exposure, has relevant implications on individual risk assessment and public health

Enzyme classification with peptide programs: a comparative study

<p>Abstract</p> <p>Background</p> <p>Efficient and accurate prediction of protein function from sequence is one of the standing problems in Biology. The generalised use of sequence alignments for inferring function promotes the propagation of errors, and there are limits to its applicability. Several machine learning methods have been applied to predict protein function, but they lose much of the information encoded by protein sequences because they need to transform them to obtain data of fixed length.</p> <p>Results</p> <p>We have developed a machine learning methodology, called peptide programs (PPs), to deal directly with protein sequences and compared its performance with that of Support Vector Machines (SVMs) and BLAST in detailed enzyme classification tasks. Overall, the PPs and SVMs had a similar performance in terms of Matthews Correlation Coefficient, but the PPs had generally a higher precision. BLAST performed globally better than both methodologies, but the PPs had better results than BLAST and SVMs for the smaller datasets.</p> <p>Conclusion</p> <p>The higher precision of the PPs in comparison to the SVMs suggests that dealing with sequences is advantageous for detailed protein classification, as precision is essential to avoid annotation errors. The fact that the PPs performed better than BLAST for the smaller datasets demonstrates the potential of the methodology, but the drop in performance observed for the larger datasets indicates that further development is required.</p> <p>Possible strategies to address this issue include partitioning the datasets into smaller subsets and training individual PPs for each subset, or training several PPs for each dataset and combining them using a bagging strategy.</p

The X-ray properties of z > 6 quasars: no evident evolution of accretion physics in the first Gyr of the Universe

Context. X-ray emission from quasars (QSOs) has been used to assess supermassive black hole accretion properties up to z 48 6. However, at z &gt; 6 only 4815 QSOs are covered by sensitive X-ray observations, preventing a statistically significant investigation of the X-ray properties of the QSO population in the first Gyr of the Universe. Aims: We present new Chandra observations of a sample of 10 z &gt; 6 QSOs, selected to have virial black-hole mass estimates from Mg II line spectroscopy (log {MBH}/{M_&09}=8.5-9.6) . Adding archival X-ray data for an additional 15 z &gt; 6 QSOs, we investigate the X-ray properties of the QSO population in the first Gyr of the Universe. In particular, we focus on the LUV - LX relation, which is traced by the \u3b1ox parameter, and the shape of their X-ray spectra. Methods: We performed photometric analyses to derive estimates of the X-ray luminosities of our z &gt; 6 QSOs, and thus their \u3b1ox values and bolometric corrections (Kbol = Lbol/LX). We compared the resulting \u3b1ox and Kbol distributions with the results found for QSO samples at lower redshift, and ran several statistical tests to check for a possible evolution of the LUV - LX relation. Finally, we performed a basic X-ray spectral analysis of the brightest z &gt; 6 QSOs to derive their individual photon indices, and joint spectral analysis of the whole sample to estimate the average photon index. Results: We detect seven of the new Chandra targets in at least one standard energy band, while two more are detected discarding energies E &gt; 5 keV, where background dominates. We confirm a lack of significant evolution of \u3b1ox with redshift, which extends the results from previous works up to z &gt; 6 with a statistically significant QSO sample. Furthermore, we confirm the trend of an increasing bolometric correction with increasing luminosity found for QSOs at lower redshifts. The average power-law photon index of our sample (\u27e8\u393\u27e9 = 2.20-0.34+0.39 and \u27e8\u393\u27e9 = 2.13-0.13+0.13 for sources with &lt; 30 and &gt; 30 net counts, respectively) is slightly steeper than, but still consistent with, typical QSOs at z = 1 - 6. Conclusions: All of these results indicate a lack of substantial evolution of the inner accretion-disk and hot-corona structure in QSOs from low redshift to z &gt; 6. Our data hint at generally high Eddington ratios at z &gt; 6

Elevated levels of eEF1A2 protein expression in triple negative breast cancer relate with poor prognosis

Eukaryotic elongation factor 1 alpha 2 (eEF1A2) is a translation factor selectively expressed by heart, skeletal muscle, nervous system and some specialized cells. Its ectopic expression relates with tumorigenesis in several types of human cancer. No data are available about the role of eEF1A2 in Triple Negative Breast Cancers (TNBC). This study investigated the relation between eEF1A2 protein levels and the prognosis of TNBC. A total of 84 TNBC diagnosed in the period 2002-2011 were included in the study. eEF1A2 protein level was measured in formalin-fixed paraffin-embedded tissues by immunohistochemistry in a semi-quantitative manner (sum of the percentage of positive cells x staining intensity) on a scale from 0 to 300. Cox regression assessed the association between eEF1A2 levels and disease-free survival (DFS) and breast cancer-specific survival (BCSS). Elevated values of eEF1A2 were associated with older age at diagnosis (p = 0.003), and androgen receptors positivity (p = 0.002). At univariate Cox analysis, eEF1A2 levels were not significantly associated with DFS and BCSS (p = 0.11 and p = 0.08, respectively) whereas adjusting for stage of disease, elevated levels of eEF1A2 protein resulted associated with poor prognosis (HR = 1.05, 95% CI: 1.01-1.11, p = 0.04 and HR = 1.07, 95% CI: 1.01-1.14, p = 0.03 for DFS and BCSS, respectively). This trend was confirmed analyzing negative versus positive samples by using categorized scores. Our data showed a negative prognostic role of eEF1A2 protein in TNBC, sustaining further investigations to confirm this result by wider and independent cohorts of patients

Overview of the VIRMOS instrument and data reduction software packages

VIMOS is a spectrograph with imaging capabilities which will be mounted on the Nasmyth B focus of VLT UT. The main characteristics of VIMOS are the multiplexing spectral capabilities up to spectra per exposure and the presence of an Integral Field Unit IFU which allows spectrophotometry of 1 squared arcmin field. To reach the goal of 800 spectra per field VIMOS has been designed with a large field of view divided into quadrants each quadrant being by all means a full spectrograph on its own Spectra are obtained using masks with slits which are designed by the astronomer. The ESO VLT Project has devised a general Data Flow within which all VLT instruments have to operate During design and development of VIMOS instrument software we had to deal with the VLT general concept and adapt it to our needs