Greedy Online Algorithms for Routing Permanent Virtual Circuits

We analyze the competitive ratio of two greedy online algorithms for routing permanent virtual circuits in a network with arbitrary topology and uniform capacity links. We show that the competitive ratio of the first algorithm, with respect to network congestion, is in \Omega\Gamma p Dm) and O( p DLm), where m is the number of links in the network, D is the maximum ratio, over all requests, of the length of the longest path for the request to the length of the shortest path for the request, and L is the ratio of the maximum to minimum bandwidth requirement. We show that the competitive ratio of the second greedy algorithm is in \Omega\Gamma d + log(n \Gamma d)) and min n O(d log n); O( p DLm) o when the optimal route assignment is pairwise edge disjoint, where n is the number of network nodes and d is the length of the longest path that can be assigned to a request. It is known that the optimal competitive ratio for this problem is \Theta(log n). Aspnes, et al. [1, 2] designed a..

\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