Clustering, Hamming Embedding, Generalized LSH and the Max Norm

We study the convex relaxation of clustering and hamming embedding, focusing on the asymmetric case (co-clustering and asymmetric hamming embedding), understanding their relationship to LSH as studied by (Charikar 2002) and to the max-norm ball, and the differences between their symmetric and asymmetric versions.Comment: 17 page

Helly-Type Theorems in Property Testing

Helly's theorem is a fundamental result in discrete geometry, describing the ways in which convex sets intersect with each other. If $S$ is a set of $n$ points in $R^d$, we say that $S$ is $(k,G)$-clusterable if it can be partitioned into $k$ clusters (subsets) such that each cluster can be contained in a translated copy of a geometric object $G$. In this paper, as an application of Helly's theorem, by taking a constant size sample from $S$, we present a testing algorithm for $(k,G)$-clustering, i.e., to distinguish between two cases: when $S$ is $(k,G)$-clusterable, and when it is $\epsilon$-far from being $(k,G)$-clusterable. A set $S$ is $\epsilon$-far $(0<\epsilon\leq1)$ from being $(k,G)$-clusterable if at least $\epsilon n$ points need to be removed from $S$ to make it $(k,G)$-clusterable. We solve this problem for $k=1$ and when $G$ is a symmetric convex object. For $k>1$, we solve a weaker version of this problem. Finally, as an application of our testing result, in clustering with outliers, we show that one can find the approximate clusters by querying a constant size sample, with high probability

A topological central point theorem

In this paper a generalized topological central point theorem is proved for maps of a simplex to finite-dimensional metric spaces. Similar generalizations of the Tverberg theorem are considered.Comment: In this version some typos were corrected after the official publicatio

Coloring translates and homothets of a convex body

We obtain improved upper bounds and new lower bounds on the chromatic number as a linear function of the clique number, for the intersection graphs (and their complements) of finite families of translates and homothets of a convex body in \RR^n.Comment: 11 pages, 2 figure

Hadron Spectroscopy with Dynamical Chirally Improved Fermions

We simulate two dynamical, mass degenerate light quarks on 16^3x32 lattices with a spatial extent of 2.4 fm using the Chirally Improved Dirac operator. The simulation method, the implementation of the action and signals of equilibration are discussed in detail. Based on the eigenvalues of the Dirac operator we discuss some qualitative features of our approach. Results for ground state masses of pseudoscalar and vector mesons as well as for the nucleon and delta baryons are presented.Comment: 26 pages, 17 figures, 10 table

A luciferase-based quick potency assay to predict chondrogenic differentiation.

Chondrogenic differentiation of adipose derived stem cells (ASC) is challenging but highly promising for cartilage repair. Large donor variability of chondrogenic differentiation potential raises the risk for transplantation of cells with reduced efficacy and a low chondrogenic potential. Therefore quick potency assays are required in order to control the potency of the isolated cells before cell transplantation. Current in vitro methods to analyze the differentiation potential are time consuming and thus, a novel enhancer and tissue-specific promoter combination was employed for the detection of chondrogenic differentiation of ASC in a novel quick potency bioassay. Human primary ASC were co-transfected with the Metridia luciferase based collagen type II reporter gene pCMVE_ACDCII-MetLuc together with a Renilla control plasmid and analyzed for their chondrogenic potential. On day 3 after chondrogenic induction, the luciferase activity was induced in all tested donors under three dimensional (3D) culture conditions and in a second approach also under 2D culture conditions. With our newly developed quick potency bioassay we can determine chondrogenic potential already after 3 days of chondrogenic induction and under 2D culture conditions. This will enhance the efficiency of testing cell functionality, which should allow in the future to predict the suitability of cells derived from individual patients for cell therapies, in a very short time and at low costs

Synthesis, structural characterization, antimicrobial and cytotoxic effects of aziridine, 2-aminoethylaziridine and azirine complexes of copper(II) and palladium(II).

The synthesis, spectroscopic and X-ray structural characterization of copper(II) and palladium(II) complexes with aziridine ligands as 2-dimethylaziridine HNCH2CMe2 (a), the bidentate N-(2-aminoethyl)aziridines C2H4NC2H4NH2 (b) or CH2CMe2NCH2CMe2NH2 (c) as well as the unsaturated azirine NCH2CPh (d) are reported. Cleavage of the cyclometallated Pd(II) dimer [μ-Cl(C6H4CHMeNMe2-C,N)Pd]2 with ligand a yielded compound [Cl(NHCH2CMe2)(C6H4CHMe2NMe2-C,N)Pd] (1a). The reaction of the aziridine complex trans-[Cl2Pd(HNC2H4)2] with an excess of aziridine in the presence of AgOTf gave the ionic chelate complex trans-[(C2H4NC2H4NH2-N,N′)2Pd](OTf)2 (2b) which contains the new ligand b formed by an unexpected insertion and ring opening reaction of two aziridines (“aziridine dimerization”). CuCl2 reacted in pure HNC2H4 or HNCH2CMe2 (b) again by “dimerization” to give the tris-chelated ionic complex [Cu(C2H4NC2H4NH2-N,N′)3]Cl2 (3b) or the bis-chelated complex [CuCl(C2H2Me2NC2H2Me2NH2-N,N′)2]Cl (4c). By addition of 2H-3-phenylazirine (d) to PdCl2, trans-[Cl2Pd(NCH2CPh)2] (5d) was formed. All new compounds were characterized by NMR, IR and mass spectra and also by X-ray structure analyses (except 3b). Additionally the cytotoxic effects of these complexes were examined on HL-60 and NALM-6 human leukemia cells and melanoma WM-115 cells. The antimicrobial activity was also determined. The growth of Gram-positive bacterial strains (S. aureus, S. epidermidis, E. faecalis) was inhibited by almost all tested complexes at the concentrations of 37.5–300.0 μg mL−1. However, MIC values of complexes obtained for Gram-negative E. coli and P. aeruginosa, as well as for C. albicans yeast, mostly exceeded 300 μg mL−1. The highest antibacterial activity was achieved by complexes 1a and 2b. Complex 2b also inhibited the growth of Gram-negative bacteria. Graphical abstract: Synthesis, structural characterization, antimicrobial and cytotoxic effects of aziridine, 2-aminoethylaziridine and azirine complexes of copper(ii) and palladium(ii

Afferent signalling from the acid-challenged rat stomach is inhibited and gastric acid elimination is enhanced by lafutidine

<p>Abstract</p> <p>Background</p> <p>Lafutidine is a histamine H₂receptor antagonist, the gastroprotective effect of which is related to its antisecretory activity and its ability to activate a sensory neuron-dependent mechanism of defence. The present study investigated whether intragastric administration of lafutidine (10 and 30 mg/kg) modifies vagal afferent signalling, mucosal injury, intragastric acidity and gastric emptying after gastric acid challenge.</p> <p>Methods</p> <p>Adult rats were treated with vehicle, lafutidine (10 – 30 mg/kg) or cimetidine (10 mg/kg), and 30 min later their stomachs were exposed to exogenous HCl (0.25 M). During the period of 2 h post-HCl, intragastric pH, gastric volume, gastric acidity and extent of macroscopic gastric mucosal injury were determined and the activation of neurons in the brainstem was visualized by c-Fos immunocytochemistry.</p> <p>Results</p> <p>Gastric acid challenge enhanced the expression of c-Fos in the nucleus tractus solitarii but caused only minimal damage to the gastric mucosa. Lafutidine reduced the HCl-evoked expression of c-Fos in the NTS and elevated the intragastric pH following intragastric administration of excess HCl. Further analysis showed that the gastroprotective effect of lafutidine against excess acid was delayed and went in parallel with facilitation of gastric emptying, measured indirectly via gastric volume changes, and a reduction of gastric acidity. The H₂receptor antagonist cimetidine had similar but weaker effects.</p> <p>Conclusion</p> <p>These observations indicate that lafutidine inhibits the vagal afferent signalling of a gastric acid insult, which may reflect an inhibitory action on acid-induced gastric pain. The ability of lafutidine to decrease intragastric acidity following exposure to excess HCl cannot be explained by its antisecretory activity but appears to reflect dilution and/or emptying of the acid load into the duodenum. This profile of actions emphasizes the notion that H₂receptor antagonists can protect the gastric mucosa from acid injury independently of their ability to suppress gastric acid secretion.</p

Sequence Capture and Next Generation Resequencing of the MHC Region Highlights Potential Transplantation Determinants in HLA Identical Haematopoietic Stem Cell Transplantation

How cells coordinate the immune system activities is important for potentially life-saving organ or stem cell transplantations. Polymorphic immunoregulatory genes, many of them located in the human major histocompatibility complex, impact the process and assure the proper execution of tolerance-versus-activity mechanisms. In haematopoietic stem cell transplantation, on the basis of fully human leukocyte antigen (HLA)-matched donor–recipient pairs, adverse effects like graft versus leukaemia and graft versus host are observed and difficult to handle. So far, high-resolution HLA typing was performed with Sanger sequencing, but for methodological reasons information on additional immunocompetent major histocompatibility complex loci has not been revealed. Now, we have used microarray sequence capture and targeted enrichment combined with next generation pyrosequencing for 3.5 million base pair human major histocompatibility complex resequencing in a clinical transplant setting and describe 3025 variant single nucleotide polymorphisms, insertions and deletions among recipient and donor in a single sequencing experiment. Taken together, the presented data show that sequence capture and massively parallel pyrosequencing can be used as a new tool for risk assessment in the setting of allogeneic stem cell transplantation