Flooding in dynamic graphs with arbitrary degree sequence

This paper addresses the flooding problem in dynamic graphs, where flooding is the basic mechanism in which every node becoming aware of a piece of information at step t$t$ forwards this information to all its neighbors at all forthcoming steps t^′>t$t^{\prime }>t$. We show that a technique developed in a previous paper, for analyzing flooding in a Markovian sequence of Erdös–Rényi graphs, is robust enough to be used also in different contexts. We establish this fact by analyzing flooding in a sequence of graphs drawn independently at random according to a model of random graphs with given expected degree sequence. In the prominent case of power-law degree distributions, we prove that flooding takes almost surely O(logn)$O(logn)$ steps even if, almost surely, none of the graphs in the sequence is connected. In the general case of graphs with an arbitrary degree sequence, we prove several upper bounds on the flooding time, which depend on specific properties of the degree sequence.     

Parsimonious flooding in dynamic graphs

An edge-Markovian process with birth-rate p and death-rate q generates infinite sequences of graphs (G ₀, G ₁, G ₂,…) with the same node set [n] such that G _t is obtained from G _t-1 as follows: if e ? E(G_t-1){e\notin E(G_{t-1})} then e ? E(G_t){e\in E(G_{t})} with probability p, and if e ? E(G_t-1){e\in E(G_{t-1})} then e ? E(G_t){e\notin E(G_{t})} with probability q. In this paper, we establish tight bounds on the complexity of flooding in edge-Markovian graphs, where flooding is the basic mechanism in which every node becoming aware of an information at step t forwards this information to all its neighbors at all forthcoming steps t′ > t. These bounds complete previous results obtained by Clementi et al. Moreover, we also show that flooding in dynamic graphs can be implemented in a parsimonious manner, so that to save bandwidth, yet preserving efficiency in term of simplicity and completion time. For a positive integer k, we say that the flooding protocol is k-active if each node forwards an information only during the k time steps immediately following the step at which the node receives that information for the first time. We define the reachability threshold for the flooding protocol as the smallest integer k such that, for any source s ? [n]{s\in [n]} , the k-active flooding protocol from s completes (i.e., reaches all nodes), and we establish tight bounds for this parameter. We show that, for a large spectrum of parameters p and q, the reachability threshold is by several orders of magnitude smaller than the flooding time. In particular, we show that it is even constant whenever the ratio p/(p + q) exceeds log n/n. Moreover, we also show that being active for a number of steps equal to the reachability threshold (up to a multiplicative constant) allows the flooding protocol to complete in optimal time, i.e., in asymptotically the same number of steps as when being perpetually active. These results demonstrate that flooding can be implemented in a practical and efficient manner in dynamic graphs. The main ingredient in the proofs of our results is a reduction lemma enabling to overcome the time dependencies in edge-Markovian dynamic graphs.     

WRAPPER INFERENCE FOR AMBIGUOUS WEB PAGES

Several studies have concentrated on the generation of wrappers for web data sources. As wrappers can be easily described as grammars, the grammatical inference heritage could play a significant role in this research field. Recent results have identified a new subclass of regular languages, called prefix mark-up languages, that nicely abstract the structures usually found in HTML pages of large web sites. This class has been proven to be identifiable in the limit, and a PTIME unsupervised learning algorithm has been previously developed. Unfortunately, many real-life web pages do not fall in this class of languages. In this article we analyze the roots of the problem and we propose a technique to transform pages in order to bring them into the class of prefix mark-up languages. In this way, we have a practical solution without renouncing to the formal background defined within the grammatical inference framework. We report on some experiments that we have conducted on real-life web pages to evaluate the approach; the results of this activity demonstrate the effectiveness of the presented techniques.     

Sperner's lemma and robust machines

Sperner's lemma states that any admissible coloring of any triangulation of the unit triangle has a 3‐colored triangle. In this paper, we first show that any algorithm to find this 3‐colored triangle that treats the coloring itself as an oracle must be in the worst case linear in the size of the triangulation. Successively, we apply this lower bound to solve three open questions on robust machines posed by Hartmanis and Hemachandra. Received: November 4, 1993     

Cytospray fixation of frozen intraoperative sections

Preservation of cellular morphologic features is well known to be a limit of intraoperative frozen sections. Various techniques have been proposed to improve tissue details, the most common being ethanol immersion of cryostatic slide. We tested fixation with spray formulation for cytology smears on intraoperative frozen section from different organs to obtain a quick alcoholic fixation and a ready-to-use method. Our results of comparative study showed that cytospray fixation of frozen sections provide a significant improvement of cellular details, that it is quick, simple, economic, and that it does not require preorganization.     

Control of acidity development on solid sulfur due to bacterial action

The global production of sulfur, which is currently obtained almost exclusively as an involuntary byproduct of the oil and gas industry, is exceeding the market demand so that long term storage or even definitive disposal of elemental sulfur is often needed to handle production surplus. The storage of large quantities of elemental sulfur calls for solidifying liquid sulfur in huge blocks, hundred meters wide on each side and as high as 20 meters. Sulfur, in presence of water and air, can be oxidized to sulfuric acid by a ubiquitous microorganism: Thiobacillus. On large blocks, this natural phenomenon may lead to soil and water acidification. Research projects have addressed suppression of Thiobacilli activity to prevent acidification, but no industrial applications have been reported. This work describes the inhibition of sulfur biological oxidation attainable by exposing sulfur to a high ionic strength environment. The bacteriostatic action is produced by contacting sulfur with a solution of an inorganic salt, such as sodium chloride, having an ionic strength similar to sea water. Possible ways to exploit the inhibitory effect to prevent the generation of acidity from sulfur storage blocks are suggested.     

Mutagenesis of endopolygalacturonase from Fusarium moniliforme: histidine residue 234 is critical for enzymatic and macerating activities and not for binding to polygalacturonase-inhibiting protein (PGIP)

The sequence encoding the endopolygalacturonase (PG) of Fusarium moniliforme was cloned into the E. coli/yeast shuttle vector Yepsec1 for secretion in yeast. The recombinant plasmid (pCC6) was used to transform Saccharomyces cerevisiae strain S150-2B; transformed yeast cells were able to secrete PG activity into the culture medium. The enzyme (wtY-PG) was purified, characterized, and shown to possess biochemical properties similar to those of the PG purified from F. moniliforme. The wtY-PG was able to macerate potato medullary tissue disks and was inhibited by the polygalacturonase-inhibiting protein (PGIP) purified from Phaseolus vulgaris. The sequence encoding PG in pCC6 was subjected to site-directed mutagenesis. Three residues in a region highly conserved in all the sequences known to encode PGs were separately mutated: His 234 was mutated into Lys (H 234-->K), and Ser 237 and Ser 240 into Gly (S 237-->G and S 240-->G). Each of the mutated sequences was used to transform S. cerevisiae and the mutated enzymes were purified and characterized. Replacement of His 234 with Lys abolished the enzymatic activity, confirming the biochemical evidence that a His residue is critical for enzyme activity. Replacement of either Ser 237 or Ser 240 with Gly reduced the enzymatic activity to 48% and 6%, respectively, of the wtY-PG. When applied to potato medullary tissue, F. moniliforme PG and wtY-PG caused comparable maceration, while the variant PGs exhibited a limited (S 234-->G and S 240-->G) or null (H 234-->K) macerating activity. The interaction between the variant enzymes and the P. vulgaris PGIP was investigated using a biosensor based on surface plasmon resonance (BIAlite). The three variant enzymes were still able to interact and bind to PGIP with association constants comparable to that of the wild type enzyme.     

Heat of dilution and density data for poly(β-propiolactone) and poly(ε-caprolactone) in dioxane

Solution properties of two polyesters, poly(β-propiolactone) and poly(?-caprolactone) in dioxane have been studied. Data reported are: polymer densities, thermal expansion coefficients, thermal pressure coefficients, solution densities (volume changes on mixing: (ΔV_M) and heats of dilution (ΔH₁). It is found that the solution properties of the two polyesters in dioxane differ; e.g. poly(β-propiolactone): ΔV_M < 0; ΔH₁ > 0; poly(?-caprolactone): ΔV_u > 0; ΔH₁ < 0. Flory's theory is used to interpret these results. The theory contains one adjustable parameter (X₁₂) which is fixed by fitting the theory to the heat of dilution data. Sign and order of magnitude of the volume changes on mixing are then correctly predicted.     

Overexpression, one-step purification and characterization of UDP-glucose dehydrogenase and UDP-N-acetylglucosamine pyrophosphorylase

HASPP28 (heat- and acid-stable phosphoprotein of 28 kDa) has been purified to near homogeneity from the acid-stable protein fraction of rat brain extract. Based on the N-terminal 40 amino acid sequence, a pair of highly degenerate primers was used to generate a 107-bp probe from rat brain RNA by RT-PCR. From the rat brain lambda gt11 library, this probe identified two positive clones that together provided a cDNA of 837 bp with an open reading frame of 546 bp. This cDNA was extended by 3'RACE to 1.2 kb that included a polyadenylation signal and a poly(A) tail. The 180-amino-acid sequence derived from the open reading frame, which did not correspond to any known protein, was predicted to have phosphorylation sites for protein kinase C, casein kinase II (CKII), and protein kinase A. Indeed, both the purified rat brain HASPP28 and the recombinant HASPP28 (rHASPP28) can be phosphorylated by these kinases. Northern blot analysis indicated that HASPP28 was present in all rat tissues tested, including those from the brain, lung, spleen, kidney, liver, heart, and muscle, in decreasing order of abundance. Phosphopeptide analysis of rHASPP28 phosphorylated in vitro by various kinases showed different tryptic patterns on two-dimensional mapping and isoelectric focusing gels. From [32P]PO4-labeled N1E115 neuroblastoma cells, HASPP28 can be immunoprecipitated with a polyclonal antiserum raised against rHASPP28. The immunoprecipitated protein showed a phosphopeptide pattern similar to that of rHASPP28 phosphorylated by CK II in vitro. Furthermore, the immunoprecipitates from cells treated with phorbol 12-myristate 13-acetate or 8-bromo-cAMP did not show any increased phosphorylation over those of untreated ones, and the phosphopeptide patterns of the immunoprecipitates again were similar to that of CK II phosphorylated protein. These results suggest that HASPP28 is a novel phosphoprotein that can be phosphorylated by several kinases in vitro. In intact cells, CK II seems to be solely responsible for the phosphorylation of HASPP28.     

Determination of clenbuterol in bovine liver by combining matrix solid-phase dispersion and molecular imprinted solid-phase extraction followed by liquid chromatography/electrospray ion trap multiple-stage mass spectrometry

Matrix solid-phase dispersion (MSPD) is a new sample pretreatment for solid samples. This technique greatly simplifies sample pretreatment but, nonetheless, the extracts often still require an extra cleanup step that is both laborious and time-consuming. The potential of combining MSPD with molecularly imprinted solid-phase extraction (MISPE) was investigated in this study. Liver samples were ground in a mortar with C18 sorbent and the homogenized mixture packed into an SPE cartridge and placed on top of a MISPE cartridge. Subsequently, clenbuterol was eluted from the MSPD cartridge onto the MISPE cartridge using acetonitrile containing 1% acetic acid. The ability of the molecularly imprinted polymer to selectively adsorb analyte in acetonitrile was exploited for re-extracting clenbuterol directly from this acetonitrile extract via the double cartridge tandem system. The analyte was eluted from the MISPE cartridge using acidified methanol. A clear eluate was obtained, which was subsequently evaporated, redissolved, and analyzed by HPLC electrochemical detection (ECD) or ion trap mass spectrometry (LC/IT-MS). The MISPE cartridge used in this study was imprinted using bromoclenbuterol, a structural analogue of clenbuterol, as the template. These MISPE cartridges showed excellent stability. The complete extraction procedure was rapid, and recoveries exceeded 90% for the target analyte. The method detection limit for the LC/IT-MS procedure was < 0.1 microg/kg. This method, therefore, satisfies the stringent requirements of European Union regulation EEC 2377/90.