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.

Model and performance of a no-reference quality assessment metric for video streaming

Video streaming via Transmission Control Protocol (TCP) networks has become a popular and highly demanded service, but its quality assessment in both objective and subjective terms has not been properly addressed. In this paper, based on statistical analysis a full analytic model of a no-reference objective metric, namely pause intensity (PI), for video quality assessment is presented. The model characterizes the video playout buffer behavior in connection with the network performance (throughput) and the video playout rate. This allows for instant quality measurement and control without requiring a reference video. PI specifically addresses the need for assessing the quality issue in terms of the continuity in the playout of TCP streaming videos, which cannot be properly measured by other objective metrics such as peak signal-to-noise-ratio, structural similarity, and buffer underrun or pause frequency. The performance of the analytical model is rigidly verified by simulation results and subjective tests using a range of video clips. It is demonstrated that PI is closely correlated with viewers' opinion scores regardless of the vastly different composition of individual elements, such as pause duration and pause frequency which jointly constitute this new quality metric. It is also shown that the correlation performance of PI is consistent and content independent. © 2013 IEEE.

Identifying the Structure and Fate of Wastewater Derived Organic Micropollutants by High-resolution Mass Spectrometry

Human activities represent a significant burden on the global water cycle, with large and increasing demands placed on limited water resources by manufacturing, energy production and domestic water use. In addition to changing the quantity of available water resources, human activities lead to changes in water quality by introducing a large and often poorly-characterized array of chemical pollutants, which may negatively impact biodiversity in aquatic ecosystems, leading to impairment of valuable ecosystem functions and services. Domestic and industrial wastewaters represent a significant source of pollution to the aquatic environment due to inadequate or incomplete removal of chemicals introduced into waters by human activities. Currently, incomplete chemical characterization of treated wastewaters limits comprehensive risk assessment of this ubiquitous impact to water. In particular, a significant fraction of the organic chemical composition of treated industrial and domestic wastewaters remains uncharacterized at the molecular level. Efforts aimed at reducing the impacts of water pollution on aquatic ecosystems critically require knowledge of the composition of wastewaters to develop interventions capable of protecting our precious natural water resources.

The goal of this dissertation was to develop a robust, extensible and high-throughput framework for the comprehensive characterization of organic micropollutants in wastewaters by high-resolution accurate-mass mass spectrometry. High-resolution mass spectrometry provides the most powerful analytical technique available for assessing the occurrence and fate of organic pollutants in the water cycle. However, significant limitations in data processing, analysis and interpretation have limited this technique in achieving comprehensive characterization of organic pollutants occurring in natural and built environments. My work aimed to address these challenges by development of automated workflows for the structural characterization of organic pollutants in wastewater and wastewater impacted environments by high-resolution mass spectrometry, and to apply these methods in combination with novel data handling routines to conduct detailed fate studies of wastewater-derived organic micropollutants in the aquatic environment.

In Chapter 2, chemoinformatic tools were implemented along with novel non-targeted mass spectrometric analytical methods to characterize, map, and explore an environmentally-relevant “chemical space” in municipal wastewater. This was accomplished by characterizing the molecular composition of known wastewater-derived organic pollutants and substances that are prioritized as potential wastewater contaminants, using these databases to evaluate the pollutant-likeness of structures postulated for unknown organic compounds that I detected in wastewater extracts using high-resolution mass spectrometry approaches. Results showed that application of multiple computational mass spectrometric tools to structural elucidation of unknown organic pollutants arising in wastewaters improved the efficiency and veracity of screening approaches based on high-resolution mass spectrometry. Furthermore, structural similarity searching was essential for prioritizing substances sharing structural features with known organic pollutants or industrial and consumer chemicals that could enter the environment through use or disposal.

I then applied this comprehensive methodological and computational non-targeted analysis workflow to micropollutant fate analysis in domestic wastewaters (Chapter 3), surface waters impacted by water reuse activities (Chapter 4) and effluents of wastewater treatment facilities receiving wastewater from oil and gas extraction activities (Chapter 5). In Chapter 3, I showed that application of chemometric tools aided in the prioritization of non-targeted compounds arising at various stages of conventional wastewater treatment by partitioning high dimensional data into rational chemical categories based on knowledge of organic chemical fate processes, resulting in the classification of organic micropollutants based on their occurrence and/or removal during treatment. Similarly, in Chapter 4, high-resolution sampling and broad-spectrum targeted and non-targeted chemical analysis were applied to assess the occurrence and fate of organic micropollutants in a water reuse application, wherein reclaimed wastewater was applied for irrigation of turf grass. Results showed that organic micropollutant composition of surface waters receiving runoff from wastewater irrigated areas appeared to be minimally impacted by wastewater-derived organic micropollutants. Finally, Chapter 5 presents results of the comprehensive organic chemical composition of oil and gas wastewaters treated for surface water discharge. Concurrent analysis of effluent samples by complementary, broad-spectrum analytical techniques, revealed that low-levels of hydrophobic organic contaminants, but elevated concentrations of polymeric surfactants, which may effect the fate and analysis of contaminants of concern in oil and gas wastewaters.

Taken together, my work represents significant progress in the characterization of polar organic chemical pollutants associated with wastewater-impacted environments by high-resolution mass spectrometry. Application of these comprehensive methods to examine micropollutant fate processes in wastewater treatment systems, water reuse environments, and water applications in oil/gas exploration yielded new insights into the factors that influence transport, transformation, and persistence of organic micropollutants in these systems across an unprecedented breadth of chemical space.

Using multifractals to evaluate oceanographic model skill

We are in an era of unprecedented data volumes generated from observations and model simulations. This is particularly true from satellite Earth Observations (EO) and global scale oceanographic models. This presents us with an opportunity to evaluate large scale oceanographic model outputs using EO data. Previous work on model skill evaluation has led to a plethora of metrics. The paper defines two new model skill evaluation metrics. The metrics are based on the theory of universal multifractals and their purpose is to measure the structural similarity between the model predictions and the EO data. The two metrics have the following advantages over the standard techniques: a) they are scale-free, b) they carry important part of information about how model represents different oceanographic drivers. Those two metrics are then used in the paper to evaluate the performance of the FVCOM model in the shelf seas around the south-west coast of the UK.

Using multifractals to evaluate oceanographic model skill

We are in an era of unprecedented data volumes generated from observations and model simulations. This is particularly true from satellite Earth Observations (EO) and global scale oceanographic models. This presents us with an opportunity to evaluate large scale oceanographic model outputs using EO data. Previous work on model skill evaluation has led to a plethora of metrics. The paper defines two new model skill evaluation metrics. The metrics are based on the theory of universal multifractals and their purpose is to measure the structural similarity between the model predictions and the EO data. The two metrics have the following advantages over the standard techniques: a) they are scale-free, b) they carry important part of information about how model represents different oceanographic drivers. Those two metrics are then used in the paper to evaluate the performance of the FVCOM model in the shelf seas around the south-west coast of the UK.

Spam campaign detection, analysis, and formalization

Les courriels Spams (courriels indésirables ou pourriels) imposent des coûts annuels extrêmement lourds en termes de temps, d’espace de stockage et d’argent aux utilisateurs privés et aux entreprises. Afin de lutter efficacement contre le problème des spams, il ne suffit pas d’arrêter les messages de spam qui sont livrés à la boîte de réception de l’utilisateur. Il est obligatoire, soit d’essayer de trouver et de persécuter les spammeurs qui, généralement, se cachent derrière des réseaux complexes de dispositifs infectés, ou d’analyser le comportement des spammeurs afin de trouver des stratégies de défense appropriées. Cependant, une telle tâche est difficile en raison des techniques de camouflage, ce qui nécessite une analyse manuelle des spams corrélés pour trouver les spammeurs. Pour faciliter une telle analyse, qui doit être effectuée sur de grandes quantités des courriels non classés, nous proposons une méthodologie de regroupement catégorique, nommé CCTree, permettant de diviser un grand volume de spams en des campagnes, et ce, en se basant sur leur similarité structurale. Nous montrons l’efficacité et l’efficience de notre algorithme de clustering proposé par plusieurs expériences. Ensuite, une approche d’auto-apprentissage est proposée pour étiqueter les campagnes de spam en se basant sur le but des spammeur, par exemple, phishing. Les campagnes de spam marquées sont utilisées afin de former un classificateur, qui peut être appliqué dans la classification des nouveaux courriels de spam. En outre, les campagnes marquées, avec un ensemble de quatre autres critères de classement, sont ordonnées selon les priorités des enquêteurs. Finalement, une structure basée sur le semiring est proposée pour la représentation abstraite de CCTree. Le schéma abstrait de CCTree, nommé CCTree terme, est appliqué pour formaliser la parallélisation du CCTree. Grâce à un certain nombre d’analyses mathématiques et de résultats expérimentaux, nous montrons l’efficience et l’efficacité du cadre proposé.

Determinação de motivos de ligação à quitina em vicilinas de Canavalia ensiformis e Vigna unguiculata através de métodos in silico e relação com suas toxicidades para o bruquídeo Callosobruchus maculatus (Coleoptera:Bruchidae)

Chitin is an important structural component of the cellular wall of fungi and exoskeleton of many invertebrate plagues, such as insects and nematodes. In digestory systems of insects it forms a named matrix of peritrophic membrane. One of the most studied interaction models protein-carbohydrate is the model that involves chitin-binding proteins. Among the involved characterized domains already in this interaction if they detach the hevein domain (HD), from of Hevea brasiliensis (Rubber tree), the R&R consensus domain (R&R), found in cuticular proteins of insects, and the motif called in this study as conglicinin motif (CD), found in the cristallography structure of the β-conglicinin bounded with GlcNac. These three chitin-binding domains had been used to determine which of them could be involved in silico in the interaction of Canavalia ensiformis and Vigna unguiculata vicilins with chitin, as well as associate these results with the WD50 of these vicilins for Callosobruchus maculatus larvae. The technique of comparative modeling was used for construction of the model 3D of the vicilin of V. unguiculata, that was not found in the data bases. Using the ClustalW program it was gotten localization of these domains in the vicilins primary structure. The domains R&R and CD had been found with bigger homology in the vicilins primary sequences and had been target of interaction studies. Through program GRAMM models of interaction ( dockings ) of the vicilins with GlcNac had been gotten. The results had shown that, through analysis in silico, HD is not part of the vicilins structures, proving the result gotten with the alignment of the primary sequences; the R&R domain, although not to have structural similarity in the vicilins, probably it has a participation in the activity of interaction of these with GlcNac; whereas the CD domain participates directly in the interaction of the vicilins with GlcNac. These results in silico show that the amino acid number, the types and the amount of binding made for the CD motif with GlcNac seem to be directly associates to the deleterious power that these vicilins show for C. maculatus larvae. This can give an initial step in the briefing of as the vicilins interact with alive chitin in and exert its toxic power for insects that possess peritrophic membrane

Efeito anti-inflamatório do heparinóide isolado do camarão Litopenaeus vannamei sobre a peritonite aguda

In recent years the heparin has been the subject of several studies that aim to expand its use as a therapeutic agent, due to its ability to modulate the activity of various proteins that play important roles in the regulation of pathophysiological processes. In several experiments and preclinical trials, heparin has demonstrated an anti-inflammatory role. However, its clinical use is limited, due to its strong anticoagulant activity and hemorrhagic complications. For this reason, considerable efforts have been employed in discovery of heparin analogous (heparinoid) with reduced side effects, that retain the anti-inflammatory properties of heparin. In this context, a heparinoid obtained from the head of Litopenaeus vannamei shrimp, which presents a structural similarity to heparin, showed, in previous studies, anti-inflammatory activity in a model of acute peritonitis with reduced anticoagulant effect in vitro and low hemorrhagic activity. Thus, the present work had as objective to evaluate the effect the heparinoid of the cephalothorax of gray shrimp on the acute inflammatory response in different times (3 or 6 hours after the induction of inflammatory stimulus), using the model of acute peritonitis induced in mice. It was also analyzed the HL effect over the activity of elastase, an enzyme involved in leukocyte recruitment. Furthermore to check if the different doses of heparin and heparinoid change the hemostatic balance in vivo, was assessed the effect of these compounds on the plasma clotting time in animals submitted to inflammation. The results show that in 3 hours, all doses of heparinoid were able to prevent efficiently in the acute inflammatory process without any anticoagulant effects, unlike the extrapolation dose of heparin, which has induced a large hemorrhage due its high anticoagulant activity. However, 6 hours after induction of inflammation, only the dosages of 0.1 and 1.0 μg/Kg of heparin and 1.0 μg/Kg of heparinoid kept anti-migratory effect, without changing of the hemostatic balance. These results indicate that the anti-migratory effect of theses compounds depends on the dosage and time of inflammatory stimulus. The HL and heparin were also able to inhibit the activity of the enzyme elastase. The discovery of this bioactive compound in the cephalothorax of shrimps can arouse great interest in biotechnology, since this compound could be useful as a structural model interesting for the development of new therapeutic agents for peritonitis

Prediction of peptide and protein propensity for amyloid formation

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Structural aspects and floristic similarity among tropical dry forest fragments with different management histories in northern Minas Gerais, Brazil

In order to produce useful knowledge to the initiatives of protection and management of forest fragments, more specifically for tropical dry forests which suffer with frequent anthropic activities, and due to the lack of specific studies, this article aimed describe the structure and the floristic similarity among three areas of dry forest with different management histories. The study was developed in Capitão Enéas municipality, Northern Minas Gerais, Brazil, where three fragments were evaluated, being one in regeneration for 30 years, another submitted to occasional fire and the third with selective cut in small scale. The sampling was developed through the point quarter method considering all the alive phanerophyte individuals with circumference at breast height (CBH) > 15 cm. In the three fragments, 512 individuals, distributed in 60 species, 47 genera, and 23 families were sampled. The most representative families were Fabaceae (26), Anacardiaceae (4), Bignoniaceae (3) and Combretaceae (3). However, fourteen families were represented by only one species. Only eight species were common to all fragments - Myracrodruon urundeuva standed out with 26.9% of all sampled individuals - while a great number of species were exclusive of each fragment. The floristic and structural differences between the fragments are possibly related to the history and intensity of management in each area besides the topography variations and the presence or absence of limestone outcrops. These results show the importance of each fragment, indicating that the loss of anyone would cause negative impacts on the regional flora and consequently to the associated biodiversity.

Morphosyntactic processing in advanced second language (L2) learners: An event-related potential investigation of the effects of L1-L2 similarity and structural distance

Different theoretical accounts of second language (L2) acquisition differ with respect to whether or not advanced learners are predicted to show native like processing for features not instantiated in the native language (L1). We examined how native speakers of English, a language with number but not gender agreement, process number and gender agreement in Spanish. We compare agreement within a determiner phrase (órgano muy complejo “[DP organ-MASC-SG very complex-MASC-SG]”) and across a verb phrase (cuadro es auténtico “painting-MASC-SG [VP is authentic-MASC-SG]”) in order to investigate whether native like processing is limited to local domains (e.g. within the phrase), in line with Clahsen and Felser (2006). We also examine whether morphological differences in how the L1 and L2 realize a shared feature impact processing by comparing number agreement between nouns and adjectives, where only Spanish instantiates agreement, and between demonstratives and nouns, where English also instantiates agreement. Similar to Spanish natives, advanced learners showed a P600 for both number and gender violations overall, in line with the Full Transfer/Full Access Hypothesis (Schwartz and Sprouse, 1996), which predicts that learners can show native-like processing for novel features. Results also show that learners can establish syntactic dependencies outside of local domains, as suggested by the presence of a P600 for both within and across phrase violations. Moreover, similar to native speakers, learners were impacted by the structural distance (number of intervening phrases) between the agreeing elements, as suggested by the more positive waveforms for within than across-phrase agreement overall. These results are consistent with the proposal that learners are sensitive to hierarchical structure.

Enzymatic and structural characterization of a basic phospholipase A(2) from the sea anemone Condylactis gigantea

This work aimed at the isolation and structural/functional characterization of a phospholipase A(2) (CgPLA(2)) from the extract of the anemone Condylactis gigantea. CgPLA2 was isolated with a high purity level through three chromatographic steps, showing pT8.6 and molecular weights of 14,500 and 29,000 for the monomer and dimer, respectively. CgPLA2 showed a high catalytic activity upon fluorescent phospholipids inducing no direct hemolytic activity. This enzyme, which is Ca2+-dependent, showed a lower stability against temperature and pH variations when compared with snake venom enzymes. The enzymatic activity was significantly reduced or completely abolished after chemical modification of CgPLA2 with BPB. Its cDNA was then obtained, with 357 base pairs which codified for a mature protein of 119 amino acid residues. A comparative analysis of the primary structure of CgPLA2 revealed 84%, 61%, 43% and 42% similarity to the PLA2s from Adamsia carciniopados, Nematostella vectensis, Vipera russelli russelli and Both raps jararacussu, respectively. (C) 2010 Elsevier Masson SAS. All rights reserved.

An alpha-type phospholipase A(2) inhibitor from Bothrops jararacussu snake plasma: Structural and functional characterization

An inhibitory protein that neutralizes the enzymatic, toxic and pharmacological activities of several phospholipases A(2) from Bothrops venoms was isolated from B. jararacussu snake plasma by affinity chromatography using the immobilized myotoxin BthTX-I on Sepharose gel. Biochemical characterization of this inhibitory protein, denominated alpha BjussuMIP, showed it to be an oligomeric glycoprotein with M-r of 24,000 for the monomeric subunit. Secondary structural analysis by circular dichroism revealed 44% alpha-helix, 18% beta-sheet, 10% beta-turn and 28% random coil structures. Circular dichroism spectroscopy indicated that no significant alterations in the secondary structure of either alpha BjussuMIP or the target protein occur following their interaction. The product from the reaction with reverse transcriptase produced a cDNA fragment of 432 bp that codifies for a mature protein of 144 amino acid residues. The first 21 amino acid residues from the N-terminal and five tryptic peptides were characterized by mass spectrometry of the mature protein and confirmed by the nucleotide sequence. Alignment of alpha BjussuMIP with other snake inhibitors showed a sequence similarity of 73-92% with these alpha PLIs. alpha BjussuMIP was relatively stable within the pH range of 6-12 and temperatures from 0 degrees C to 80 degrees C, even after deglycosylation. The results showed effects against Bothrops phospholipase A(2) activities (enzymatic, edema inducing, myotoxic, cytotoxic and bactericidal), suggesting that alpha BjussuMIP may prove useful in the treatment of snakebite envenomations. (C) 2008 Elsevier Masson SAS. All rights reserved.

Thermal ecology and structural habitat use of two sympatric lizards (Carlia vivax and Lygisaurus foliorum) in subtropical Australia

The thermal ecology and structural habitat use of two closely related sympatric lizards, Carlia vivax (de Vis) and Lygisaurus foliorum de Vis, were examined in an open sclerophyll forest in subtropical Australia. Comparable mean body temperatures (T-b) and habitat temperatures (T-hab) at the point of capture were recorded for both species. However, sex- related differences in the thermal variables for C. vivax, with females displaying higher temperatures than males, resulted in some significant differences in T-b and T-hab between the species. Variation in T-b and T-hab within and between species was unrelated to time of capture. The difference in T-hab within C. vivax suggested that females were selecting warmer thermal environments than males. Both C. vivax and L. foliorum used most structural features of their habitat randomly as indicated by a similarity in canopy, shrub, ground, log and litter cover and litter depth between habitat surveys and random surveys. However, C. vivax displayed a preference for ground vegetation (height

Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information

The three-dimensional structures of leucine-rich repeat (LRR) -containing proteins from five different families were previously predicted based on the crystal structure of the ribonuclease inhibitor. using an approach that combined homology-based modeling, structure-based sequence alignment of LRRs, and several rational assumptions. The structural models have been produced based on very limited sequence similarity, which, in general. cannot yield trustworthy predictions. Recently, the protein structures from three of these five families have been determined. In this report we estimate the quality of the modeling approach by comparing the models with the experimentally determined structures. The comparison suggests that the general architecture, curvature, interior/exterior orientations of side chains. and backbone conformation of the LRR structures can be predicted correctly. On the other hand. the analysis revealed that, in some cases. it is difficult to predict correctly the twist of the overall super-helical structure. Taking into consideration the conclusions from these comparisons, we identified a new family of bacterial LRR proteins and present its structural model. The reliability of the LRR protein modeling suggests that it would be informative to apply similar modeling approaches to other classes of solenoid proteins.