A method of encoding generalized link diagrams

We describe a method of encoding various types of link diagrams, including those with classical, flat, rigid, welded, and virtual crossings. We show that this method may be used to encode link diagrams, up to equivalence, in a notation whose length is a cubic function of the number of 'riser marks'. For classical knots, the minimal number of such marks is twice the bridge index, and a classical knot diagram in minimal bridge form with bridge index $b$ may be encoded in space $\mathcal{O}(b^2)$. A set of moves on the notation is defined. As a demonstration of the utility of the notation we give another proof that the Kishino virtual knot is non-classical.Comment: 17 pages, 13 figures; to appear in the Journal of Knot Theory & Its Ramification

A Note on the Total Detection Numbers of Cycles

Let G be a connected graph of size at least 2 and c :E(G)→{0, 1, . . . , k− 1} an edge coloring (or labeling) of G using k labels, where adjacent edges may be assigned the same label. For each vertex v of G, the color code of v with respect to c is the k-vector code(v) = (a0, a1, . . . , ak−1), where ai is the number of edges incident with v that are labeled i for 0 ≤ i ≤ k − 1. The labeling c is called a detectable labeling if distinct vertices in G have distinct color codes. The value val(c) of a detectable labeling c of a graph G is the sum of the labels assigned to the edges in G. The total detection number td(G) of G is defined by td(G) = min{val(c)}, where the minimum is taken over all detectable labelings c of G. We investigate the problem of determining the total detection numbers of cycles

\u3ci\u3eDrosophila\u3c/i\u3e Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu