A coupled boundary element/differential equation method formulation for plate-beam interaction analysis

In this work, a new boundary element formulation for the analysis of plate-beam interaction is presented. This formulation uses a three nodal value boundary elements and each beam element is replaced by its actions on the plate, i.e., a distributed load and end of element forces. From the solution of the differential equation of a beam with linearly distributed load the plate-beam interaction tractions can be written as a function of the nodal values of the beam. With this transformation a final system of equation in the nodal values of displacements of plate boundary and beam nodes is obtained and from it, all unknowns of the plate-beam system are obtained. Many examples are analyzed and the results show an excellent agreement with those from the analytical solution and other numerical methods. (C) 2009 Elsevier Ltd. All rights reserved.

Structure, Dynamics, and RNA Interaction Analysis of the Human SBDS Protein

Shwachman-Bodian-Diamond syndrome is an autosomal recessive genetic syndrome with pleiotropic phenotypes, including pancreatic deficiencies, bone marrow dysfunctions with increased risk of myelodysplasia or leukemia, and skeletal abnormalities. This syndrome has been associated with mutations in the SBDS gene, which encodes a conserved protein showing orthologs in Archaea and eukaryotes. The Shwachman-Bodian-Diamond syndrome pleiotropic phenotypes may be an indication of different cell type requirements for a fully functional SBDS protein. RNA-binding activity has been predicted for archaeal and yeast SBDS orthologs, with the latter also being implicated in ribosome biogenesis. However, full-length SBDS orthologs function in a species-specific manner, indicating that the knowledge obtained from model systems may be of limited use in understanding major unresolved issues regarding SBDS function, namely, the effect of mutations in human SBDS on its biochemical function and the specificity of RNA interaction. We determined the solution structure and backbone dynamics of the human SBDS protein and describe its RNA binding site using NMR spectroscopy. Similarly to the crystal structures of Archaea, the overall structure of human SBDS comprises three well-folded domains. However, significant conformational exchange was observed in NMR dynamics experiments for the flexible linker between the N-terminal domain and the central domain, and these experiments also reflect the relative motions of the domains. RNA titrations monitored by heteronuclear correlation experiments and chemical shift mapping analysis identified a classic RNA binding site at the N-terminal FYSH (fungal, Yhr087wp, Shwachman) domain that concentrates most of the mutations described for the human SBDS. (C) 2010 Elsevier Ltd. All rights reserved.

Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual

Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with alterations present in non-tumor genomes. A comparison of the two would be crucial to better characterize the genetic alterations driving tumorigenesis. We sequenced the genomes of a lymphoblastoid (HCC1954BL) and a breast tumor (HCC1954) cell line derived from the same patient and compared the somatic alterations present in both. The lymphoblastoid genome presents a comparable number and similar spectrum of nucleotide substitutions to that found in the tumor genome. However, a significant difference in the ratio of non-synonymous to synonymous substitutions was observed between both genomes (P = 0.031). Protein-protein interaction analysis revealed that mutations in the tumor genome preferentially affect hub-genes (P = 0.0017) and are co-selected to present synergistic functions (P < 0.0001). KEGG analysis showed that in the tumor genome most mutated genes were organized into signaling pathways related to tumorigenesis. No such organization or synergy was observed in the lymphoblastoid genome. Our results indicate that endogenous mutagens and replication errors can generate the overall number of mutations required to drive tumorigenesis and that it is the combination rather than the frequency of mutations that is crucial to complete tumorigenic transformation.

Qualitative Analysis of the Interdisciplinary Interaction between Data Analysis Specialists and Novice Clinical Researchers

Background: The inherent complexity of statistical methods and clinical phenomena compel researchers with diverse domains of expertise to work in interdisciplinary teams, where none of them have a complete knowledge in their counterpart's field. As a result, knowledge exchange may often be characterized by miscommunication leading to misinterpretation, ultimately resulting in errors in research and even clinical practice. Though communication has a central role in interdisciplinary collaboration and since miscommunication can have a negative impact on research processes, to the best of our knowledge, no study has yet explored how data analysis specialists and clinical researchers communicate over time. Methods/Principal Findings: We conducted qualitative analysis of encounters between clinical researchers and data analysis specialists (epidemiologist, clinical epidemiologist, and data mining specialist). These encounters were recorded and systematically analyzed using a grounded theory methodology for extraction of emerging themes, followed by data triangulation and analysis of negative cases for validation. A policy analysis was then performed using a system dynamics methodology looking for potential interventions to improve this process. Four major emerging themes were found. Definitions using lay language were frequently employed as a way to bridge the language gap between the specialties. Thought experiments presented a series of ""what if'' situations that helped clarify how the method or information from the other field would behave, if exposed to alternative situations, ultimately aiding in explaining their main objective. Metaphors and analogies were used to translate concepts across fields, from the unfamiliar to the familiar. Prolepsis was used to anticipate study outcomes, thus helping specialists understand the current context based on an understanding of their final goal. Conclusion/Significance: The communication between clinical researchers and data analysis specialists presents multiple challenges that can lead to errors.

Structure-Function Analysis of the HrpB2-HrcU Interaction in the Xanthomonas citri Type III Secretion System

Bacterial type III secretion systems deliver protein virulence factors to host cells. Here we characterize the interaction between HrpB2, a small protein secreted by the Xanthomonas citri subsp. citri type III secretion system, and the cytosolic domain of the inner membrane protein HrcU, a paralog of the flagellar protein FlhB. We show that a recombinant fragment corresponding to the C-terminal cytosolic domain of HrcU produced in E. coli suffers cleavage within a conserved Asn264-Pro265-Thr266-His267 (NPTH) sequence. A recombinant HrcU cytosolic domain with N264A, P265A, T266A mutations at the cleavage site (HrcU(AAAH)) was not cleaved and interacted with HrpB2. Furthermore, a polypeptide corresponding to the sequence following the NPTH cleavage site also interacted with HrpB2 indicating that the site for interaction is located after the NPTH site. Non-polar deletion mutants of the hrcU and hrpB2 genes resulted in a total loss of pathogenicity in susceptible citrus plants and disease symptoms could be recovered by expression of HrpB2 and HrcU from extrachromossomal plasmids. Complementation of the Delta hrcU mutant with HrcU(AAAH) produced canker lesions similar to those observed when complemented with wild-type HrcU. HrpB2 secretion however, was significantly reduced in the Delta hrcU mutant complemented with HrcU(AAAH), suggesting that an intact and cleavable NPTH site in HrcU is necessary for total functionally of T3SS in X. citri subsp. citri. Complementation of the Delta hrpB2 X. citri subsp. citri strain with a series of hrpB2 gene mutants revealed that the highly conserved HrpB2 C-terminus is essential for T3SS-dependent development of citrus canker symptoms in planta.

Learning Profile Identification Based on the Analysis of the User Context of Interaction

One of the e-learning environment goal is to attend the individual needs of students during the learning process. The adaptation of contents, activities and tools into different visualization or in a variety of content types is an important feature of this environment, bringing to the user the sensation that there are suitable workplaces to his profile in the same system. Nevertheless, it is important the investigation of student behaviour aspects, considering the context where the interaction happens, to achieve an efficient personalization process. The paper goal is to present an approach to identify the student learning profile analyzing the context of interaction. Besides this, the learning profile could be analyzed in different dimensions allows the system to deal with the different focus of the learning.

Generation and Analysis of Interaction Energy Maps of p-Substituted Benzoic Acid [(5-Nitro-thiophen-2-yl)-methylene]-Hydrazides Active against MRSA

In this preliminary study eighteen p-substituted benzoic acid [(5-nitro-thiophen-2-yl)-methylene]-hydrazides with antimicrobial activity were evaluated against multidrug-resistant Staphylococcus aureus, correlating the three-dimensional characteristics of the ligands with their respective bioactivities. The computer programs Sybyl and CORINA were used, respectively, for the design and three-dimensional conversion of the ligands. Molecular interaction fields were calculated using GRID program. Calculations using Volsurf resulted in a statistically consistent model with 48 structural descriptors showing that hydrophobicity is a fundamental property in the analyzed biological response.

Interaction between Tobacco and Alcohol Use and the Risk of Head and Neck Cancer: Pooled Analysis in the International Head and Neck Cancer Epidemiology Consortium

Background: The magnitude of risk conferred by the interaction between tobacco and alcohol use on the risk of head and neck cancers is not clear because studies have used various methods to quantify the excess head and neck cancer burden. Methods: We analyzed individual-level pooled data from 17 European and American case-control studies (11,221 cases and 16,168 controls) participating in the International Head and Neck Cancer Epidemiology consortium. We estimated the multiplicative interaction parameter (psi) and population attributable risks (PAR). Results: A greater than multiplicative joint effect between ever tobacco and alcohol use was observed for head and neck cancer risk (psi = 2.15; 95% confidence interval, 1.53-3.04). The PAR for tobacco or alcohol was 72% (95% confidence interval, 61-79%) for head and neck cancer, of which 4% was due to alcohol alone, 33% was due to tobacco alone, and 35% was due to tobacco and alcohol combined. The total PAR differed by subsite (64% for oral cavity cancer, 72% for pharyngeal cancer, 89% for laryngeal cancer), by sex (74% for men, 57% for women), by age (33% for cases < 45 years, 73% for cases > 60 years), and by region (84% in Europe, 51% in North America, 83% in Latin America). Conclusions: Our results confirm that the joint effect between tobacco and alcohol use is greater than multiplicative on head and neck cancer risk. However, a substantial proportion of head and neck cancers cannot be attributed to tobacco or alcohol use, particularly for oral cavity cancer and for head and neck cancer among women and among young-onset cases. (Cancer Epidemiol Biomarkers Prev 2009;18(2):541-50)

Magnetic interaction in exchange-biased bilayers: a first-order reversal curve analysis

The distributions of coercivities and magnetic interactions in a set of polycrystalline Ni(0.8)Fe(0.2)/FeMn bilayers have been determined using the first-order reversal curve (FORC) formalism. The thickness of the permalloy (Py) film was fixed at 10 nm (nominal), while that of the FeMn film varied within the range 0-20 nm. The FORC diagrams of each bilayer displayed two clearly distinguishable regions. The main region was generated by Py particles whose coercivities were enhanced in comparison with those in which the FeMn film was absent (sample O). The minor region was produced by Py particles with coercivities similar to or slightly higher than those of particles in the Py film of sample O. Each sample presented two distributions of interaction fields, one for each region, and both were centred slightly below the exchange-bias field, thus indicating a prevalence of magnetizing interactions. These results are consistent with a grain size distribution in the Py layer and the presence of uncompensated antiferromagnetic moments.

Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases

Suramin is a hexasulfonated naphthylurea which has been recently characterized as a non-competitive inhibitor of human alpha-thrombin activity over fibrinogen, although its binding site and mode of interaction with the enzyme remain elusive. Here, we determined two X-ray structure of the thrombin: suramin complex, refined at 2.4 angstrom resolution. While a single thrombin: suramin complex was found in the asymmetric unit cell of the crystal, some of the crystallographic contacts with symmetrically related molecules are mediated by both the enzyme and the ligand. Molecular dynamics simulations with the 1:1 complex demonstrate a large rearrangement of suramin in the complex, but with the protein scaffold and the more extensive protein-ligand regions keep unchanged. Small-angle X-ray scattering measurements at high micromolar concentration demonstrate a suramin-induced dimerization of the enzyme. These data indicating a dissimilar binding mode in the monomeric and oligomeric states, with a monomeric, 1:1 complex to be more likely to exist at the thrombin physiological, nanomolar concentration range. Collectively, close understanding on the structural basis for interaction is given which might establish a basis for design of suramin analogues targeting thrombin. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

The interaction between atoms of Au and Cu with clean Si(111) surface: A study combining synchrotron radiation grazing incidence X-ray fluorescence analysis and theoretical calculations

In order to evaluate the interactions between Au/Cu atoms and clean Si(l 11) surface, we used synchrotron radiation grazing incidence X-ray fluorescence analysis and theoretical calculations. Optimized geometries and energies on different adsorption sites indicate that the binding energies at different adsorption sites are high, suggesting a strong interaction between metal atom and silicon surface. The Au atom showed higher interaction than Cu atom. The theoretical and experimental data showed good agreement. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Interaction between staining and degradation of a composite resin in contact with colored foods

Composite resins might be susceptible to degradation and staining when in contact with some foods and drinks. This study evaluated color alteration and changes in microhardness of a microhybrid composite after immersion in different colored foods and determined whether there was a correlation between these two variables. Eighty composite disks were randomly divided into 8 experimental groups (n = 10): kept dry; deionized water; orange juice; passion fruit juice; grape juice; ketchup; mustard and soy sauce. The disks were individually immersed in their respective test substance at 37 ºC, for a period of 28 days. Superficial analysis of the disk specimens was performed by taking microhardness measurements (Vickers, 50 g load for 45 seconds) and color alterations were determined with a spectrophotometer (CINTRA 10- using a CIEL*a*b* system, 400-700 nm wavelength, illuminant d65 and standard observer of 2º) at the following times: baseline (before immersion), 1, 7, 14, 21 and 28 days. Results were analyzed by ANOVA and Tukey's test (p < 0.05). Both variables were also submitted to Pearson's correlation test (p < 0.05). The passion fruit group underwent the greatest microhardness change, while the mustard group suffered the greatest color alteration. Significant positive correlation was found between the two variables for the groups deionized water, grape juice, soy sauce and ketchup. Not all color alteration could be associated with surface degradation.

The optical analysis of the abdominal wall using the biospeckle after implants of polypropylene mesh in rats

PURPOSE: To evaluate an experimental animal model to study the abdominal tissue activity considering its interaction with a polypropylene mesh, through the use of one of the optical phenomena of light Laser, the biospeckle. METHODS: Fifty Wistar male rats were divided into four groups: Group 1: ten animals not submitted to surgery; Group 2: ten animals submitted to surgery without polypropylene mesh; Group 3: 20 animals submitted to surgery followed by the mesh placement; Group 4: (sham) with ten animals. None of the animals presented post surgical complications being submitted to the optical tests at the 20th postoperative day. RESULTS: The analysis from the biospeckle tests, comparing the medians and standard deviations with T Student test, indicated that no significative difference was observed on the abdominal wall tissue activity in the four groups considered, with and without polypropylene mesh prosthesis implantation. CONCLUSION: The animal model is viable and the biospeckle open ways for a great number of experiments to be developed in evaluating tissue activity.

Alluvial-eolian interaction in a Cambrian rift margin: the Pedra das Torrinhas and Pedra Pintada formations (Guaritas Group, RS)

This work presents a study of selected outcrops from the Pedra das Torrinhas Formation of the Guaritas Group (Cambrian, Camaquã Basin), near the basin bordering Encantadas Fault Zone. The studied succession includes alluvial fan deposits that pass laterally into eolian deposits. Sedimentary facies and architectural element analysis were performed, followed by sedimentary petrography and microscopic porosity analysis, aiming to characterize the porosity of the deposits and its spatial distribution. The main objective was to contribute to a better understanding of the porosity spatial distribution in depositional systems characterized by the interaction between alluvial and eolian processes, with special reference to deposits formed prior to the development of terrestrial plants. Porosity values are related to depositional processes, with higher porosities associated to eolian dune deposits (mean of 8.4%), and lower porosity related to interdunes (mean of 3.4%) and alluvial fans (mean of 4.3%). Architectural elements analysis revealed the spatial relationships of these deposits, a response to the interplay of the eolian and alluvial processes. The integration of porosity data reveals that the interaction of alluvial and eolian processes results in heterogeneous distribution of porosity at the facies association scale. Eolian reworking of alluvial facies increases porosity whereas sheet-flood and other alluvial processes in the interdune areas reduce porosity.

A century of research: what have we learned about the interaction of Trypanosoma cruzi with host cells?

Since the discovery of Trypanosoma cruzi and the brilliant description of the then-referred to "new tripanosomiasis" by Carlos Chagas 100 years ago, a great deal of scientific effort and curiosity has been devoted to understanding how this parasite invades and colonises mammalian host cells. This is a key step in the survival of the parasite within the vertebrate host, and although much has been learned over this century, differences in strains or isolates used by different laboratories may have led to conclusions that are not as universal as originally interpreted. Molecular genotyping of the CL-Brener clone confirmed a genetic heterogeneity in the parasite that had been detected previously by other techniques, including zymodeme or schizodeme (kDNA) analysis. T. cruzi can be grouped into at least two major phylogenetic lineages: T. cruzi I, mostly associated with the sylvatic cycle and T. cruzi II, linked to human disease; however, a third lineage, T. cruziIII, has also been proposed. Hybrid isolates, such as the CL-Brener clone, which was chosen for sequencing the genome of the parasite (Elias et al. 2005, El Sayed et al. 2005a), have also been identified. The parasite must be able to invade cells in the mammalian host, and many studies have implicated the flagellated trypomastigotes as the main actor in this process. Several surface components of parasites and some of the host cell receptors with which they interact have been described. Herein, we have attempted to identify milestones in the history of understanding T. cruzi- host cell interactions. Different infective forms of T. cruzi have displayed unexpected requirements for the parasite to attach to the host cell, enter it, and translocate between the parasitophorous vacuole to its final cytoplasmic destination. It is noteworthy that some of the mechanisms originally proposed to be broad in function turned out not to be universal, and multiple interactions involving different repertoires of molecules seem to act in concert to give rise to a rather complex interplay of signalling cascades involving both parasite and cellular components.