Propagation, structural similarity and image quality

Póster presentado en SPIE Photonics Europe, Brussels, 16-19 April 2012.

Retinal image quality assessment through a visual similarity index

Retinal image quality is commonly analyzed through parameters inherited from instrumental optics. These parameters are defined for ‘good optics’ so they are hard to translate into visual quality metrics. Instead of using point or artificial functions, we propose a quality index that takes into account properties of natural images. These images usually show strong local correlations that help to interpret the image. Our aim is to derive an objective index that quantifies the quality of vision by taking into account the local structure of the scene, instead of focusing on a particular aberration. As we show, this index highly correlates with visual acuity and allows inter-comparison of natural images around the retina. The usefulness of the index is proven through the analysis of real eyes before and after undergoing corneal surgery, which usually are hard to analyze with standard metrics.

Mouse alarm pheromone shares structural similarity with predator scents.

Sensing the chemical warnings present in the environment is essential for species survival. In mammals, this form of danger communication occurs via the release of natural predator scents that can involuntarily warn the prey or by the production of alarm pheromones by the stressed prey alerting its conspecifics. Although we previously identified the olfactory Grueneberg ganglion as the sensory organ through which mammalian alarm pheromones signal a threatening situation, the chemical nature of these cues remains elusive. We here identify, through chemical analysis in combination with a series of physiological and behavioral tests, the chemical structure of a mouse alarm pheromone. To successfully recognize the volatile cues that signal danger, we based our selection on their activation of the mouse olfactory Grueneberg ganglion and the concomitant display of innate fear reactions. Interestingly, we found that the chemical structure of the identified mouse alarm pheromone has similar features as the sulfur-containing volatiles that are released by predating carnivores. Our findings thus not only reveal a chemical Leitmotiv that underlies signaling of fear, but also point to a double role for the olfactory Grueneberg ganglion in intraspecies as well as interspecies communication of danger.

The relationship between L3 transfer and structural similarity across L3 development: raising across an experience in Brazilian Portuguese

The present study examines three competing models of morphosyntactic transfer in third language (L3) acquisition, examining the particular domain of the feature configuration of embedded T in L3 Brazilian Portuguese (BP) at the initial stages and then through development. The methodology alternates Spanish and English as the L1 and L2 to tease apart the source of transfer to L3 BP. Results from a scalar grammaticality acceptability task show unequivocal transfer of Spanish irrespective of Spanish’s status as an L1 or L2. The data thus support the Typological Primacy Model (Rothman 2010, 2011, 2013a, 2013b), which proposes that multilingual transfer is selected by factors related to comparative structural similarity. Given that Spanish transfer at the L3 initial stages creates the need for feature reconfiguration to converge on the target BP grammar, the second part of this chapter examines the developmental consequences of what the TPM models in cases of non-facilitative initial transfer, that is, the developmental path of feature reconfiguration of embedded T in L3 BP by English/Spanish bilinguals. Given what these data reveal, we address the role of regressive transfer as a correlate of L3 proficiency gains.

Color ad spectral image assessment using novel quality and fidelity techniques

The ongoing development of the digital media has brought a new set of challenges with it. As images containing more than three wavelength bands, often called spectral images, are becoming a more integral part of everyday life, problems in the quality of the RGB reproduction from the spectral images have turned into an important area of research. The notion of image quality is often thought to comprise two distinctive areas – image quality itself and image fidelity, both dealing with similar questions, image quality being the degree of excellence of the image, and image fidelity the measure of the match of the image under study to the original. In this thesis, both image fidelity and image quality are considered, with an emphasis on the influence of color and spectral image features on both. There are very few works dedicated to the quality and fidelity of spectral images. Several novel image fidelity measures were developed in this study, which include kernel similarity measures and 3D-SSIM (structural similarity index). The kernel measures incorporate the polynomial, Gaussian radial basis function (RBF) and sigmoid kernels. The 3D-SSIM is an extension of a traditional gray-scale SSIM measure developed to incorporate spectral data. The novel image quality model presented in this study is based on the assumption that the statistical parameters of the spectra of an image influence the overall appearance. The spectral image quality model comprises three parameters of quality: colorfulness, vividness and naturalness. The quality prediction is done by modeling the preference function expressed in JNDs (just noticeable difference). Both image fidelity measures and the image quality model have proven to be effective in the respective experiments.

Arcabouço para aprovisionamento de QoS e QoE em redes sem fio heterogêneas WiMAX/Wi-Fi com garantia de equidade entre vazões

Recentemente a sociedade está vivendo em meio a um aglomerado de dispositivos móveis com múltiplas interfaces sem fio que permitem que clientes móveis domésticos e corporativos solucionem problemas rotineiros no menor espaço de tempo e em diversas localizações. Por outro lado, a disponibilidade de diversas tecnologias de acesso sem fio como: Wi-Fi (Wireless Fidelity), WiMAX (Worldwide Interoperability for Microwave Access) e LTE (Long Term Evolution), proporcionam um cenário heterogêneo com diversas oportunidades de conectividade para o usuário de dispositivos com múltiplas interfaces. Alguns dos desafios atuais no contexto da concepção da então denominada NGN (Next Generation Networks) são o desenvolvimento de arcabouços e mecanismos que viabilizem tanto o suporte adequado à Qualidade de Serviço (QoS – Quality of Service) e à Qualidade de Experiência (QoE – Quality of Experience) para aplicações multimídia, quanto a garantia de equidade entre vazões de diferentes aplicações em ambiente heterogêneo. Esta dissertação propõe um arcabouço para o aprovisionamento de QoS e QoE em redes sem fio heterogêneas formada por redes WiMAX e Wi-Fi. Especificamente, nossa solução provê mapeamento estático de QoS entre as classes de serviços WiMAX e categorias de acesso Wi-Fi. Além disso, nossa proposta também combina funcionalidades de equidade entre vazões com a solução de mapeamento, a fim de alcançar um bom compromisso tanto para o operador da rede, quanto para o usuário, através de uma nova metodologia de coleta e calculo de vazão agregada e algoritmo de decisão de handover vertical. A avaliação quantitativa da proposta foi realizada através de modelos de simulação no ns-2 (Network Simulator). Os resultados de desempenho demonstram a eficiência da arquitetura em termos de métricas de QoS (vazão, vazão média e atraso) e QoE (PSRN - Peak Signal to Noise Ratio, SSIM - Structural Similarity Index e VQM - Video Quality Metric).

Applying enhancement filters in the pre-processing of images of lymphoma

Lymphoma is a type of cancer that affects the immune system, and is classified as Hodgkin or non-Hodgkin. It is one of the ten types of cancer that are the most common on earth. Among all malignant neoplasms diagnosed in the world, lymphoma ranges from three to four percent of them. Our work presents a study of some filters devoted to enhancing images of lymphoma at the pre-processing step. Here the enhancement is useful for removing noise from the digital images. We have analysed the noise caused by different sources like room vibration, scraps and defocusing, and in the following classes of lymphoma: follicular, mantle cell and B-cell chronic lymphocytic leukemia. The filters Gaussian, Median and Mean-Shift were applied to different colour models (RGB, Lab and HSV). Afterwards, we performed a quantitative analysis of the images by means of the Structural Similarity Index. This was done in order to evaluate the similarity between the images. In all cases we have obtained a certainty of at least 75%, which rises to 99% if one considers only HSV. Namely, we have concluded that HSV is an important choice of colour model at pre-processing histological images of lymphoma, because in this case the resulting image will get the best enhancement.

A comparison of denoising methods for X-ray fluoroscopic images

Fluoroscopic images exhibit severe signal-dependent quantum noise, due to the reduced X-ray dose involved in image formation, that is generally modelled as Poisson-distributed. However, image gray-level transformations, commonly applied by fluoroscopic device to enhance contrast, modify the noise statistics and the relationship between image noise variance and expected pixel intensity. Image denoising is essential to improve quality of fluoroscopic images and their clinical information content. Simple average filters are commonly employed in real-time processing, but they tend to blur edges and details. An extensive comparison of advanced denoising algorithms specifically designed for both signal-dependent noise (AAS, BM3Dc, HHM, TLS) and independent additive noise (AV, BM3D, K-SVD) was presented. Simulated test images degraded by various levels of Poisson quantum noise and real clinical fluoroscopic images were considered. Typical gray-level transformations (e.g. white compression) were also applied in order to evaluate their effect on the denoising algorithms. Performances of the algorithms were evaluated in terms of peak-signal-to-noise ratio (PSNR), signal-to-noise ratio (SNR), mean square error (MSE), structural similarity index (SSIM) and computational time. On average, the filters designed for signal-dependent noise provided better image restorations than those assuming additive white Gaussian noise (AWGN). Collaborative denoising strategy was found to be the most effective in denoising of both simulated and real data, also in the presence of image gray-level transformations. White compression, by inherently reducing the greater noise variance of brighter pixels, appeared to support denoising algorithms in performing more effectively. © 2012 Elsevier Ltd. All rights reserved.

Structural analysis of the vegetation on a highland granitic rock outcrop in Southeast Brazil

Granitic rock outcrops of the Brazilian southeast are either coastal or inland. The latter can often have high altitudes, such as in the summits of "Serra do Mar" and "Serra da Mantiqueira", where they are known as "Campos de Altitude". The landscape on these high altitude plateaux is often a mosaic of shrubs and treelets within a bunchgrass matrix, with sparse pteridophytes and other herbs, interspersed with variable extensions of rock outcrops. Despite the pervasiveness of rock outcrops in the Brazilian landscape, studies on the structural analysis of the vegetation on such formations are scarce. This study aimed to analyze the structure of the vegetation on a highland granitic rock outcrop in "Parque Estadual da Serra do Brigadeiro", state of Minas Gerais, Southeast Brazil (42°20' - 42°40' S and 20°20' - 21°00' W, 1,722 m of elevation ). Quantitative parameters of absolute and relative frequency and dominance (cover) were estimated. The group analysis used the Jaccard similarity index. Trilepis lhotzkiana, Panicum sp. 1, and Vellozia variegata presented the highest relative frequencies, relative dominances and importance values. These three species, along with Dyckia bracteata, Rhynchospora emaciate, and Tibouchina cf. manicata, represented 98.3% of the relative dominance. The remaining 1.7% referred to 22 remaining species. The distinction among quadrats within formed groups by cluster analysis was due to the great number of low frequency species.

Structural basis for selective inhibition of trypanosomatid glyceraldehyde-3-phosphate dehydrogenase: Molecular docking and 3D QSAR studies

The glycolytic enzyme glyceraldehyde-3 -phosphate dehydrogenase (GAPDH) is as an attractive target for the development of novel antitrypanosomatid agents. In the present work, comparative molecular field analysis and comparative molecular similarity index analysis were conducted on a large series of selective inhibitors of trypanosomatid GAPDH. Four statistically significant models were obtained (r(2) > 0.90 and q(2) > 0.70), indicating their predictive ability for untested compounds. The models were then used to predict the potency of an external test set, and the predicted values were in good agreement with the experimental results. Molecular modeling studies provided further insight into the structural basis for selective inhibition of trypanosomatid GAPDH.

Rigid pavements distresses - pavement condition index evaluation

Pavements require maintenance in order to provide good service levels during their life period. Because of the significant costs of this operation and the importance of a proper planning, a pavement evaluation methodology, named Pavement Condition Index (PCI), was created by the U.S. Army Corps of Engineers. This methodology allows for the evaluation of the pavement condition along the life period, generally yearly, with minimum costs and, in this way, it is possible to plan the maintenance action and to adopt adequate measures, minimising the rehabilitation costs. The PCI methodology provides an evaluation based on visual inspection, namely on the distresses observed on the pavement. This condition index of the pavement is classified from 0 to 100, where 0 it is the worst possible condition and 100 the best possible condition. This methodology of pavement assessment represents a significant tool for management methods such as airport pavement management system (APMS) and life-cycle costs analysis (LCCA). Nevertheless, it has some limitations which can jeopardize the correct evaluation of the pavement behavior. Therefore the objective of this dissertation is to help reducing its limitations and make it easier and faster to use. Thus, an automated process of PCI calculation was developed, avoiding the abaci consultation, and consequently, minimizing the human error. To facilitate also the visual inspection a Tablet application was developed to replace the common inspection data sheet and thus making the survey easier to be undertaken. Following, an airport pavement condition was study accordingly with the methodology described at Standard Test Method for Airport Pavement Condition Index Surveys D5340, 2011 where its original condition level is compared with the condition level after iterate possible erroneous considered distresses as well as possible rehabilitations. Afterwards, the results obtained were analyzed and the main conclusions presented together with some future developments.

Horizontal and vertical tree community structure in a lowland atlantic rain forest, southeastern Brazil

The horizontal and vertical tree community structure in a lowland Atlantic Rain Forest was investigated through a phytosociological survey in two 0.99 ha plots in the Intervales State Park, São Paulo State. All trees > 5 cm diameter at breast height were recorded. 3,078 individuals belonging to 172 species were identified and recorded. The Shannon diversity index was H' = 3.85 nat.ind.-1. The Myrtaceae family showed the greatest floristic richness (38 species) and the highest density (745 individuals) in the stand. Euterpe edulis Mart. had the highest importance value (33.98%) accounting for 21.8% of all individuals recorded. The quantitative similarity index was higher than the qualitative index, showing little structural variation between plots. However, the large number of uncommon species resulted in pronounced floristic differences. A detrended correspondence analysis (DCA) generated three arbitrary vertical strata. Stratum A (> 26 m), where Sloanea guianensis (Aubl.) Benth. and Virola bicuhyba (Schott. ex A.DC.) Warb. were predominant showed the lowest density. Stratum B (8 m < h < 26 m) had the greatest richness and diversity, and stratum C (< 8 m) showed the highest density. Euterpe edulis, Guapira opposita (Vell.) Reitz, Garcinia gardneriana (Planch. & Triana) Zappi, and Eugenia mosenii (Kausel) Sobral were abundant in strata B and C. The occurrence of strata in tropical forests is discussed and we recommend the use of DCA for others studies of the vertical distribution of tropical forest tree communities.

Molecular approaches for structural characterization of Bothrops L-amino acid oxidases with antiprotozoal activity: cDNA cloning, comparative sequence analysis, and molecular modeling

Two L-amino acid oxidases (LAAOs) were identified by random sequencing of cDNA libraries from the venom glands of Bothrops moojeni (BmooLAAO) and Bothrops jararacussu (Bjussu LAAO). Phylogenetic analysis involving other SV-LAAOs showed sequence identities within the range 83-87% being closely related to those from Agkistrodon and Trimeresurus. Molecular modeling experiments indicated the FAD-binding, substrate-binding, and helical domains of Bmoo and Bjussu LAAOs. The RMS deviations obtained by the superposition of those domains and that from Calloselasma rhodostoma LAAO crystal structure confirm the high degree of structural similarity between these enzymes. Purified BjussuLAAO-I and BmooLAAO-I exhibited antiprotozoal activities which were demonstrated to be hydrogen-peroxide mediated. This is the first report on the isolation and identification of cDNAs encoding LAAOs from Bothrops venom. The findings here reported contribute to the overall structural elucidation of SV-LAAOs and will advance the understanding on their mode of action. (c) 2006 Elsevier B.V. All rights reserved.

Horizontal and vertical tree community structure in a lowland atlantic rain forest, southeastern Brazil

A estrutura horizontal e vertical do componente arbóreo foi investigada em um trecho de Floresta Atlântica baixo-montana através de um levantamento fitossociológico em dois blocos amostrais de 0,99 ha cada no Parque Estadual Intervales. Todos os indivíduos com DAP > 5 cm foram registrados. Foram amostrados 3.078 indivíduos distribuídos em 172 espécies. O índice de diversidade de Shannon foi de H' = 3,85 nat.ind.-1. A família Myrtaceae se destacou tanto em número de espécies (38) quanto em número de indivíduos (745) no levantamento. Euterpe edulis Mart. teve o maior valor de importância (33,98%), abrangendo 21,8% do total de indivíduos registrados. O índice de similaridade quantitativo foi maior do que o qualitativo, mostrando pouca variação estrutural entre os blocos amostrais, mas a grande quantidade de espécies pouco abundantes, resultou em pronunciadas diferenças florísticas entre eles. Uma análise de correspondência retificada (DCA) gerou três estratos verticais arbitrários. O estrato A (> 26 m) teve a menor densidade e foi bem representado pelas espécies Sloanea guianensis (Aubl.) Benth. e Virola bicuhyba (Schott. ex A.DC.) Warb. O estrato B (8 m < h < 26 m) mostrou a maior riqueza e diversidade florística, e o estrato C (< 8 m) a maior densidade. Euterpe edulis, Guapira opposita (Vell.) Reitz, Garcinia gardneriana (Planch. & Triana) Zappi e Eugenia mosenii (Kausel) Sobral foram bem representadas nos estratos B e C da floresta. A existência de estratos verticais em florestas tropicais é discutida, recomendando-se o uso da DCA para estudos da estratificação vertical em outras florestas tropicais.

Structural and functional characterization of neuwiedase, a nonhemorrhagic fibrin(ogen)olytic metalloprotease from Bothrops neuwiedi snake venom

A fibrino(geno)lytic nonhemorrhagic metalloprotease (neuwiedase) was purified from Bothrops neuwiedi snake venom by a single chromatographic step procedure on a CM-Sepharose column, Neuwiedase represented 4.5% (w/w) of the crude desiccated venom, with an approximate Mr of 20,000 and pI 5.9, As regards the amino acid composition, neuwiedase showed similarities with other metalloproteases, with high proportions of Asx, Glx, Leu, and Ser, Atomic absorption spectroscopy showed that one mole of Zn2+ and one mole of Ca2+ were present per mole olf protein. The cDNA encoding neuwiedase was isolated by RT-PCR from venom gland RNA, using oligonucleotides based on the partially determined amino-acid sequences of this metalloprotease. The fall sequence contained approximately 594 bp, which codified the 198 amino acid residues with an estimated molecular weight of 22,375. Comparison of the nucleotide and amino acid sequences of neuwiedase with those of other snake venom metalloproteases showed a high level of sequential similarity, Neuwiedase has two highly conserved characteristics sequences H(142)E(143)XXH(146)XXG(140)XXH(152) and C164I165M166. The three-dimensional structure of neuwiedase was modeled based on the crystal structure of Crotalus adamanteus Adamalysin II. This model revealed that the zinc binding site region showed a I high structural similarity with other metalloproteases,, the proteolyitc specificity, using the B beta-chain of oxidized insulin as substrate, was shown to be directed to the Ala(14)-Leu(15) and Tyr(16)-Leu(17) peptide bonds which were preferentially hydrolyzed. Neuwiedase is a A alpha,B beta fibrinogenase, Its activity upon the A alpha chain of fibrinogen was detected within 15 min of incubation. The optimal temperature and pH for the degradation of both A alpha and B beta chains were 37 degrees C and 7.4-8.0, respectively. This activity was inhibited by EDTA and 1,10-phenantroline, Neuwiedase also showed proteolytic activity upon fibrin and some components of the extracellular matrix. However, it did not show TAME esterase activity and was not able to inhibit platelet aggregation. (C) 2000 Academic Press.