An O(n^3)-Time Algorithm for Tree Edit Distance

The {\em edit distance} between two ordered trees with vertex labels is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as inserting new nodes. In this paper, we present a worst-case $O(n^3)$-time algorithm for this problem, improving the previous best $O(n^3\log n)$-time algorithm~\cite{Klein}. Our result requires a novel adaptive strategy for deciding how a dynamic program divides into subproblems (which is interesting in its own right), together with a deeper understanding of the previous algorithms for the problem. We also prove the optimality of our algorithm among the family of \emph{decomposition strategy} algorithms--which also includes the previous fastest algorithms--by tightening the known lower bound of $\Omega(n^2\log^2 n)$~\cite{Touzet} to $\Omega(n^3)$, matching our algorithm's running time. Furthermore, we obtain matching upper and lower bounds of $\Theta(n m^2 (1 + \log \frac{n}{m}))$ when the two trees have different sizes $m$ and~$n$, where $m < n$.Comment: 10 pages, 5 figures, 5 .tex files where TED.tex is the main on

Deterministic and Probabilistic Binary Search in Graphs

We consider the following natural generalization of Binary Search: in a given undirected, positively weighted graph, one vertex is a target. The algorithm's task is to identify the target by adaptively querying vertices. In response to querying a node $q$, the algorithm learns either that $q$ is the target, or is given an edge out of $q$ that lies on a shortest path from $q$ to the target. We study this problem in a general noisy model in which each query independently receives a correct answer with probability $p > \frac{1}{2}$ (a known constant), and an (adversarial) incorrect one with probability $1-p$. Our main positive result is that when $p = 1$ (i.e., all answers are correct), $\log_2 n$ queries are always sufficient. For general $p$, we give an (almost information-theoretically optimal) algorithm that uses, in expectation, no more than $(1 - \delta)\frac{\log_2 n}{1 - H(p)} + o(\log n) + O(\log^2 (1/\delta))$ queries, and identifies the target correctly with probability at leas $1-\delta$. Here, $H(p) = -(p \log p + (1-p) \log(1-p))$ denotes the entropy. The first bound is achieved by the algorithm that iteratively queries a 1-median of the nodes not ruled out yet; the second bound by careful repeated invocations of a multiplicative weights algorithm. Even for $p = 1$, we show several hardness results for the problem of determining whether a target can be found using $K$ queries. Our upper bound of $\log_2 n$ implies a quasipolynomial-time algorithm for undirected connected graphs; we show that this is best-possible under the Strong Exponential Time Hypothesis (SETH). Furthermore, for directed graphs, or for undirected graphs with non-uniform node querying costs, the problem is PSPACE-complete. For a semi-adaptive version, in which one may query $r$ nodes each in $k$ rounds, we show membership in $\Sigma_{2k-1}$ in the polynomial hierarchy, and hardness for $\Sigma_{2k-5}$

A consistency architecture for hierarchical shared caches

Hierarchical Cache Consistency (HCC) is a scalable cache-con-sistency architecture for chip multiprocessors in which caches are shared hierarchically. HCC’s cache-consistency protocol is embed-ded in the message-routing network that interconnects the caches, providing a distributed and scalable alternative to bus-based and directory-based consistency mechanisms. The HCC consistency protocol is “progressive ” in that every message makes monotonic progress without timeouts, retries, negative acknowledgments, or retreating in any way. The latency is at most proportional to the di-ameter of the network. For HCC with a binary fat-tree network, the protocol requires at most 13 bits of additional state per cache line, no matter how large the system. We prove that the HCC protocol is deadlock free and provides sequential consistency

Quality Improvement of Disqualified Tiger Prawn (Penaeus Monodon Fab.) Broodstock Using Dopamine

Disqualified tiger prawn broodstock is the one that has undergone ablation after two breeding periodes, which causes high production cost, pollution of environment and difficulties in providing it continuously with enough quantity at exact time. The purpose of this study is to find the proper dosage of dopamine which will give good quality for breeding of the disqualified tiger prawn, because dopamine inhibits maturation, so it has enough time for maturation and can be improved the eggs quality. This experiment used 15 pairs the twice breeding tiger prawn, which is taken from Perigi (Central Java). The sample were treated with difference dosage of dopamine (dosage 10-9 , 10-8, 10-7, 10-6 moll and control/injected by aquabidest). The parameters were identified in this experiment are duration (days) for eggs maturation, fecundity, fertilizing rate, hatching rate, egg diameter and phototaxis respnnsive of the nauplii. The result of this research are the of the average of duration for eggs maturation on the broodstock that were injected dopamine, dosage 10-9 , 10-8, 10-7, 10-6 moll and control , were 14, 12, 4, 2, 5 days. Fecundity 561.489, 503.000, 384.205, 230.850 and 150.034. Fertilizing rate 89,8 %, 82,1 %, 56.0 %, 46,3 %, and 23,2 %. Hatching rate 79,53%, 72,53%, 47,75%, 12,27%, and 36.6% . Diameter 0,29; 0,29; 0,29; 0,27; and 0,27mm. The nauplii that had produced by injected broodstock by dosage 10-9 , 10-8, 10-7, have the positive phototaxis responsive while dosage 10-6 and control were weak

Kebiasaan Makan Tiram Mutiara Pintada Maxima di Perairan Teluk Sekotong, Lombok

Penelitian ini bertujuan untuk mengetahui kebiasaan makan tiram mutiara Pintada maxima. Penelitian dilaksanakan dari bulan Juni 2003 sampai Februari 2004 di perairan Teluk Sekotong Propinsi Lombok. Pengambilan contoh fitoplankton di perairan dilakukan setiap 3 jam sekali selama 24 jam antara pukul 06.00 - 03.00 WIB. Pada setiap pemgamatan diambil sebanyak 8 ekor tiram mutiara untuk sekali pengamatan. Untukmemperoleh gambaran kebiasaan makan tiram mutiara dilakukan analisis indeks pilihan. Pintada maxima memakan semua fitoplankton yang ada di lingkungannya. Tiram mutiara tidak melakukan seleksi terhadap jenis makanannya yang terdapat di alam, tetapi menyeleksi makanannya berdasarkan ukuran makanannya. Tiram mutiara menyukai makanan yang memiliki ukuran lebih kecil. Persentase jenis-jenis fitoplanktonyang disukai tiram mutiara berturut-turut adalah kelas Bacillariophyceae, Dinophyceae, Ciliata, Chrisophyta, Cyanophyceae, Chlorophyceae dan moluska

Weak local rules for planar octagonal tilings

We provide an effective characterization of the planar octagonal tilings which admit weak local rules. As a corollary, we show that they are all based on quadratic irrationalities, as conjectured by Thang Le in the 90s.Comment: 23 pages, 6 figure

Frateuria defendens reduces yellows disease symptoms in grapevine under field conditions

Yellows diseases in grapevine, associated with the presence of different phytoplasmas, are a major problem for growers, with no environmentally friendly means of control. Frateuria defendens (Frd), a bacterium with endophytic traits, has been shown to reduce yellows symptoms in grapevine plantlets under laboratory conditions. The objective of this study was to test whether similar effects could be achieved under field conditions. A trial was conducted in a heavily infected vineyard in northern Israel for two consecutive years. A suspension of Frd cells (108·mL-1) was applied bi-weekly by foliar spray on grapevines from bud burst to leaf senescence. Frd penetrated the leaves during the growing period but not during leaf senescence and could be detected in the leaves by PCR analysis up to 14 days post-spraying. The rate of yellows infection was lower in the treated grapevines compared to its increase in untreated grapevines and the yield of symptomatic plants was improved by 10 to 20 %. Taken together, the results suggest Frd acted as a biological control agent in vineyards under the experimental conditions tested

Satellite DNA evolution in Corvoidea inferred from short and long reads

Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satDNA causes problems during the assembly of genomes, and therefore it is still difficult to study it in detail in nonmodel organisms as well as across broad evolutionary timescales. Here, we combined the use of short- and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds-of-paradise (Paradisaeidae) and crow (Corvus) species. These avian species highlighted the presence of a GC-rich Corvoidea satellitome composed of 61 satellite families and provided a set of candidate satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satDNA of crow species rapidly diverged between closely related species while the satDNA appeared more similar between birds-of-paradise species belonging to different genera

Cell surface properties of Pseudomonas stutzeri in the process of diesel oil biodegradation

Pseudomonas stutzeri, isolated from crude oil-contaminated soil, was used to degrade diesel oil. Of three surfactants, 120 mg rhamnolipids 1−1 significantly increased degradation of diesel oil giving 88% loss after 14 days compared to 54% loss without the surfactant. The system with rhamnolipids was characterised by relatively high particle homogeneity. However, the addition of saponins to diesel oil caused the cells to aggregate (the polydispersity index: 0.542) and the biodegradation of diesel oil was only 46%. The cell yield was 0.22 g l−1