An unfitted hp-adaptive finite element method based on hierarchical B-splines for interface problems of complex geometry

Generating finite element discretizations with direct interface parameterizations constitutes a considerable computational expense in case of complex interface geometries. The paper at hand introduces a B-spline finite element method, which circumvents parameterization of interfaces and offers fast and easy meshing irrespective of the geometric complexity involved. Its core idea is the adaptive approximation of discontinuities by hierarchical grid refinement, which adds several levels of local basis functions in the close vicinity of interfaces, but unfitted to their exact location, so that a simple regular grid of knot span elements can be maintained. Numerical experiments show that an hp-refinement strategy, which simultaneously increases the polynomial degree of the B-spline basis and the levels of refinement around interfaces, achieves exponential rates of convergence despite the presence of discontinuities. It is also demonstrated that the hierarchical B-spline FEM can be used to transfer the recently introduced Finite Cell concept to geometrically nonlinear problems. Its computational performance, imposition of unfitted boundary conditions and fast hierarchical grid generation are illustrated for a set of benchmark problems in one, two and three dimensions, and the advantages of the regular grid approach for complex geometries are demonstrated by the geometrically nonlinear simulation of a voxel based foam composite.     

Value and limits of μ-CT for nondemineralized bone tissue processing

An experimental approach was performed on 20 giant rabbits to establish the possibilities and limitations of μ-CT for routine processing of nondemineralized bone tissue. Hydroxyapatite (HA) or β-tricalciumphosphate (β-TCP) bead implants or a melange of both, microchambered and solid, were implanted into a standardized and precise defect in the patellar groove. The bone-healing phase was chosen for the histology considering 1 or 2 days, and 2, 3, and 6 weeks. Normal X-ray and μ-CT were applied on all specimens; five specimens in the 6-week stage were additionally processed according to the full range of conventional nondemineralized bone processing methods. μ-CT increased the possibilities of nondemineralized histology with respect to bone morphometry and a complete sequence of sections, thus providing a complete analysis of the bone response. μ-CT was limited in differentiating bone quality, cell analyses, and mineralization stages. The investigation based on normal X-rays is limited to defining integration and excluding the fibrous and bony encapsulation of loose implants. μ-CT allows a 3D evaluation of newly formed bone which is clearly marked against the ceramic implant. It does not allow, however, for the differentiation between woven and lamellar bone, the presentation of the canalicular lacunar system, or on the cell level, revealing canaliculi or details of the mineralization process which can be documented by high-resolution microradiography. Titer dynamics of bone formation remains the domain of polychromatic sequential labeling. The complete sequence of μ-CT slices enhances the possibilities for routine histology, tremendously allowing to the focus on detail histology to topographically well-defined cuts, thus providing more precise conclusions which take into consideration the whole implant.     

Reducing Playground Bullying and Supporting Beliefs: An Experimental Trial of the Steps to Respect Program.

Six schools were randomly assigned to a multilevel bullying intervention or a control condition. Children in Grades 3-6 (N=1,023) completed pre- and posttest surveys of behaviors and beliefs and were rated by teachers. Observers coded playground behavior of a random subsample (n=544). Hierarchical analyses of changes in playground behavior revealed declines in bullying and argumentative behavior among intervention-group children relative to control-group children, increases in agreeable interactions, and a trend toward reduced destructive bystander behavior. Those in the intervention group reported enhanced bystander responsibility, greater perceived adult responsiveness, and less acceptance of bullying/aggression than those in the control group. Self-reported aggression did not differ between the groups. Implications for future research on the development and prevention of bullying are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Interactive structural learning of Bayesian networks

We propose an hybrid approach for structure learning of Bayesian networks, in which a computer system and a human expert cooperate to search for the best structure. The system builds an initial tree structure which is graphically presented to the expert, and then the expert can modify this structure according to his knowledge of the domain. The system has several tools for aiding the human in this task: it allows for graphical editing (adding, deleting, inverting arcs) of the network, it shows graphically the correlation between variables, and it gives a measure of the quality and complexity for each structure. A measure which combines both quality and complexity, that we call quality, is defined. We have tested the tool in two domains: atmospheric pollution and car insurance, with good results.     

Multipurpose modular experimental station for the DiProI beamline of Fermi@Elettra free electron laser

We present a compact modular apparatus with a flexible design that will be operated at the DiProI beamline of the Fermi@Elettra free electron laser (FEL) for performing static and time-resolved coherent diffraction imaging experiments, taking advantage of the full coherence and variable polarization of the short seeded FEL pulses. The apparatus has been assembled and the potential of the experimental setup is demonstrated by commissioning tests with coherent synchrotron radiation. This multipurpose experimental station will be open to general users after installation at the Fermi@Elettra free electron laser in 2011.     

In-house and interlaboratory validation of a method for the extraction of DNA from maize starch

Here, we describe the procedure of a DNA extraction method from maize starch including the method??s validation by in-house and interlaboratory tests. The amplifiable amount of maize DNA tested by real-time PCR was used as parameter for evaluating our method. The practical (i.e. relative) limit of detection (LOD) was used as key criterion for assessing the suitability of the extraction method with respect to genetically modified organism analysis. In a round-robin test with ten participating laboratories, satisfactory results were achieved with practical LODs in the range of 0.1?% with three native maize starch materials. In-house tests showed that this protocol??with an additional purification step??can also be applied for extracting DNA from chemically or enzymatically modified starch.     

The Innate Immune Glycoprotein Lactoferrin Represses the Helicobacter pylori cag Type IV Secretion System

Chronic infection with Helicobacter pylori increases risk of gastric diseases including gastric cancer. Despite development of a robust immune response, H. pylori persists in the gastric niche. Progression of gastric inflammation to serious disease outcomes is associated with infection with H. pylori strains which encode the cag Type IV Secretion System (cag T4SS). The cag T4SS is responsible for translocating the oncogenic protein CagA into host cells and inducing pro-inflammatory and carcinogenic signaling cascades. Our previous work demonstrated that nutrient iron modulates the activity of the T4SS and biogenesis of T4SS pili. In response to H. pylori infection, the host produces a variety of antimicrobial molecules, including the iron-binding glycoprotein, lactoferrin. Our work shows that apo-lactoferrin exerts antimicrobial activity against H. pylori under iron-limited conditions, while holo-lactoferrin enhances bacterial growth. Culturing H. pylori in the presence of holo-lactoferrin prior to co-culture with gastric epithelial cells, results in repression of the cag T4SS activity. Concomitantly, a decrease in biogenesis of cag T4SS pili at the host-pathogen interface was observed under these culture conditions by high-resolution electron microscopy analyses. Taken together, these results indicate that acquisition of alternate sources of nutrient iron plays a role in regulating the pro-inflammatory activity of a bacterial secretion system and present novel therapeutic targets for the treatment of H. pylori-related disease.     

Efficient Incorporation of Clickable Unnatural Amino Acids Enables Rapid and Biocompatible Labeling of Proteins in Vitro and in Bacteria

Site-specific incorporation of unnatural amino acids (uAAs) bearing a bioorthogonal group has enabled the attachment – typically at a single site or at a few sites per protein – of chemical groups at precise locations for protein and biomaterial labeling, conjugation, and functionalization. Herein, we report the evolution of chromosomal Methanocaldococcus jannaschii tyrosyl-tRNA synthetase (aaRS) for the alkyne-bearing uAA, 4-propargyloxy-l -phenylalanine (pPR), with ∼30-fold increased production of green fluorescent protein containing three instances of pPR compared with a previously described M. jannaschii-derived aaRS for pPR, when expressed from a single chromosomal copy. We show that when expressed from multicopy plasmids, the evolved aaRSs enable the production – using a genomically recoded Escherichia coli and the non-recoded BL21 E. coli strain – of elastin-like polypeptides (ELPs) containing multiple pPR residues in high yields. We further show that the multisite incorporation of pPR in ELPs facilitates the rapid, robust, and nontoxic fluorescent labeling of these proteins in bacteria. The evolved variants described in this work can be used to produce a variety of protein and biomaterial conjugates and to create efficient minimal tags for protein labeling.     

Exploring critical attributes during air traffic congestion with a fuzzy DEMATEL–ANP technique: a case study in Ninoy Aquino International Airport

Railway Engineering Science - The constant growth of air travel in the Philippines has brought about significant consequences to air traffic congestion. Given limited resources, major airports seek...