Inhibitors of Trypanosoma brucei trypanothione reductase: comparative molecular field analysis modeling and structural basis for selective inhibition

Background: Sleeping sickness is a major cause of death in Africa. Since no secure treatment is available, the development of novel therapeutic agents is urgent. In this context, the enzyme trypanothione reductase (TR) is a prominent molecular target that has been investigated in drug design for sleeping sickness. Results: In this study, comparative molecular field analysis models were generated for a series of Trypanosoma brucei TR inhibitors. Statistically significant results were obtained and the models were applied to predict the activity of external test sets, with good correlation between predicted and experimental results. We have also investigated the structural requirements for the selective inhibition of the parasite's enzyme over the human glutathione reductase. Conclusion: The quantitative structure-activity relationship models provided valuable information regarding the essential molecular requirements for the inhibitory activity upon the target protein, providing important insights into the design of more potent and selective TR inhibitors.

Structure-semantics interplay in complex networks and its effects on the predictability of similarity in texts

The classification of texts has become a major endeavor with so much electronic material available, for it is an essential task in several applications, including search engines and information retrieval. There are different ways to define similarity for grouping similar texts into clusters, as the concept of similarity may depend on the purpose of the task. For instance, in topic extraction similar texts mean those within the same semantic field, whereas in author recognition stylistic features should be considered. In this study, we introduce ways to classify texts employing concepts of complex networks, which may be able to capture syntactic, semantic and even pragmatic features. The interplay between various metrics of the complex networks is analyzed with three applications, namely identification of machine translation (MT) systems, evaluation of quality of machine translated texts and authorship recognition. We shall show that topological features of the networks representing texts can enhance the ability to identify MT systems in particular cases. For evaluating the quality of MT texts, on the other hand, high correlation was obtained with methods capable of capturing the semantics. This was expected because the golden standards used are themselves based on word co-occurrence. Notwithstanding, the Katz similarity, which involves semantic and structure in the comparison of texts, achieved the highest correlation with the NIST measurement, indicating that in some cases the combination of both approaches can improve the ability to quantify quality in MT. In authorship recognition, again the topological features were relevant in some contexts, though for the books and authors analyzed good results were obtained with semantic features as well. Because hybrid approaches encompassing semantic and topological features have not been extensively used, we believe that the methodology proposed here may be useful to enhance text classification considerably, as it combines well-established strategies. (c) 2012 Elsevier B.V. All rights reserved.

Tomotherapy dose distribution verification using MAGIC-f polymer gel dosimetry

Purpose: This paper presents the application of MAGIC-f gel in a three-dimensional dose distribution measurement and its ability to accurately measure the dose distribution from a tomotherapy unit. Methods: A prostate intensity-modulated radiation therapy (IMRT) irradiation was simulated in the gel phantom and the treatment was delivered by a TomoTherapy equipment. Dose distribution was evaluated by the R2 distribution measured in magnetic resonance imaging. Results: A high similarity was found by overlapping of isodoses of the dose distribution measured with the gel and expected by the treatment planning system (TPS). Another analysis was done by comparing the relative absorbed dose profiles in the measured and in the expected dose distributions extracted along indicated lines of the volume and the results were also in agreement. The gamma index analysis was also applied to the data and a high pass rate was achieved (88.4% for analysis using 3%/3 mm and of 96.5% using 4%/4 mm). The real three-dimensional analysis compared the dose-volume histograms measured for the planning volumes and expected by the treatment planning, being the results also in good agreement by the overlapping of the curves. Conclusions: These results show that MAGIC-f gel is a promise for tridimensional dose distribution measurements. (C) 2012 American Association of Physicists in Medicine. [http://dx.doi.org/10.1118/1.4704496]

Morphologic micro–computed tomography analysis of mandibular premolars with three root canals

Introduction: This study aimed to describe the anatomy of mandibular premolars with type IX canal configuration by using micro–computed tomography. Methods: Mandibular premolars with radicular grooves (n = 105) were scanned, and 16 teeth with type IX configuration were selected. Number and location of canals, distances between anatomic landmarks, occurrence of apical delta, root canal fusion, and furcation canals, as well as 2-dimensional (area, perimeter, roundness, major and minor diameters) and 3-dimensional (volume, surface area, and structuremodel index) analysis were performed. Data were statistically compared by using analysis of variance and Kruskal-Wallis tests (a = 0.05). Results: Overall, specimens had 1 root with a main canal that divided into mesiobuccal, distobuccal, and lingual canals at the furcation level. Mean length of the teeth was 22.9 2.06 mm, and the configuration of the pulp chamber was mostly triangle-shaped. Mean distances from the furcation to the apex and cementoenamel junction were 9.14 2.07 and 5.59 2.19 mm, respectively. Apical delta, root canal fusion, and furcation canals were present in 4, 5, and 10 specimens, respectively. No statistical differences were found in the 2-dimensional and 3-dimensional analyses between root canals (P > .05). Conclusions: Type IX configuration of the root canal system was found in 16 of 105 mandibular premolars with radicular grooves. Most of the specimens had a triangle-shaped pulp chamber. Within this anatomic configuration, complexities of the root canal systems such as the presence of furcation canals, fusion of canals, oval-shaped canals in the apical third, small orifices at the pulp chamber level, and apical delta were also observed

Sesquiterpene Lactones with Anti-Hepatitis C Virus Activity Using Molecular Descriptors

Hepatitis C is a worldwide public health problem. The available therapies are limited by their partial effectiveness and with meaningful side-effects. Sesquiterpene lactones (SLs) are a group of natural products with a wide variety of chemical structures and biological activities associated. There are few studies about the influence of the molecular structure of SLs for the anti-hepatitis C virus activity. In the present work, SLs are investigated in a subgenomic RNA replicon assay system and were analyzed using multiple linear regression along with self-organizing maps with DRAGON descriptors in order to identify the structural requirements for their biological activity and to predict the inhibitory potency of SLs. Characteristics such as stereochemistry and electronic effects demonstrated to be important for their anti-HCV activity, and the SOM produced a clear separation betwenn active and inactive compounds. Therefore, it is possible to use this map as a filter for virtual screening to predict the anti-HCV activity of SLs.

Using complex networks concepts to assess approaches for citations in scientific papers

The number of citations received by authors in scientific journals has become a major parameter to assess individual researchers and the journals themselves through the impact factor. A fair assessment therefore requires that the criteria for selecting references in a given manuscript should be unbiased with regard to the authors or journals cited. In this paper, we assess approaches for citations considering two recommendations for authors to follow while preparing a manuscript: (i) consider similarity of contents with the topics investigated, lest related work should be reproduced or ignored; (ii) perform a systematic search over the network of citations including seminal or very related papers. We use formalisms of complex networks for two datasets of papers from the arXiv and the Web of Science repositories to show that neither of these two criteria is fulfilled in practice. By representing the texts as complex networks we estimated a similarity index between pieces of texts and found that the list of references did not contain the most similar papers in the dataset. This was quantified by calculating a consistency index, whose maximum value is one if the references in a given paper are the most similar in the dataset. For the areas of "complex networks" and "graphenes", the consistency index was only 0.11-0.23 and 0.10-0.25, respectively. To simulate a systematic search in the citation network, we employed a traditional random walk search (i.e. diffusion) and a random walk whose probabilities of transition are proportional to the number of the ingoing edges of the neighbours. The frequency of visits to the nodes (papers) in the network had a very small correlation with either the actual list of references in the papers or with the number of downloads from the arXiv repository. Therefore, apparently the authors and users of the repository did not follow the criterion related to a systematic search over the network of citations. Based on these results, we propose an approach that we believe is fairer for evaluating and complementing citations of a given author, effectively leading to a virtual scientometry.

Genetic diversity of Stryphnodendron adstringens (Mart.) Coville determined by AFLP molecular markers

Bark extracts of Stryphnodendron adstringens (Mart) Coville a Leguminosae species, well known in Brazil as barbatimao, are popularly used as healing agent. The objective of this work was to determine the genetic diversity of S. adstringens populations and to correlate genetic distances to the production of tannins. S. adstringens accessions from populations found in Cerrado regions in the states of Goias, Minas Gerais and Sao Paulo were analyzed using the AFLP (Amplified Fragment Length Polymorphism) technique. A total of 236 polymorphic bands were scored and higher proportion of genetic diversity was found inter populations (70.9%), rather than intra populations (29.1%). F-ST value was found to be significantly greater than zero (0.2906), demonstrating the complex genetic structure of S. adstringens populations. Accessions collected in Cristalina, GO, showed higher percentage of polymorphic loci (87.3%) and the highest genetic diversity. The lowest genetic variability was detected among accessions from the population growing in Caldas Novas, GO. The genetic distance among populations was estimated using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), which grouped populations into 3 clusters. Moreover, chemotypes with tannin concentration above 40% showed higher genetic similarity. AFLP analysis proved to be an efficient gene mapping technique to determine the genetic diversity among remaining populations of S. adstringens. Obtained results may be employed to implement further strategies for the conservation of this medicinal plant. (C) 2011 Elsevier Ltd. All rights reserved.

Exploração e análise das novas interfaces digitais relacionadas à representação gráfica na arquitetura

Este trabalho integra as pesquisas desenvolvidas pelo Grupo N.elac – IAU.USP, que tem como tema estudos sobre a representação da arquitetura e da cidade. Este artigo faz análise dos novos recursos tecnológicos direcionados para o desenho e projeto arquitetônico que emulam ou fazem uso do movimento gestual humano no ato de desenho e projeto. A pesquisa testa e avalia qualitativamente o uso das novas ferramentas digitais, tais como as tablets gráficas (ex:Apple Ipad), tablets opacas (ex: Wacom Bamboo) e canetas eletrônicas (ex: Wacom Inkling) na execução de desenhos livre e de observação, orientados por uma proposta de desenvolvimento gráfico relacionados ao ato de projeto arquitetônico, de maneira que se possa construir uma análise comparativa e interpretativa por meio dos produtos gerados nesse processo.

Estudo comparativo entre as novas ferramentas digitais utilizadas no desenho à mão livre

This paper makes an analysis on the new technological resources related to architectural drawing that make use of the hand drawing. It tests and evaluates the use of new tools such as tablets (e.g. Wacom Bamboo), graphic tablets (e.g. iPad), tablet/screen hybrids (e.g. Wacom Cintiq) and electronic pens (e.g. Wacom Inkling) in the making of free drawings oriented for the developing of graphic products related to the projective act in architecture and design. The paper makes a comparative e interpretative analysis through the reading of those products.

Structure-based drug design studies on a series of aldolase inhibitors

Human African trypanosomiasis, also known as sleeping sickness, is a major cause of death in Africa, and for which there are no safe and effective treatments available. The enzyme aldolase from Trypanosoma brucei is an attractive, validated target for drug development. A series of alkyl‑glycolamido and alkyl-monoglycolate derivatives was studied employing a combination of drug design approaches. Three-dimensional quantitative structure-activity relationships (3D QSAR) models were generated using the comparative molecular field analysis (CoMFA). Significant results were obtained for the best QSAR model (r2 = 0.95, non-cross-validated correlation coefficient, and q2 = 0.80, cross-validated correlation coefficient), indicating its predictive ability for untested compounds. The model was then used to predict values of the dependent variables (pKi) of an external test set,the predicted values were in good agreement with the experimental results. The integration of 3D QSAR, molecular docking and molecular dynamics simulations provided further insight into the structural basis for selective inhibition of the target enzyme.

Biochemical characterization and comparative analysis of two distinct serine proteases from Bothrops pirajai snake venom

This study reports the isolation and biochemical characterization of two different serine proteases from Bothrops pirajai snake venom, thus providing a comparative analysis of the enzymes. The isolation process consisted of three consecutive chromatographic steps (Sephacryl S-200, Benzamidine Sepharose and C2/C18), resulting in two serine proteases, named BpirSP27 and BpirSP41 after their molecular masses by mass spectrometry (27,121 and 40,639 Da, respectively). Estimation by SDS-PAGE under denaturing conditions showed that, when deglycosylated with PNGase F, BpirSP27 and BpirSP41 had their molecular masses reduced by approximately 15 and 42%, respectively. Both are acidic enzymes, with pI of approximately 4.7 for BpirSP27 and 3.7 for BpirSP41, and their N-terminal amino acid sequences showed 57% identity to each other, with high similarity to the sequences of other snake venom serine proteases (SVSPs). The enzymes showed different actions on bovine fibrinogen, with BpirSP27 acting preferentially on the B beta chain and BpirSP41 on both A alpha and B beta chains. The two serine proteases were also able to degrade fibrin and blood clots in vitro depending on the doses and incubation periods, with higher results for BpirSP41. Both enzymes coagulated the human plasma in a dose-dependent manner, and BpirSP41 showed a higher coagulant potential, with minimum coagulant dose (MCD) of similar to 3.5 mu g versus 20 mu g for BpirSP27. The enzymes were capable of hydrolyzing different chromogenic substrates, including S-2238 for thrombin-like enzymes, but only BpirSP27 acted on the substrate S-2251 for plasmin. They also showed high stability against variations of temperature and pH, but their activities were significantly reduced after preincubation with Cu2+ ion and specific serine protease inhibitors. In addition. BpirSP27 induced aggregation of washed platelets to a greater extent than BpirSP41. The results showed significant structural and functional differences between B. pirajai serine proteases, providing interesting insights into the structure-function relationship of SVSPs. (C) 2012 Elsevier Masson SAS. All rights reserved.

Comparative analysis of rating curve and ADP estimates of instantaneous water discharge through estuaries in two contrasting Brazilian rivers

This work quantifies, using ADP and rating curve techniques, the instantaneous outflows at estuarine interfaces: higher to middle estuary and middle to lower estuary, in two medium-sized watersheds (72 000 and 66 000 km(2) of area, respectively), the Jaguaribe and Contas Rivers located in the northeastern (semi-arid) and eastern (tropical humid) Brazilian coasts, respectively. Results from ADP showed that the net water balances show the Contas River as a net water exporter, whereas the Jaguaribe River Estuary is a net water importer. At the Jaguaribe Estuary, water retention during flood tide contributes to 58% of the total volume transferred during the ebb tide from the middle to lower estuary. However, 42% of the total water volume (452 m(3) s(-1)) that entered during flood tide is retained in the middle estuary. In the Contas River, 90% of the total water is retained during the flood tide contributing to the volume transported in the ebb tide from the middle to the lower estuary. Outflows obtained with the rating curve method for the Contas and Jaguaribe Rivers were uniform through time due to river flow normalization by dams in both basins. Estimated outflows with this method are about 65% (Contas) and 95% (Jaguaribe) lower compared to outflows obtained with ADP. This suggests that the outflows obtained with the rating curve method underestimate the net water balance in both systems, particularly in the Jaguaribe River under a semi-arid climate. This underestimation is somewhat decreased due to wetter conditions in the Contas River basin. Copyright. (C) 2011 John Wiley & Sons, Ltd.

A comparative study between crack analysis and a mechanical test for assessing the polymerization stress of restorative composites

Objectives. To verify the hypothesis that crack analysis and a mechanical test would rank a series of composites in a similar order with respect to polymerization stress. Also, both tests would show similar relationships between stress and composite elastic modulus and/or shrinkage. Methods. Soda-lime glass discs (2-mm thick) with a central perforation (3.5-mm diameter) received four Vickers indentations 500 mu m from the cavity margin. The indent cracks were measured (500x) prior and 10 min after the cavity was restored with one of six materials (Kalore/KL, Gradia/GR, Ice/IC, Wave/WV, Majesty Flow/MF, and Majesty Posterior/MP). Stresses at the indent site were calculated based on glass fracture toughness and increase in crack length. Stress at the bonded interface was calculated using the equation for an internally pressurized cylinder. The mechanical test used a universal testing machine and glass rods (5-mm diameter) as substrate. An extensometer monitored specimen height (2 mm). Nominal stress was calculated dividing the maximum shrinkage force by the specimen cross-sectional area. Composite elastic modulus was determined by nanoindentation and post-gel shrinkage was measured using strain gages. Data were subjected to one-way ANOVA/Tukey or Kruskal-Wallis/Mann-Whitney tests (alpha: 5%). Results. Both tests grouped the composites in three statistical subsets, with small differences in overlapping between the intermediate subset (MF, WV) and the highest (MP, IC) or the lowest stress materials (KL, GR). Higher stresses were developed by composites with high modulus and/or high shrinkage. Significance. Crack analysis demonstrated to be as effective as the mechanical test to rank composites regarding polymerization stress. (c) 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Comparative analysis of shell occupation by two southern populations of the hermit crab Loxopagurus loxochelis (Decapoda, Diogenidae)

The present study aimed to comparatively verify the relation between the hermit crabs and the shells they use in two populations of Loxopagurus loxochelis. Samples were collected monthly from July 2002 to June 2003, at Caraguatatuba and Ubatuba Bay, Sao Paulo, Brazil. The animals sampled had their sex identified, were weighed and measured; their shells were identified, measured and weighed, and their internal volume determined. To relate the hermit crab's characteristics and the shells' variables, principal component analysis (PCA) and a regression tree were used. According to the PCA analysis, the three gastropod shells most frequently used by L. loxochelis varied in size. The regression tree successfully explained the relationship between the hermit crab's characteristics and the internal volume of the inhabited shell. It can be inferred that the relationship between the morphometry of an individual hermit crab and its shell is not straightforward and it is impossible to explain only on the basis of direct correlations between the body's and the shell's attributes. Several factors (such as the morphometry and the availability of the shell, environmental conditions and inter- and intraspecific competition) interact and seem to be taken into consideration by the hermit crabs when they choose a shell, resulting in the diversified pattern of shell occupancy shown here and elsewhere.

Comparative Genomics of Early-Diverging Brucella Strains Reveals a Novel Lipopolysaccharide Biosynthesis Pathway

Brucella species are Gram-negative bacteria that infect mammals. Recently, two unusual strains (Brucella inopinata BO1(T) and B. inopinata-like BO2) have been isolated from human patients, and their similarity to some atypical brucellae isolated from Australian native rodent species was noted. Here we present a phylogenomic analysis of the draft genome sequences of BO1(T) and BO2 and of the Australian rodent strains 83-13 and NF2653 that shows that they form two groups well separated from the other sequenced Brucella spp. Several important differences were noted. Both BO1(T) and BO2 did not agglutinate significantly when live or inactivated cells were exposed to monospecific A and Mantisera against O-side chain sugars composed of N-formyl-perosamine. While BO1(T) maintained the genes required to synthesize a typical Brucella O-antigen, BO2 lacked many of these genes but still produced a smooth LPS (lipopolysaccharide). Most missing genes were found in the wbk region involved in O-antigen synthesis in classic smooth Brucella spp. In their place, BO2 carries four genes that other bacteria use for making a rhamnose-based O-antigen. Electrophoretic, immunoblot, and chemical analyses showed that BO2 carries an antigenically different O-antigen made of repeating hexose-rich oligosaccharide units that made the LPS water-soluble, which contrasts with the homopolymeric O-antigen of other smooth brucellae that have a phenol-soluble LPS. The results demonstrate the existence of a group of early-diverging brucellae with traits that depart significantly from those of the Brucella species described thus far. IMPORTANCE This report examines differences between genomes from four new Brucella strains and those from the classic Brucella spp. Our results show that the four new strains are outliers with respect to the previously known Brucella strains and yet are part of the genus, forming two new clades. The analysis revealed important information about the evolution and survival mechanisms of Brucella species, helping reshape our knowledge of this important zoonotic pathogen. One discovery of special importance is that one of the strains, BO2, produces an O-antigen distinct from any that has been seen in any other Brucella isolates to date.