Randomized Speedup of the Bellman-Ford Algorithm

We describe a variant of the Bellman-Ford algorithm for single-source shortest paths in graphs with negative edges but no negative cycles that randomly permutes the vertices and uses this randomized order to process the vertices within each pass of the algorithm. The modification reduces the worst-case expected number of relaxation steps of the algorithm, compared to the previously-best variant by Yen (1970), by a factor of 2/3 with high probability. We also use our high probability bound to add negative cycle detection to the randomized algorithm.Comment: 12 Pages, 6 Figures, ANALCO 201

Crossing Minimization for 1-page and 2-page Drawings of Graphs with Bounded Treewidth

We investigate crossing minimization for 1-page and 2-page book drawings. We show that computing the 1-page crossing number is fixed-parameter tractable with respect to the number of crossings, that testing 2-page planarity is fixed-parameter tractable with respect to treewidth, and that computing the 2-page crossing number is fixed-parameter tractable with respect to the sum of the number of crossings and the treewidth of the input graph. We prove these results via Courcelle's theorem on the fixed-parameter tractability of properties expressible in monadic second order logic for graphs of bounded treewidth.Comment: Graph Drawing 201

Fixed parameter tractability of crossing minimization of almost-trees

We investigate exact crossing minimization for graphs that differ from trees by a small number of additional edges, for several variants of the crossing minimization problem. In particular, we provide fixed parameter tractable algorithms for the 1-page book crossing number, the 2-page book crossing number, and the minimum number of crossed edges in 1-page and 2-page book drawings.Comment: Graph Drawing 201

Small Superpatterns for Dominance Drawing

We exploit the connection between dominance drawings of directed acyclic graphs and permutations, in both directions, to provide improved bounds on the size of universal point sets for certain types of dominance drawing and on superpatterns for certain natural classes of permutations. In particular we show that there exist universal point sets for dominance drawings of the Hasse diagrams of width-two partial orders of size O(n^{3/2}), universal point sets for dominance drawings of st-outerplanar graphs of size O(n\log n), and universal point sets for dominance drawings of directed trees of size O(n^2). We show that 321-avoiding permutations have superpatterns of size O(n^{3/2}), riffle permutations (321-, 2143-, and 2413-avoiding permutations) have superpatterns of size O(n), and the concatenations of sequences of riffles and their inverses have superpatterns of size O(n\log n). Our analysis includes a calculation of the leading constants in these bounds.Comment: ANALCO 2014, This version fixes an error in the leading constant of the 321-superpattern siz

Wilful blindness: sleeping sickness and Onchocerciasis in Colonial Northern Ghana, 1909–1957

As a contribution to the existing literature on deliberate or unintended neglect, concealment and ignorance regarding significant and enduring public health problems—produced by economic marginality, lack of political power and institutional failures affecting specific places and groups—this article discusses the history of epidemic sleeping sickness and endemic onchocerciasis in colonial northern Ghana from 1909 to 1957. Despite accumulating evidence of their serious impacts on the health of northern communities, and calls to action on the part of some health officials, both diseases were only officially recognised as significant risks when it was no longer politically possible to deny them. The particular histories of each disease, in the same region over the same decades, reveal two comparable and interrelated trajectories of neglect

Comparison of chicken 7SK and U6 RNA polymerase III promoters for short hairpin RNA expression

Background: RNA polymerase III (pol III) type 3 promoters such as U6 or 7SK are commonly used to express short-hairpin RNA (shRNA) effectors for RNA interference (RNAi). To extend the use of RNAi for studies of development using the chicken as a model system, we have developed a system for expressing shRNAs using the chicken 7SK (ch7SK) promoter. Results: We identified and characterised the ch7SK promoter sequence upstream of the full-length 7SK small nuclear RNA (snRNA) sequence in the chicken genome and used this to construct vectors to express shRNAs targeting enhanced green fluorescent protein (EGFP). We transfected chicken DF-1 cells with these constructs and found that anti-EGFP-shRNAs (shEGFP) expressed from the ch7SK promoter could induce efficient knockdown of EGFP expression. We further compared the efficiency of ch7SK-directed knockdown to that of chicken U6 (cU6) promoters and found that the efficiency of the ch7SK promoter was not greater than, but comparable to the efficiency of cU6 promoters. Conclusion: In this study we have demonstrated that the ch7SK promoter can express shRNAs capable of mediating efficient RNAi in a chicken cell line. However, our finding that RNAi driven by the ch7SK promoter is not more efficient than cU6 promoters contrasts previous comparisons of mammalian U6 and 7SK promoters. Since the ch7SK promoter is the first non-mammalian vertebrate 7SK promoter to be characterised, this finding may be helpful in understanding the divergence of pol III promoter activities between mammalian and non-mammalian vertebrates. This aside, our results clearly indicate that the ch7SK promoter is an efficient alternative to U6-based shRNA expression systems for inducing efficient RNAi activity in chicken cells.<br /

A pulsed NMR relaxation and diffusion study of water in treated and untreated waterlogged wood

Freezing curve, NMR relaxation data, and steady field gradient and pulsed field gradient experiments were conducted on samples of water-logged woods excavated from the Tudor warship, the Mary Rose and on similar samples impregnated with Polyethylene-Glycol solutions: the polymer used as a bulking agent to prevent decay. At least two distinguishable populations of water molecules are found in wood. Freezing curves indicate the presence of approximately 0.38 g/g of hydration water, close to that observed in fresh timbers. Relaxation measurements on pre-treated samples provides evidence of a very tightly bound fraction, present at water contents of below 0.14 g/g 0i hydration water, with a second population of hydration water being present up to 0.1.8 9/9. Above this value a third ‘free' population is observed. The relaxation decays in longitudinal and transverse direction have been analysed in terms of a sum of exponentials. These indicate the presence of two populations of water which do not correspond to populations observed in freezing curve analysis. Exchange mechanisms dominate the temperature dependency of the relaxation behaviour in pre-treated samples, which is similar to that observed in other fibrous materials such as meat. However, t he different components do not appear to correspond to the physical characteristics of the wood and the spin populations cannot be associated with a distribution between identifiable compartments within the system. In PEG impregnated samples the contribution to the signal from the polymer is not resolvable on the equipment used. Samples treated with PEGs for which the degree of polymerisation is greater than 1540 show a dependency of relaxation characteristics on the water content of the sample. At low water contents PEGs of low molecular weight impart a mobility to the "bound" water molecules which is not seen in untreated samples. . Belt diffusion coefficients for water molecules in wood are anisotropic, and are reduced from those observed in distilled water. This reduction is brought about because water molecules are both held in a hydration layer, and bounded by the cellular structure of the wood. In impregnated samples the diffusion rates are lowered by a factor of 10, though this is not reflected in the relaxation behaviour. The anisotropy is reduced, and proton exchange mechanisms are blocked