Some Notes on the Formal Properties of Bidirectional Optimality Theory

In this paper, we discuss some formal properties of the model ofbidirectional Optimality Theory that was developed inBlutner (2000). We investigate the conditions under whichbidirectional optimization is a well-defined notion, and we give aconceptually simpler reformulation of Blutner's definition. In thesecond part of the paper, we show that bidirectional optimization can bemodeled by means of finite state techniques. There we rely heavily onthe related work of Frank and Satta (1998) about unidirectionaloptimization.     

Granulocyte colony-stimulating factor worsens the outcome of experimental Klebsiella pneumoniae pneumonia through direct interaction with the bacteria

Besides its well-established effects on granulocytopoiesis, granulocyte colony-stimulating factor (G-CSF) has been shown to have direct effects on the recruitment and bactericidal ability of neutrophils, resulting in improved survival of experimentally infected animals. We studied the effect of G-CSF on the course of experimental pneumonia induced by Klebsiella pneumoniae, an important gram-negative bacillary pulmonary pathogen. Using a highly reproducible murine model, we here show the paradoxical finding that mortality from infection was significantly increased when animals received G-CSF before induction of pneumonia. Administration of G-CSF promoted replication of bacteria in the liver and spleen, thus indicating an impairment rather than an enhancement of antibacterial mechanisms. By contrast, a monoclonal antibody against Klebsiella K2 capsule significantly reduced bacterial multiplication in the lung, liver, and spleen, and abrogated the increased mortality caused by G-CSF. In vitro studies showed a direct effect of G-CSF on K pneumoniae resulting in increased capsular polysaccharide (CPS) production. When bacteria were coincubated with therapeutically achievable concentrations of G-CSF, phagocytic uptake and killing by neutrophils was impaired. Western blot analysis showed three binding sites of G-CSF to K pneumoniae. Binding of 125I-G-CSF to K pneumoniae was displaced by an excess of unlabeled G-CSF, whereas an unrelated cytokine, interleukin-1alpha, did not compete with G-CSF binding to the bacteria. Thus, in this model, the direct effect of G-CSF on a bacterial virulence factor, CPS production, outweighed any beneficial effect of G-CSF on recruitment and stimulation of leukocytes.     

Differential time course of angiotensin-induced AP-1 and Krox proteins in the rat lamina terminalis and hypothalamus

Binding to olfactory receptors is the first step in odorant and pheromonal recognition and discrimination. These receptors constitute one of the most important, although poorly known, families of neuronal receptors. In this study we used degenerated oligonucleotides and a RT-PCR approach to selectively amplify olfactory receptors in the nasal epithelium of the domestic pig Sus scrofa. Several combinations of oligonucleotide were tested and allowed the isolation of eleven different partial sequences belonging to the seven transmembrane olfactory receptor family. These receptors formed a separate family within the seven transmembrane receptor superfamily in pigs. Using the criteria of Ben Arie et al. [Ben-Arie N., Lancet D., Taylor C., Khen M., Walker N., Ledbetter DH., Carrozzo R., Patel K., Sheer D., Lehrah H. and North M., Hum. Mol. Genet., 3 (1994) 229-235], the 11 receptors described here can be classified into three known families and seven subfamilies (one known and six new).     

Graffiti: graph-based classification in heterogeneous networks

We address the problem of multi-label classification in heterogeneous graphs, where nodes belong to different types and different types have different sets of classification labels. We present a novel approach that aims to classify nodes based on their neighborhoods. We model the mutual influence of nodes as a random walk in which the random surfer aims at distributing class labels to nodes while walking through the graph. When viewing class labels as “colors”, the random surfer is essentially spraying different node types with different color palettes; hence the name Graffiti of our method. In contrast to previous work on topic-based random surfer models, our approach captures and exploits the mutual influence of nodes of the same type based on their connections to nodes of other types. We show important properties of our algorithm such as convergence and scalability. We also confirm the practical viability of Graffiti by an experimental study on subsets of the popular social networks Flickr and LibraryThing. We demonstrate the superiority of our approach by comparing it to three other state-of-the-art techniques for graph-based classification.     

Provably correct and complete transaction rules for updating 3D city models

The shapes of our cities change very frequently. These changes have to be reflected in data sets representing urban objects. However, it must be assured that frequent updates do not affect geometric-topological consistency. This important aspect of spatial data quality guarantees essential assumptions on which users and applications of 3D city models rely: viz. that objects do not intersect, overlap or penetrate mutually, or completely cover one another. This raises the question how to guarantee that geometric-topological consistency is preserved when data sets are updated. Hence, there is a certain risk that plans and decisions which are based on these data sets are erroneous and that the tremendous efforts spent for data acquisition and updates become vain. In this paper, we solve this problem by presenting efficient transaction rules for updating 3D city models. These rules guarantee that geometric-topological consistency is preserved (Safety) and allow for the generation of arbitrary consistent 3D city models (Completeness). Safety as well as completeness is proven with mathematical rigor, guaranteeing the reliability of our method. Our method is applicable to 3D city models, which define—besides the terrain surface—complex spatial objects like buildings with rooms and storeys as interior structures, as well as bridges and tunnels. Those objects are represented as aggregations of solids, and their surfaces are complex from a topology point of view. 3D GIS models like CityGML, which are widely used to represent cities, provide the means to define semantics, geometry and topology, but do not address the problem of maintaining consistency. Hence, our approach complements CityGML.     

A fast audio similarity retrieval method for millions of music tracks

We present a filter-and-refine method to speed up nearest neighbor searches with the Kullback–Leibler divergence for multivariate Gaussians. This combination of features and similarity estimation is of special interest in the field of automatic music recommendation as it is widely used to compute music similarity. However, the non-vectorial features and a non-metric divergence make using it with large corpora difficult, as standard indexing algorithms can not be used. This paper proposes a method for fast nearest neighbor retrieval in large databases which relies on the above approach. In its core the method rescales the divergence and uses a modified FastMap implementation to speed up nearest-neighbor queries. Overall the method accelerates the search for similar music pieces by a factor of 10–30 and yields high recall values of 95–99% compared to a standard linear search.     

Exploring the Biomaterial-Induced Secretome: Physical Bone Substitute Characteristics Influence the Cytokine Expression of Macrophages

In addition to their chemical composition various physical properties of synthetic bone substitute materials have been shown to influence their regenerative potential and to influence the expression of cytokines produced by monocytes, the key cell-type responsible for tissue reaction to biomaterials in vivo. In the present study both the regenerative potential and the inflammatory response to five bone substitute materials all based on β-tricalcium phosphate (β-TCP), but which differed in their physical characteristics (i.e., granule size, granule shape and porosity) were analyzed for their effects on monocyte cytokine expression. To determine the effects of the physical characteristics of the different materials, the proliferation of primary human osteoblasts growing on the materials was analyzed. To determine the immunogenic effects of the different materials on human peripheral blood monocytes, cells cultured on the materials were evaluated for the expression of 14 pro- and anti-inflammatory cytokines, i.e., IL-6, IL-10, IL-1β, VEGF, RANTES, IL-12p40, I-CAM, IL-4, V-CAM, TNF-α, GM-CSF, MIP-1α, Il-8 and MCP-1 using a Bio-Plex^® Multiplex System. The granular shape of bone substitutes showed a significant influence on the osteoblast proliferation. Moreover, smaller pore sizes, round granular shape and larger granule size increased the expression of GM-CSF, RANTES, IL-10 and IL-12 by monocytes, while polygonal shape and the larger pore sizes increased the expression of V-CAM. The physical characteristics of a bone biomaterial can influence the proliferation rate of osteoblasts and has an influence on the cytokine gene expression of monocytes in vitro. These results indicate that the physical structure of a biomaterial has a significant effect of how cells interact with the material. Thus, specific characteristics of a material may strongly affect the regenerative potential in vivo.     

Liver Lipids of Patients with Hepatitis B and C and Associated Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) still remains a difficult to cure malignancy. In recent years, the focus has shifted to lipid metabolism for the treatment of HCC. Very little is known about hepatitis B virus (HBV) and C virus (HCV)-related hepatic lipid disturbances in non-malignant and cancer tissues. The present study showed that triacylglycerol and cholesterol concentrations were similar in tumor adjacent HBV and HCV liver, and were not induced in the HCC tissues. Higher levels of free cholesterol, polyunsaturated phospholipids and diacylglycerol species were noted in non-tumorous HBV compared to HCV liver. Moreover, polyunsaturated phospholipids and diacylglycerols, and ceramides declined in tumors of HBV infected patients. All of these lipids remained unchanged in HCV-related HCC. In HCV tumors, polyunsaturated phosphatidylinositol levels were even induced. There were no associations of these lipid classes in non-tumor tissues with hepatic inflammation and fibrosis scores. Moreover, these lipids did not correlate with tumor grade or T-stage in HCC tissues. Lipid reprogramming of the three analysed HBV/HCV related tumors mostly resembled HBV-HCC. Indeed, lipid composition of non-tumorous HCV tissue, HCV tumors, HBV tumors and HBV/HCV tumors was highly similar. The tumor suppressor protein p53 regulates lipid metabolism. The p53 and p53S392 protein levels were induced in the tumors of HBV, HCV and double infected patients, and this was significant in HBV infection. Negative correlation of tumor p53 protein with free cholesterol indicates a role of p53 in cholesterol metabolism. In summary, the current study suggests that therapeutic strategies to target lipid metabolism in chronic viral hepatitis and associated cancers have to consider disease etiology.