Efficiently navigating a random Delaunay triangulation

Planar graph navigation is an important problem with significant implications to both point location in geometric data structures and routing in networks. However, whilst a number of algorithms and existence proofs have been proposed, very little analysis is available for the properties of the paths generated and the computational resources required to generate them under a random distribution hypothesis for the input. In this paper we analyse a new deterministic planar navigation algorithm with constant spanning ratio (w.r.t the Euclidean distance) which follows vertex adjacencies in the Delaunay triangulation. We call this strategy cone walk. We prove that given n uniform points in a smooth convex domain of unit area, and for any start point z and query point q; cone walk applied to z and q will access at most sites with complexity with probability tending to 1 as n goes to infinity. We additionally show that in this model, cone walk is ‐memoryless with high probability for any pair of start and query point in the domain, for any positive ξ. We take special care throughout to ensure our bounds are valid even when the query points are arbitrarily close to the border. © 2016 Wiley Periodicals, Inc. Random Struct. Alg., 49, 95–136, 2016     

Imaging cytoplasmic cAMP in mouse brainstem neurons

Background  

cAMP is an ubiquitous second messenger mediating various neuronal functions, often as a consequence of increased intracellular Ca²⁺ levels. While imaging of calcium is commonly used in neuroscience applications, probing for cAMP levels has not yet been performed in living vertebrate neuronal tissue before.     

Stable isotopic studies of earthworm feeding ecology in tropical ecosystems of Puerto Rico

Feeding strategies of earthworms and their influence on soil processes are often inferred from morphological, behavioral and physiological traits. We used (13)C and (15)N natural abundance in earthworms, soils and plants to explore patterns of resource utilization by different species of earthworms in three tropical ecosystems in Puerto Rico. In a high altitude dwarf forest, native earthworms Trigaster longissimus and Estherella sp. showed less (15)N enrichment ((15)N = 3-6 per thousand) than exotic Pontoscolex corethrurus ((15)N =7-9 per thousand) indicating different food sources or stronger isotopic discrimination by the latter. Conversely, in a lower altitude tabonuco forest, Estherella sp. and P. corethrurus overlapped completely in (15)N enrichment ((15)N = 6-9 per thousand), suggesting the potential for interspecific competition for N resources. A tabonuco forest converted to pasture contained only P. corethrurus which were less enriched in (15)N than those in the forest sites, but more highly enriched in (13)C suggesting assimilation of C from the predominant C(4) grass. These results support the utility of stable isotopes to delineate resource partitioning and potential competitive interactions among earthworm species. Copyright 1999 John Wiley & Sons, Ltd.     

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity: in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide-MHC binding affinity. The ISC-PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide-MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms--q2, SEP, and NC--ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).     

Ultra-porous hollow particles

Hollow particles with porous shells have been prepared by a simple modification to the surfactant-free polymerisation of styrene by the incorporation of water-soluble natural polymers and the use of high stirring speeds. The particle morphology has been characterised by scanning electron microscopy (SEM). When styrene is polymerised in the presence of either carboxymethyl cellulose (CMC) or sodium alginate at high stirring speeds, small homogeneous (solid) particles (diameter ~200 nm) and large porous particles (diameter~10 m) are both formed. However, at low stirring speeds only the small homogeneous (solid) particles are formed. Further, only the small homogeneous (solid) particles are formed when non-adsorbing polymers such as starch and poly(vinyl alcohol) are present. In contrast, polymers that strongly adsorb onto polystyrene particles cause the polymerising mixture to flocculate. It is proposed that the porous character is a direct result of the polymerisation of a multiple emulsion in the presence of a depletion interaction. Moreover, addition of a high concentration of surfactant to the CMC system simply results in the spherical homogenous particles, suggesting that the surfactant removes the depletion effect.