Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 angstrom. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP. (C) 2009 Elsevier Inc. All rights reserved.

Face Detection and Facial Feature Localization for multi-pose faces and complex backgroundimages

The objective of this thesis work, is to propose an algorithm to detect the faces in a digital image with complex background. A lot of work has already been done in the area of face detection, but drawback of some face detection algorithms is the lack of ability to detect faces with closed eyes and open mouth. Thus facial features form an important basis for detection. The current thesis work focuses on detection of faces based on facial objects. The procedure is composed of three different phases: segmentation phase, filtering phase and localization phase. In segmentation phase, the algorithm utilizes color segmentation to isolate human skin color based on its chrominance properties. In filtering phase, Minkowski addition based object removal (Morphological operations) has been used to remove the non-skin regions. In the last phase, Image Processing and Computer Vision methods have been used to find the existence of facial components in the skin regions.This method is effective on detecting a face region with closed eyes, open mouth and a half profile face. The experiment’s results demonstrated that the detection accuracy is around 85.4% and the detection speed is faster when compared to neural network method and other techniques.

Identification of cause of impairment in spiral drawings, using non-stationary feature extraction approach

Parkinson’s disease is a clinical syndrome manifesting with slowness and instability. As it is a progressive disease with varying symptoms, repeated assessments are necessary to determine the outcome of treatment changes in the patient. In the recent past, a computer-based method was developed to rate impairment in spiral drawings. The downside of this method is that it cannot separate the bradykinetic and dyskinetic spiral drawings. This work intends to construct the computer method which can overcome this weakness by using the Hilbert-Huang Transform (HHT) of tangential velocity. The work is done under supervised learning, so a target class is used which is acquired from a neurologist using a web interface. After reducing the dimension of HHT features by using PCA, classification is performed. C4.5 classifier is used to perform the classification. Results of the classification are close to random guessing which shows that the computer method is unsuccessful in assessing the cause of drawing impairment in spirals when evaluated against human ratings. One promising reason is that there is no difference between the two classes of spiral drawings. Displaying patients self ratings along with the spirals in the web application is another possible reason for this, as the neurologist may have relied too much on this in his own ratings.

Spiral drawing during self-rated dyskinesia is more impaired than during self-rated off

Background: A mobile device test battery, consisting of a patient diary collection section with disease-related questions and a fine motor test section (including spiral drawing tasks), was used by 65 patients with advanced Parkinson's disease (PD)(treated with intraduodenal levodopa/carbidopa gel infusion, Duodopa®, or candidates for this treatment) on 10439 test occasions in their home environments. On each occasion, patients traced three pre-drawn Archimedes spirals using an ergonomic stylus and self-assessed their motor function on a global Treatment Response Scale (TRS) ranging from -3 = very 'off' to 0 = 'on' to +3 = very dyskinetic. The spirals were processed by a computer-based method that generates a "spiral score" representing the PD-related drawing impairment. The scale for the score was based on a modified Bain & Findley rating scale in the range from 0 = no impairment to 5 = moderate impairment to 10 = extremely severe impairment. Objective: To analyze the test battery data for the purpose to find differences in spiral drawing performance of PD patients in relation to their self-assessments of motor function. Methods: Three motor states were used in the analysis; OFF state (including moderate and very 'off'), ON state ('on') and a dyskinetic (DYS) state (moderate and very dyskinetic). In order to avoid the problem of multiple test occasions per patient, 200 random samples of single test occasions per patient were drawn. One-way analysis of variance, ANOVA, test followed by Tukey multiple comparisons test was used to test if mean values of spiral test parameters, i.e. the spiral score and drawing completion times (in seconds), were different among the three motor states. Statistical significance was set at p<0.05. To investigate changes in the spiral score over the time-of-day test sessions for the three motor states, plots of statistical summaries were inspected. Results: The mean spiral score differed significantly across the three self-assessed motor states (p<0.001, ANOVA test). Tukey post-hoc comparisons indicate that the mean spiral score (mean ± SD; [95% CI for mean]) in DYS state (5.2 ± 1.8; [5.12, 5.28]) was higher than the mean spiral score in OFF (4.3 ± 1.7; [4.22, 4.37]) and ON (4.2 ± 1.7; [4.17, 4.29]) states. The mean spiral score was also significantly different among individual TRS values of slightly 'off' (4.02 ± 1.63), 'on' (4.07 ± 1.65) and slightly dyskinetic (4.6 ± 1.71), (p<0.001). There were no differences in drawing completion times among the three motor states (p=0.509). In the OFF and ON states, patients drew slightly more impaired spirals in the afternoon whereas in the DYS state the spiral drawing performance was more impaired in the morning. Conclusion: It was found that when patients considered themselves as being dyskinetic spiral drawing was more impaired (nearly one unit change in a 0-10 scale) compared to when they considered themselves as being 'off' and 'on'. The spiral drawing at patients that self-assessed their motor state as dyskinetic was slightly more impaired in the morning hours, between 8 and 12 o'clock, a situation possibly caused by the morning dose effect.

Rule versus interaction function : evaluating regional aggregations of commuting flows in Sweden

The aim of this paper is to evaluate the performance of two divergent methods for delineating commuting regions, also called labour market areas, in a situation that the base spatial units differ largely in size as a result of an irregular population distribution. Commuting patterns in Sweden have been analyzed with geographical information system technology by delineating commuting regions using two regionalization methods. One, a rule-based method, uses one-way commuting flows to delineate local labour market areas in a top-down procedure based on the selection of predefined employment centres. The other method, the interaction-based Intramax analysis, uses two-way flows in a bottom-up procedure based on numerical taxonomy principles. A comparison of these methods will expose a number of strengths and weaknesses. For both methods, the same data source has been used. The performance of both methods has been evaluated for the country as a whole using resident employed population, self-containment levels and job ratios for criteria. A more detailed evaluation has been done in the Goteborg metropolitan area by comparing regional patterns with the commuting fields of a number of urban centres in this area. It is concluded that both methods could benefit from the inclusion of additional control measures to identify improper allocations of municipalities.

Plane detection from monocular image sequences

AIRES, Kelson R. T. ; ARAÚJO, Hélder J. ; MEDEIROS, Adelardo A. D. . Plane Detection from Monocular Image Sequences. In: VISUALIZATION, IMAGING AND IMAGE PROCESSING, 2008, Palma de Mallorca, Spain. Proceedings..., Palma de Mallorca: VIIP, 2008

Plane Detection Using Affine Homography

AIRES, Kelson R. T.; ARAÚJO, Hélder J.; MEDEIROS, Adelardo A. D. Plane Detection Using Affine Homography. In: CONGRESSO BRASILEIRO DE AUTOMÁTICA, 2008, Juiz de Fora, MG: Anais... do CBA 2008.

Neuronal Assembly Detection and Cell Membership Specification by Principal Component Analysis

LOPES-DOS-SANTOS, V. , CONDE-OCAZIONEZ, S. ; NICOLELIS, M. A. L. , RIBEIRO, S. T. , TORT, A. B. L. . Neuronal assembly detection and cell membership specification by principal component analysis. Plos One, v. 6, p. e20996, 2011.

Mapping Macrophyte Species in the Amazon Floodplain Wetlands Using Fully Polarimetric ALOS/PALSAR Data

The purpose of this paper was to evaluate attributes derived from fully polarimetric PALSAR data to discriminate and map macrophyte species in the Amazon floodplain wetlands. Fieldwork was carried out almost simultaneously to the radar acquisition, and macrophyte biomass and morphological variables were measured in the field. Attributes were calculated from the covariance matrix [C] derived from the single-look complex data. Image attributes and macrophyte variables were compared and analyzed to investigate the sensitivity of the attributes for discriminating among species. Based on these analyses, a rule-based classification was applied to map macrophyte species. Other classification approaches were tested and compared to the rule-based method: a classification based on the Freeman-Durden and Cloude-Pottier decomposition models, a hybrid classification (Wishart classifier with the input classes based on the H/a plane), and a statistical-based classification (supervised classification using Wishart distance measures). The findings show that attributes derived from fully polarimetric L-band data have good potential for discriminating herbaceous plant species based on morphology and that estimation of plant biomass and productivity could be improved by using these polarimetric attributes.

Oxidation of melatonin and its catabolites, N-1-acetyl-N (2)-formyl-5-methoxykynuramine and N-1-acetyl-5-methoxykynuramine, by activated leukocytes

N-1-acetyl-N-2-formyl-5-methoxykynuramine (AFMK) and N-1-acetyl-5-methoxykynuramine (AMK), two melatonin catabolites, have been described as potent antioxidants. We aimed to follow the kinetics of AFMK and AMK formation when melatonin is oxidized by phorbol myristate acetate (PMA) and lipopolysaccharide (LPS)-activated leukocytes. An HPLC-based method was used for AFMK and AMK determination in neutrophil and peripheral blood mononuclear cell cultures supernatants. Samples were separated isocratically on a C18 reverse-phase column using acetonitrile/H2O (25:75) as the mobile phase. AFMK was detected by fluorescence (excitation 340 nm and emission 460 nm) and AMK by UV-VIS absorbance (254 nm). Activation of neutrophils and mononuclear cells with PMA produces larger amounts of AFMK than activation with LPS, probably due to the lower levels of reactive oxygen species formation and myeloperoxidase (MPO) degranulation that occurs when cells are stimulated with LPS. The concentration of AMK found in the supernatant was about 5-10% (from 18-hr cultures) compared with AFMK. This result may reflect its reactivity. Indeed AMK, but not AFMK, is easily oxidized by activated neutrophils in a MPO and hydrogen peroxide-dependent reaction. In conclusion, we defined a simple procedure for the determination of AFMK and AMK in biological samples and demonstrated the capacity of leukocytes to oxidize melatonin and AMK.

Métodos numéricos para resolução de equações diferenciais ordinárias lineares baseados em interpolação por spline

In this work we have elaborated a spline-based method of solution of inicial value problems involving ordinary differential equations, with emphasis on linear equations. The method can be seen as an alternative for the traditional solvers such as Runge-Kutta, and avoids root calculations in the linear time invariant case. The method is then applied on a central problem of control theory, namely, the step response problem for linear EDOs with possibly varying coefficients, where root calculations do not apply. We have implemented an efficient algorithm which uses exclusively matrix-vector operations. The working interval (till the settling time) was determined through a calculation of the least stable mode using a modified power method. Several variants of the method have been compared by simulation. For general linear problems with fine grid, the proposed method compares favorably with the Euler method. In the time invariant case, where the alternative is root calculation, we have indications that the proposed method is competitive for equations of sifficiently high order.

Amniotic Fluid Interleukin-1 Beta and Interleukin-6, but not Interleukin-8 Correlate with Microbial Invasion of the Amniotic Cavity in Preterm Labor

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genetic structure in a tropical lek-breeding bird, the blue manakin (Chiroxiphia caudata) in the Brazilian Atlantic Forest

Determining the genetic structure of tropical bird populations is important for assessing potential genetic effects of future habitat fragmentation and for testing hypotheses about evolutionary mechanisms promoting diversification. Here we used 10 microsatellite DNA loci to describe levels of genetic differentiation for five populations of the lek-mating blue manakin (Chiroxiphia caudata), sampled along a 414-km transect within the largest remaining continuous tract of the highly endangered Atlantic Forest habitat in southeast Brazil. We found small but significant levels of differentiation between most populations. F-ST values varied from 0.0 to 0.023 (overall F-ST = 0.012) that conformed to a strong isolation by distance relationship, suggesting that observed levels of differentiation are a result of migration-drift equilibrium. N(e)m values estimated using a coalescent-based method were small (<= 2 migrants per generation) and close to the minimum level required to maintain genetic similarity between populations. An implication of these results is that if future habitat fragmentation reduces dispersal between populations to even a small extent, then individual populations may undergo a loss of genetic diversity due to an increase in the relative importance of drift, since inbreeding effective population sizes are relatively small (N-e similar to 1000). Our findings also demonstrate that population structuring can occur in a tropical bird in continuous habitat in the absence of geographical barriers possibly due to behavioural features of the species.

Determination of pesticides multiresidues in shallow groundwater in a cotton-growing region of Mato Grosso, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Loss of imprinting and loss of heterozygosity on 11p15.5 in head and neck squamous cell carcinomas

Background. IGF2 and H19 are reciprocal imprinted genes with paternal and maternal monoallelic expression, respectively. This is interesting, because IGF2 is known as a growth factor, and H19 encodes a RNA with putative tumor suppressor action. Furthermore, IGF2 and H19 are linked genes located on chromosome 11p15.5, a common site of loss of heterozygosity in human cancers.Methods. We performed an allelic-typing assay using a PCR-RFLP-based method for identification of heterozygous Informative cases in head and neck squamous cell carcinomas. Tumoral total RNA was extracted from each of the heterozygotes and further studied by RT-PCR analysis.Results. We detected the expression of the IGF2 gene in 10 of 10 informative cases. Two cases exhibited LOI of the IGF2 gene as evidenced by biallelic expression, and in another case, LOH was coupled with monoallelic expression of this growth factor. LOI for the H19 gene was observed in 1 of 14 informative samples analyzed. In this case, we also detected parallel mono-allelic expression of the IGF2 gene. Down-regulation of the H19 gene was observed in 10 of 14 cases.Conclusion. These findings support the hypothesis that H19 may be a tumor suppressor gene involved In head and neck carcinogenesis. Furthermore, our data showed that genetic and epigenetic chances at 11p15.5 could lead to abnormal expression of imprinted genes in HNSCC. (C) 2001 John Wiley & Sons, Inc.