High performance subgraph mining in molecular compounds

Structured data represented in the form of graphs arises in several fields of the science and the growing amount of available data makes distributed graph mining techniques particularly relevant. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiver-initiated, load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening dataset, where the approach attains close-to linear speedup in a network of workstations.

Utilisation by ruminants of nitrogen compounds in silage-based diets

This paper considers the various complex changes that occur to nitrogen (N) containing compounds in forages through the processes of ensiling, rumen degradation and microbial synthesis, post-ruminal digestion and absorption and synthesis into milk protein. Particular emphasis is placed on reviewing recent data on the efficiency of utilisation of N-containing compounds in silages by rumen microbes, since low efficiency here is believed to be a major cause of large N losses to the environment on some silage-based diets. Data are reviewed which show that although rumen degradation of N compounds in silage is rapid and extensive, up to 10% of the soluble N can escape the rumen by being associated with the liquid phase. There is now firm evidence that the composition of the amino acids (AAs) absorbed is heavily dependent on the process of ensiling and that witting or use of certain silage additives conserve the initial amino acid profile of the forage. This provides an opportunity to manipulate the amino acid supply to better match demand thus potentially enhancing utilisation. This review confirms that utilisation of the N fractions in grass and legume silages in particular, is poor and the efficiency of microbial protein synthesis (EMPS) is consistently higher on maize silage-based diets. It is concluded that the way in which grass and legume silages in particular are produced and used in the future needs a radical rethink. New research needs to be aimed at enhancing the utilisation of N in the rumen through a better understanding of N/carbohydrate relationships and the ability of forages to supply degraded carbohydrate. Also more emphasis is needed on understanding of the potentially different role of the different N fractions that exist in silages. (C) 2004 Elsevier B.V. All rights reserved.

Role of polyhydroxybutyrate and glycogen as carbon storage compounds in pea and bean bacteroids

Rhizobium leguminosarum synthesizes polyhydroxybutyrate and glycogen as its main carbon storage compounds. To examine the role of these compounds in bacteroid development and in symbiotic efficiency, single and double mutants of R. legumosarum bv. viciae were made which lack polyhydroxybutyrate synthase (phaC), glycogen synthase (glgA), or both. For comparison, a single phaC mutant also was isolated in a bean-nodulating strain of R. leguminosarum bv. phaseoli. In one large glasshouse trial, the growth of pea plants inoculated with the R. leguminosarum bv. viciae phaC mutant were significantly reduced compared with wild-type-inoculated plants. However, in subsequent glasshouse and growth-room studies, the growth of pea plants inoculated with the mutant were similar to wildtype-inoculated plants. Bean plants were unaffected by the loss of polyhydroxybutyrate biosynthesis in bacteroids. Pea plants nodulated by a glycogen synthase mutants or the glgA/phaC double mutant, grew as well as the wild type in growth-room experiments. Light and electron micrographs revealed that pea nodules infected with the glgA mutant accumulated large amounts of starch in the II/III interzone. This suggests that glycogen may be the dominant carbon storage compound in pea bacteroids. Polyhydroxybutyrate was present in bacteria in the infection thread of pea plants but was broken down during bacteroid formation. In nodules infected with a phaC mutant of R. leguminosarum bv. viciae, there was a drop in the amount of starch in the II/III interzone, where bacteroids form. Therefore, we propose a carbon burst hypothesis for bacteroid formation, where polyhydroxybutyrate accumulated by bacteria is degraded to fuel bacteroid differentiation.

Splanchnic metabolism of nitrogenous compounds and urinary nitrogen excretion in steers fed alfalfa under conditions of increased absorption of ammonia and L-arginine supply across the portal-drained viscera

Effects of increased ammonia and/or arginine absorption across the portal-drained viscera (PDV) on net splanchnic (PDV and liver) metabolism of nitrogenous compounds and urinary N excretion were investigated in six cathetenzed Hereford x Angus steers (501 +/- 1 kg BW) fed a 75% alfalfa:25% (as-fed basis) corn-soybean meal diet (0.523 MJ of ME/[kg BW0.15.d]) every 2 h without (27.0 g of N/kg of dietary DM) and with 20 g of urea/kg of dietary DM (35.7 g of N/kg of dietary DM) in a split-plot design. Net splanchnic flux measurements were obtained immediately before beginning and ending a 72-h mesenteric vein infusion of L-arginine (15 mmol/h). For 3 d before and during arginine infusion, daily urine voided was measured and analyzed for N composition. Feeding urea increased PDV absorption (P < 0.01) and hepatic removal (P < 0.01) of ammonia N, accounting for 80% of increased hepatic urea N output (P < 0.01). Numerical increases in net hepatic removal of AA N could account for the remaining portion of increased hepatic urea N output. Arginine infusion increased hepatic arginine removal (P < 0.01) and hepatic urea N output (P < 0.03) and switched hepatic ornithine flux from net uptake to net output (P < 0.01), but numerical changes in net hepatic removal of ammonia and AA N could not account fully for the increase in hepatic urea N output. Increases in urine N excretion equaled quantities of N fed as urea or infused as arginine. Estimated salivary urea N excretion was not changed by either treatment. Urea cycle regulation occurs via a complex interaction of mechanisms and requires N sources other than ammonia, but the effect of increased ammonia absorption on hepatic catabolism of individual AA in the present study was not significant.

In vitro antioxidant activity of coffee compounds and their metabolites

In this paper we report the antioxidant activity of different compounds which are present in coffee or are produced as a result of the metabolism of this beverage. In vitro methods such as the ABTS(center dot+) [ABTS = 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid)] decolorization assay and the oxygen radical absorbance capacity assay (ORAC) were used to assess the capacity of coffee compounds to scavenge free radicals. The importance of caffeine metabolites and colonic metabolites in the overall antioxidant activity associated with coffee consumption is shown. Colonic metabolites such as m-coumaric acid and dihydroferulic acid showed high antioxidant activity. The ability of these compounds to protect human low-density lipoprotein (LDL) oxidation by copper and 2,2'-azobis(2-amidinopropane) dihydrochloride was also explored. 1-Methyluric acid was particularly effective at inhibiting LDL oxidative modification. Different experiments showed that this caffeine metabolite is not incorporated into LDL particles. However, at physiologically relevant concentrations, it was able to delay for more than 13 h LDL oxidation by copper.

Role of polyhydroxybutyrate and glycogen as carbon storage compounds in pea and bean bacteroids

Rhizobium leguminosarum synthesizes polyhydroxybutyrate and glycogen as its main carbon storage compounds. To examine the role of these compounds in bacteroid development and in symbiotic efficiency, single and double mutants of R. legumosarum bv. viciae were made which lack polyhydroxybutyrate synthase (phaC), glycogen synthase (glgA), or both. For comparison, a single phaC mutant also was isolated in a bean-nodulating strain of R. leguminosarum bv. phaseoli. In one large glasshouse trial, the growth of pea plants inoculated with the R. leguminosarum bv. viciae phaC mutant were significantly reduced compared with wild-type-inoculated plants. However, in subsequent glasshouse and growth-room studies, the growth of pea plants inoculated with the mutant were similar to wildtype-inoculated plants. Bean plants were unaffected by the loss of polyhydroxybutyrate biosynthesis in bacteroids. Pea plants nodulated by a glycogen synthase mutants or the glgA/phaC double mutant, grew as well as the wild type in growth-room experiments. Light and electron micrographs revealed that pea nodules infected with the glgA mutant accumulated large amounts of starch in the II/III interzone. This suggests that glycogen may be the dominant carbon storage compound in pea bacteroids. Polyhydroxybutyrate was present in bacteria in the infection thread of pea plants but was broken down during bacteroid formation. In nodules infected with a phaC mutant of R. leguminosarum bv. viciae, there was a drop in the amount of starch in the II/III interzone, where bacteroids form. Therefore, we propose a carbon burst hypothesis for bacteroid formation, where polyhydroxybutyrate accumulated by bacteria is degraded to fuel bacteroid differentiation.

The role of polyphenolic compounds in the diet as inhibitors of platelet function

Platelets play a substantial role in cardiovascular disease, and for many years there has been a search for dietary components that are able to inhibit platelet function and therefore decrease the risk of cardiovascular disease. Platelets can be inhibited by alcohol, dietary fats and some antioxidants, including a group of compounds, the polyphenols, found in fruits and vegetables. A number of these compounds have been shown to inhibit platelet function both in vitro and in vivo. In the present study the effects of the hydroxycinnamates and the flavonoid quercetin on platelet activation and cell signalling in vitro were investigated. The hydroxycinnamates inhibited platelet function, although not at levels that can be achieved in human plasma by dietary intervention. However, quercetin inhibited platelet aggregation at levels lower than those previously reported. Quercetin was also found to inhibit intracellular Ca mobilisation and whole-cell tyrosine protein phosphorylation in platelets, which are both processes essential for platelet activation. The effect of polyphenols on platelet aggregation in vivo was also investigated. Twenty subjects followed a low-polyphenol diet for 3 d before and also during supplementation. All subjects were supplemented with a polyphenol-rich meal every lunchtime for 5 d. Platelet aggregation and plasma flavonols were measured at baseline and after 5 d of dietary supplementation. Total plasma flavonoids increased significantly after the dietary intervention period (P = 0.001). However, no significant changes in ex vivo platelet aggregation were observed. Further investigation of the effects of individual polyphenolic compounds on platelet function, both in vitro and in vivo, is required in order to elucidate their role in the relationship between diet and the risk of cardiovascular disease.

Some transition metal complexes derived from mono- and di-ethynyl perfluorobenzenes

Transition metal alkynyl complexes containing perfluoroaryl groups have been prepared directly from trimethylsilyl-protected mono- and di-ethynyl perfluoroarenes by simple desilylation/metallation reaction sequences. Reactions between Me3SiC CC6F5 and RuCl(dppe)Cp'[Cp' = Cp, Cp*] in the presence of KF in MeOH give the monoruthenium complexes Ru(C CC6F5)(dppe)Cp'[Cp' = Cp (2); Cp* (3)], which are related to the known compound Ru(C CC6F5)(PPh3)(2)Cp (1). Treatment of Me3SiC CC6F5 with Pt-2(mu-dppm)(2)Cl-2 in the presence of NaOMe in MeOH gave the bis(alkynyl) complex Pt-2(mu-dppm)(2)(C CC6F5)(2) (4). The Pd(0)/Cu(I)-catalysed reactions between Au(C CC6F5)(PPh3) and Mo( CBr)(CO)(2) Tp* [Tp* = hydridotris(3.5-dimethylpyrazoyl)borate], Co-3(mu(3)-CBr)(mu-dppm)(CO)(7) or IC CFc [Fc = (eta(5)-C5H4)FeCp] afford Mo( CC CC6F5)(CO)(2)Tp* (5), Co-3(mu 3-CC CC6F5)(mu-dppm)(CO)(7) (6) and FcC CC CC6F5 (7), respectively. The diruthenium complexes 1,4-{Cp'(PP)RuC C}(2)C6F4 [(PP)Cp'=(PPh3)(2)Cp (8); (dppe)Cp (9); (dppe)Cp* (10)] are prepared from 1,4-(Me3SiC C)(2)C6F4 in a manner similar to that described for the monoruthenium complexes 1-3. The non-fluorinated complexes 1,4-{Cp'(PP)RuC C}(2)C6H4 [(PP)Cp' = (PPh3)(2)Cp (11); ( dppe) Cp (12); ( dppe) Cp* (13)], prepared for comparison, are obtained from 1,4-(Me3SiC C)(2)C6H4. Spectro-electrochemical studies of the ruthenium aryl and arylene alkynyl complexes 2-3 and 8-13, together with DFT-based computational studies on suitable model systems, indicate that perfluorination of the aromatic ring has little effect on the electronic structures of these compounds, and that the frontier orbitals have appreciable diethynylphenylene character. Molecular structure determinations are reported for the fluoroaromatic complexes 1, 2, 3, 6 and 10.

1-(2 '-pyridylazo)-2-naphtholate complexes of ruthenium: synthesis, characterization, and DNA binding properties

Reaction of 1-(2'-pyridylazo)-2 -naphthol (Hpan) with [Ru(dmso)(4)Cl-2] (dmso=dimethylsulfoxide), [Ru(trpy)Cl-3] (trpy=2,2',2 ''-terpyridine), [Ru(bpy)Cl-3] (bpy=2,2'-bipyridine) and [Ru(PPh3)(3)Cl-2] in refluxing ethanol in the presence of a base (NEt3) affords, respectively, the [Ru(pan)(2)], [Ru(trpy)(pan)](+) (isolated as perchlorate salt), [Ru(bpy)(pan)Cl] and [Ru(PPh3)(2)(pan)Cl] complexes. Structures of these four complexes have been determined by X-ray crystallography. in each of these complexes, the pan ligand is coordinated to the metal center as a monoanionic tridentate N,N,O-donor. Reaction of the [Ru(bpy)(pan)Cl] complex with pyridine (py) and 4-picoline (pic) in the presence of silver ion has yielded the [Ru(bpy)(pan)(py)](+) and [Ru(bpy)(pan)(pic)](+) complexes (isolated as perchlorate salts), respectively. All the complexes are diamagnetic (low-spin d(6), S = 0) and show characteristic H-1 NMR signals and intense MLCT transitions in the visible region. Cyclic voltammetry on all the complexes shows a Ru(II)-Ru(III) oxidation on the positive side of SCE. Except in the [Ru(pan)(2)] complex, a second oxidative response has been observed in the other five complexes. Reductions of the coordinated ligands have also been observed on the negative side of SCE. The [Ru(trpy)(pan)]ClO4, [Ru(bpy)(pan)(py)]ClO4 and [Ru(bpy) (pan)(pic)]ClO4 complexes have been observed to bind to DNA, but they have not been able to cleave super-coiled DNA on UV irradiation. (c) 2008 Elsevier Ltd. All rights reserved.

First 5f-element complexes with the tetradentate BTBP ligand. Synthesis and crystal structure of uranyl(VI) compounds with CyMe4BTBP

Treatment of [UO2(OTf)(2)] or [UO2I2(thf)(3)] with 1 equiv. of CyMe4BTBP in anhydrous acetonitrile led to the formation of [UO2(CyMe4BTBP)(OTf)(2)] (1) and [UO2(CyMe4BTBP)I-2] (2) which crystallized as the cationic forms [UO2(CyMe4BTBP)(py)][OTf](2) (3) and [UO2I(CyMe4BTBP)][I] (4) in pyridine and acetonitrile, respectively. These compounds are unique examples of structurally characterized actinide complexes with a BTBP molecule; this ligand adopts a planar conformation in the equatorial plane of the {UO2}(2+) ion. In pyridine, 1 is dissociated into [UO2(OTf)(2)(PY)(3)] and free CyMe4BTBP and the thermodynamic parameters (K, Delta H, Delta S) of this equilibrium have been determined by H-1 NMR spectroscopy. The ethoxide derivative [UO2(OEt)(CyMe4BTBP)][OTf] (5) crystallized from a solution of I in a mixture of ethanol and acetone under air, and the dinuclear mu-oxo complex [{UO2(CyMe4BTBP)}(2)(mu-O)][I](2) (6) was obtained from [UO2I(thf)(2.7)] and CyMe4BTBP. The crystal structures of 6 and of the analogous derivatives [{UO2(py)(4)}(2)(mu-O)][I](2)(7) and [{UO2(TPTZ)(py)}(2)(mu-O)][I-3](2)(8) exhibit a flexible [{UO2}-O-{UO2}](2+) moiety.

Pyrene-functionalised, alternating copolyimide for sensing nitroaromatic compounds

A novel, pyrene-functionalised copolymer has been synthesised in a single step via imidisation of poly(maleic anhydride-alt-1-octadecene) with 1-pyrenemethylamine, and its potential for the detection of volatile nitro aromatic compounds (NACs) evaluated. The new copolymer forms complexes in solution with NACs such as 2,5-dinitrobenzonitrile, as shown by H-1 NMR, UV-vis and fluorescence spectroscopy. Moreover, thin films of this copolymer, cast from THF solution, undergo almost instantaneous fluorescence quenching when exposed to the vapour of 2,5-dinitrobenzonitrile (a model for TNT) at ambient temperatures and pressures.

Ruthenium (III) complexes of tetradentate NSNO pyridylthioazophenolates: Synthesis, spectral studies, crystal structure and redox properties

A family of ruthenium (III) complexes of tetradentate monobasic NSNO donor chelators (HL) have been synthesized and isolated in their pure form. On chromatographic separation, trans-dichloro and cis-dichloro ruthenium (111) complexes of pyridylthioazophenolates are eluted using 19:1 and 7:3 (v/v) DCM-MeOH mixtures, respectively. Both cis and trans isomers of the dark brown colored ruthenium (111) complexes, having the general formula of [Ru(L)Cl-2], have been characterized by elemental analyses, spectroscopic and other physico-chemical tools. The magnetic moments of both the cis- and trans-[Ru(L)Cl-2] complexes are in the range of 1.71-1.79 BM. One of the complexes, trans-[Ru(L1)Cl-2] (2a), has been subjected to single-crystal X-ray analysis which confirms that the chlorines are in mutually trans positions in the molecule. The EPR spectra of the cis-[Ru(L)Cl-2] complexes (1) in DMF are consistent with the fact that the complexes are low-spin octahedral with one unpaired electron having three different g values (g(x) not equal g(y) not equal g(z)) complexes are monomeric with an octahedral coordination sphere. The electrochemical studies of [Ru(L)Cl,] in DMF show a quasi-reversible voltammogram. The reduction potentials for the cis-isomers are comparatively lower than those of the corresponding trans isomers. On reaction with the bidentate bipyridyl ligand in the presence of AgNO3, the cis-[Ru(L)Cl-2] complexes (1) produce a series of complexes with the general formula [Ru(L)(bpy)(2)](PF6)(2) (3). which have also been characterized by elemental analyses, spectroscopic and other physico-chemical tools. (c) 2006 Elsevier Ltd. All rights reserved.

A DFT study of free radicals formed from artemisinin and related compounds

Ab initio calculations using density functional theory have shown that the reactions that occur between artemisinin, 1, a cyclic trioxane active against malaria, and some metal ions and complexes lead to a series of radicals which are probably responsible for its therapeutic activity. In particular it has been shown that the interaction of Fe(H) with artemisinin causes the O-O bond to be broken as indeed does Fe(III) and Cu(I), while Zn(II) does not. Calculations were carried out with Fe(II) in several different forms including the bare ion, [Fe(H2O)(5)](2+) and [FeP(Im)] (P, porphyrin; Im, imadazole) and similar results were obtained. The resulting oxygen-based radicals are readily converted to more stable carbon-based radicals and/or. stable products. Similar radicals and products are also formed from two simple model trioxanes 2 and 3 that show little or no therapeutic action against malaria although some subtle differences were obtained. This suggests that the scaffold surrounding the pharmacophore may be involved in molecular recognition events allowing efficient uptake of this trioxane warhead into the parasite. (C) 2004 Elsevier B.V. All rights reserved.

Use of HNO3 as the source of NO to prepare a nitric oxide complex of ruthenium

Reaction of cis-Ru(bisox)(2)Cl-2, where bisox is 4,4,4',4'-tetramethyl-2,2'-bisoxazoline, with HNO3 in 1 : 4 molar proportion in boiling water under N-2 atmosphere and subsequent addition of an excess of NaClO4 center dot H2O yields [Ru(bisox)(HL)(NO)](ClO4)(NO3) (1). HL is a hydrolysed form of bisox where one of the oxazoline rings opens up. X-Ray crystallography shows that 1 contains an octahedral RuN5O core. HL binds the metal through an imino N, an amide N and an alcoholic O atom. Reaction of cis-Ru(bisox)(2)Cl-2 with an excess of NaNO2 in water gives cis-Ru(bisox)(2)(NO2)(2) (2). On acidification by HClO4 in methanol, 2 is smoothly converted to cis-[Ru(bisox)(2)(NO2)(NO)](ClO4)(2) (3) due to equilibrium (1).

A deliberate synthesis of a mononuclear trans-dimethoxide complex of ruthenium(III). X-ray crystal structure, electrochemistry and electron paramagnetic resonance

Using bis(3,5-dimethylpyrazol-1-yl) methane as the bidentate N donor ligand L, the yellow compound trans-[(RuL2)-L-III(OMe)(2)]ClO4 center dot CH2Cl2 is synthesized. It is a rare example of a mononuclear dialkoxo complex of Ru(III). It shows a quasireversible Ru(II/III) couple at -0.65 V versus NHE in acetonitrile at a Pt electrode. Its magnetic moment at room temperature corresponds to one unpaired electron. It displays a rhombic EPR spectrum in acetone at 77 K with g = 2.219, 2.062 and 1.855. (C) 2009 Elsevier B. V. All rights reserved.