TOWARD SEMANTIC WEB SERVICES AS MVC APPLICATIONS: FROM OWL-S VIA UML

OWL-S is an application of OWL, the Web Ontology Language, that describes the semantics of Web Services so that their discovery, selection, invocation and composition can be automated. The research literature reports the use of UML diagrams for the automatic generation of Semantic Web Service descriptions in OWL-S. This paper demonstrates a higher level of automation by generating complete complete Web applications from OWL-S descriptions that have themselves been generated from UML. Previously, we proposed an approach for processing OWL-S descriptions in order to produce MVC-based skeletons for Web applications. The OWL-S ontology undergoes a series of transformations in order to generate a Model-View-Controller application implemented by a combination of Java Beans, JSP, and Servlets code, respectively. In this paper, we show in detail the documents produced at each processing step. We highlight the connections between OWL-S specifications and executable code in the various Java dialects and show the Web interfaces that result from this process.

Stability and interface properties of thin cellulose ester films adsorbed from acetone and ethyl acetate solutions

Stability and interface properties of cellulose acetate propionate (CAP) and cellulose acetate butyrate (CAB) films adsorbed from acetone or ethyl acetate onto Si wafers have been investigated by means of contact angle measurements and atomic force microscopy (AFM). Surface energy (gamma(total)(S)) values determined for CAP adsorbed from acetone are larger than those from ethyl acetate. In the case of CAB films adsorbed from ethyl acetate and acetone were similar. Dewetting was observed by AFM only for CAP films prepared from ethyl acetate. Positive values of effective Hamaker constant (A(eff)) were found only for CAP prepared from ethyl acetate, corroborating with dewetting phenomena observed by AFM. Oil the contrary, negative values of A(eff) were determined for CAP and CAB prepared from acetone and for CAB prepared from ethyl acetate, Corroborating with experimental observations. Sum frequency generation (SFG) vibrational spectra indicated that CAP and CAB films prepared from ethyl acetate present more alkyl groups oriented perpendicularly to the polymer-air interface than those films prepared from acetone. Such preferential orientation corroborates with macroscopic contact angle measurements. Moreover, SFG spectra showed that acetone hinds strongly to Si wafers, creating a new surface for CAP and CAB films. (C) 2008 Elsevier Inc. All rights reserved.

Evaluation of petrogenetic models for intermediate and silicic plutonic rocks from the Sierra de Valle Fertil-La Huerta, Argentina: Petrologic constraints on the origin of igneous rocks in the Ordovician Famatinian-Puna paleoarc

The whole Valle Fertil-La Huerta section appears as a calc-alkaline plutonic suite typical of a destructive plate margin. New Sr and Nd isotopic whole-rock data and published whole-rock geochemistry suggest that the less-evolved intermediate (dioritic) rocks can be derived by magmatic differentiation, mainly by hornblende + plagioclase +/- Fe-Ti oxide fractional crystallization, from mafic (gabbroic) igneous precursors. Closed-system differentiation, however, cannot produce the typical intermediate (tonalitic) and silicic (granodioritic) plutonic rocks, which requires a preponderant contribution of crustal components. Intermediate and silicic plutonic rocks from Valle Fertil-La Huerta section have formed in a plate subduction setting where the thermal and material input of mantle-derived magmas promoted fusion of fertile metasedimentary rocks and favored mixing of gabbroic or dioritic magmas with crustal granitic melts. Magma mixing is observable in the field and evident in variations of chemical elemental parameters and isotopic ratios, revealing that hybridization coupled with fractionation of magmas took place in the crust. Consideration of the whole-rock geochemical and isotopic data in the context of the Famatinian-Puna magmatic belt as a whole demonstrates that the petrologic model postulated for the Sierra Valle Fertil-La Huerta section has the potential to explain the generation of plutonic and volcanic rocks across the Early Ordovician paleoarc from central and northwestern Argentina. As the petrologic model does not require the intervention of old Precambrian continental crust, the nature of the basement on which thick accretionary turbiditic sequences were deposited remains a puzzling aspect. Discussion in this paper provides insights into the nature of magmatic source rocks and mechanisms of magma generation in Cordilleran-type volcano-plutonic arcs of destructive plate margins. (C) 2010 Elsevier Ltd. All rights reserved.

The link between partial melting, granitization and granulite development in central Ribeira Fold Belt, SE Brazil: New evidence from elemental and Sr-Nd isotopic geochemistry

Elemental and Sr-Nd isotopic data on metatexites, diatexites, orthogneisses and charnockites from the central Ribeira Fold Belt indicate that they are LILE-enriched weakly peraluminous granodiorites. Harker and Th-Hf-La correlation trends suggest that these rocks represent a co-genetic sequence, whereas variations on CaO, MnO, Y and HREE for charnockites can be explained by garnet consumption during granulitic metamorphism. Similar REE patterns and isotopic results of epsilon(565)(Nd) = -5.4 to -7.3 and (87)Sr/(86)Sr(565) = 0.706-0.711 for metatexites, diatexites, orthogneisses and charnockites, as well as similar T(DM) ages between 2.0 and 1.5 Ga are consistent with evolution from a relatively homogeneous and enriched common crustal (metasedimentary) protolith. Results suggest a genetic link between metatexites, diatexites, orthogneisses and charnockites and a two-step process for charnockite development: (a) generation of the hydrated igneous protoliths by anatexis of metasedimentary rocks; (b) continuous high-grade metamorphism that transformed the ""S-type granitoids"" (leucosomes and diatexites) into orthogneisses and, as metamorphism and dehydration progressed, into charnockites. (C) 2011 Elsevier Ltd. All rights reserved.

Trace element geochemistry and Sr-Nd characteristics of Mesoproterozoic mafic intrusive rocks from Rondonia, Brazil, SW Amazonian Craton: Petrogenetic and tectonic inferences

The Amazonian Craton comprises an Archean domain surrounded by four successively younger Proterozoic tectonic provinces. Within the Rio-Negro-Juruena province the Serra da Providencia Intrusive Suite (1.60 and 1.53 Ga) consists of A-type rapakivi granites, charnockites and mangerites genetically associated with diabase dikes, gabbros and amphibolites lites. The original mafic melts were derived from a depleted mantle source (epsilon(Nd(T)) + 2.5 to +2.8; epsilon(Sr(T)) - 12.1). Underplated mafic magma induced melting of a short-lived fielsic crust, thus originating coeval felsic-inafic magmatism in a continental intraplate setting. The Colorado Complex, assigned to the Rondonian-San Ignacio province, comprises 1.35-1.36 Ga intrusive bimodal magmatism represented by monzonite gneisses associated with amphibolite, gabbro and metadiabase dikes intercalated with metasediments with detrital zircon that yield U-Pb ages of 1.35 to 1.42 Ga. Mafic samples display juvenile signatures (epsilon(Nd(T)) 0.0 to +5.2; epsilon(Sr(T)) -5.0 to -30.7) and are less contaminated than the Serra da Previdencia and Nova Brasiladndia ones. The generation of the basaltic magma is related to the subduction of an oceanic slab below the peridotite wedge (intraoceanic arc setting). Fluids and/or small melts from the slab impregnated the mantle. The Nova Brasilandia Sequence (Sunsas-Aguapei province) comprises a metasedimentary sequence intruded by 1.10-1.02 Ga metadiabases, gabbros, meta-gabbros, and amphibolites associated with granitic plutons (bimodal magmatism). The original tholeiitic magmas, derived from a depleted source (epsilon(Nd(T)) = +3.1 to +5.0), in a proto-oceanic setting, underwent subsequent contamination by the host rocks, as indicated by the isotopic and trace element data.

Grain size and heavy minerals of the Late Quaternary eolian sediments from the Imbituba-Jaguaruna coast, Southern Brazil: Depositional controls linked to relative sea-level changes

The stratigraphic subdivision and correlation of dune deposits is difficult, especially when age datings are not available. A better understanding of the controls on texture and composition of eolian sands is necessary to interpret ancient eolian sediments. The Imbituba-Jaguaruna coastal zone (Southern Brazil, 28 degrees-29 degrees S) stands out due to its four well-preserved Late Pleistocene (eolian generation 1) to Holocene eolian units (eolian generations 2, 3, and 4). In this study, we evaluate the grain-size and heavy-mineral characteristics of the Imbituba-Jaguartma eolian units through statistical analysis of hundreds of sediment samples. Grain-size parameters and heavy-mineral content allow us to distinguish the Pleistocene from the Holocene units. The grain size displays a pattern of fining and better sorting from generation 1 (older) to 4 (younger), whereas the content of mechanically stable (dense and hard) heavy minerals decreases from eolian generation 1 to 4. The variation in grain size and heavy-mineral content records shifts in the origin and balance (input versus output) of eolian sediment supply attributable mainly to relative sea-level changes. Dunefields submitted to relative sea-level lowstand conditions (eolian generation 1) are characterized by lower accumulation rates and intense post-depositional dissection by fluvial incision. Low accumulation rates favor deflation in the eolian system, which promotes concentration of denser and stable heavy minerals (increase of ZTR index) as well as coarsening of eolian sands. Dissection involves the selective removal of finer sediments and less dense heavy minerals to the coastal source area. Under a high rate of relative sea-level rise and transgression (eolian generation 2), coastal erosion prevents deflation through high input of sediments to the coastal eolian source. This condition favors dunefield growth. Coastal erosion feeds sand from local sources to the eolian system. including sands from previous dunefields (eolian generation 1) and from drowned incised valleys. Therefore, dunefields corresponding to transgressive phases inherit the grain-size and heavy-mineral characteristics of previous dunefields, leading to selective enrichment of finer sands and lighter minerals. Eolian generations 3 and 4 developed during a regressive-progradational phase (Holocene relative sea level highstand). The high rate of sediment supply during the highstand phase prevents deflation. The lack of coastal erosion favors sediment supply from distal sources (fluvial sediments rich in unstable heavy minerals). Thus, dunefields of transgressive and highstand systems tracts may be distinguished from dunefields of the lowstand systems tract through high rates of accumulation (low deflation) in the former. The sediment source of the transgressive dunefields (high input of previously deposited coastal sands) differs from that of the highstand dunefields (high input of fluvial distal sands). Based on this case study, we propose a general framework for the relation between relative sea level, sediment supply and the texture and mineralogy of eolian sediments deposited in siliciclastic wet coastal zones similar to the Imbituba-Jaguaruna coast (C) 2009 Elsevier B.V. All rights reserved.

Symmetry in biology: from genetic code to stochastic gene regulation

Mathematical models, as instruments for understanding the workings of nature, are a traditional tool of physics, but they also play an ever increasing role in biology - in the description of fundamental processes as well as that of complex systems. In this review, the authors discuss two examples of the application of group theoretical methods, which constitute the mathematical discipline for a quantitative description of the idea of symmetry, to genetics. The first one appears, in the form of a pseudo-orthogonal (Lorentz like) symmetry, in the stochastic modelling of what may be regarded as the simplest possible example of a genetic network and, hopefully, a building block for more complicated ones: a single self-interacting or externally regulated gene with only two possible states: ` on` and ` off`. The second is the algebraic approach to the evolution of the genetic code, according to which the current code results from a dynamical symmetry breaking process, starting out from an initial state of complete symmetry and ending in the presently observed final state of low symmetry. In both cases, symmetry plays a decisive role: in the first, it is a characteristic feature of the dynamics of the gene switch and its decay to equilibrium, whereas in the second, it provides the guidelines for the evolution of the coding rules.

Tissue-, substrate-, and site-specific characteristics of mitochondrial reactive oxygen species generation

Reactive oxygen species are a by-product of mitochondrial oxidative phosphorylation, derived from a small quantity of superoxide radicals generated during electron transport. We conducted a comprehensive and quantitative study of oxygen consumption, inner membrane potentials, and H(2)O(2) release in mitochondria isolated from rat brain, heart, kidney, liver, and skeletal muscle, using various respiratory substrates (alpha-ketoglutarate, glutamate, succinate, glycerol phosphate, and palmitoyl carnitine). The locations and properties of reactive oxygen species formation were determined using oxidative phosphorylation and the respiratory chain modulators oligomycin, rotenone, myxothiazol, and antimycin A and the Uncoupler CCCP. We found that in mitochondria isolated from most tissues incubated under physiologically relevant conditions, reactive oxygen release accounts for 0.1-0.2% of O(2) consumed. Our findings support an important participation of flavoenzymes and complex III and a substantial role for reverse electron transport to complex I as reactive oxygen species sources. Our results also indicate that succinate is an important substrate for isolated mitochondrial reactive oxygen production in brain, heart, kidney, and skeletal muscle, whereas fatty acids generate significant quantities of oxidants in kidney and liver. Finally, we found that increasing respiratory rates is an effective way to prevent mitochondrial oxidant release under many, but not all, conditions. Altogether, our data uncover and quantify many tissue-, substrate-, and site-specific characteristics of mitochondrial ROS release. (C) 2009 Elsevier Inc. All rights reserved.

Protoporphyrin IX Nanoparticle Carrier: Preparation, Optical Properties, and Singlet Oxygen Generation

The present study is focused on developing a nanoparticle carrier for the photosensitizer protoporphyrin IX for use in photodynamic therapy. The entrapment of protoporphyrin IX (Pp IX) in silica spheres was achieved by modification of Pp IX molecules with an organosilane reagent. The immobilized drug preserved its optical properties and the capacity to generate singlet oxygen, which was detected by a direct method from its characteristic phosphorescence decay curve at near-infrared and by a chemical method using 1,3-diphenylisobenzofuran to trap singlet oxygen. The lifetime of singlet oxygen when a suspension of Pp IX-loaded particles in acetonitrile was excited at 532 nm was determined as 52 mu s, which is in good agreement with the value determined for methylene blue in acetonitrile solution under the same conditions. The Pp IX-loaded silica particles have an efficiency of singlet oxygen generation (eta Delta) higher than the quantum yield of free porphyrins. This high efficiency of singlet oxygen generation was attributed to changes on the monomer-dimer equilibrium after photosentisizer immobilization.

Singlet oxygen generation in the reaction centers of Rhodobacter sphaeroides

Singlet oxygen ((1)O(2)) generation in the reaction centers (RCs) of Rhodobacter sphaeroides wild type was characterized by luminescent emission in the near infrared region (time resolved transients and emission spectra) and quantified to have quantum yield of 0.03 +/- 0.005. (1)O(2) emission was measured as a function of temperature, ascorbate, urea and potassium ferricyanide concentrations and as a function of incubation time in H(2)O: D(2)O mixtures. (1)O(2) was shown to be affected by the RC dynamics and to originate from the reaction of molecular oxygen with two sources of triplets: photoactive dimer formed by singlet-triplet mixing and bacteriopheophytin formed by direct photoexcitation and intersystem crossing.

Generation and suppression of singlet oxygen in hair by photosensitization of melanin

We have studied the spectroscopic properties of hair (white, blond, red, brown, and black) under illumination with visible light, giving special emphasis to the photoinduced generation of singlet oxygen ((1)O(2)). Irradiation of hair shafts (lambda(ex)>400 nm) changed their properties by degrading the melanin. Formation of C3 hydroperoxides in the melanin indol groups was proven by (1)H NMR. After 532-nm excitation, all hair shafts presented the characteristic (1)O(2) emission (lambda(em) = 1270 nm), whose intensity varied inversely with the melanin content. (1)O(2) lifetime was also shown to vary with hair type, being five times shorter in black hair than in blond hair, indicating the role of melanin as a (1)O(2) suppressor. Lifetime ranged from tenths of a nanosecond to a few microseconds, which is much shorter than the lifetime expected for (1)O(2) in the solvents in which the hair shafts were suspended, indicating that (1)O(2) is generated and suppressed inside the hair structure. Both eumelanin and pheomelanin were shown to produce and to suppress (1)O(2), with similar efficiencies. The higher amount of (1)O(2) generated in blond hair and its longer lifetime is compatible with the stronger damage that light exposure causes in blond hair. We propose a model to explain the formation and suppression of (1)O(2) in hair by photosensitization of melanin with visible light and the deleterious effects that an excess of visible light may cause in hair and skin. 2011 Published by Elsevier Inc.

Relationship between structure and photoactivity of porphyrins derived from protoporphyrin IX

Protoporphyrin (Pp IX) derivatives were prepared to study the relationship between photosensitizer structure and photoactivity, with an emphasis on understanding the role of membrane interactions in the efficiency of photosensitizers used in photodynamic therapy (PDT). The synthetic strategies described here aimed at changing protoporphyrin periferic groups, varying overall charge and oil/water partition, while maintaining their photochemical properties. Three synthetic routes were used: (1) modification of Pp IX at positions 3(1) and 8(1) by addition of alkyl amine groups of different lengths (compounds 2-5), (2) change of Pp IX at positions 13(3) and 17(3), generating alkyl amines (compounds 6 and 7), a phosphate amine (compound 8), and quarternary ammonium compounds (compounds 9 and 10), and (3) amine-alkylation of Hematoporphyrin IX (Hp IX) at positions 3(1), 8(1), 13(3) and 17(3) (compound 12). Strategy 1 leads to hydrophobic compounds with low photocytotoxicity. Strategy 2 leads to compounds 6-10 that have high levels of binding/incorporation in vesicles, mitochondria and cells, which are indicative of high bioavailability. Addition of the phosphate group (compound 8), generates an anionic compound that has low liposome and cell incorporation, plus low photocytotoxicity. Compound 12 has intermediate incorporation and photocytotoxic properties. Compound modification is also associated with changes in their sub-cellular localization: 30% of 8 (anionic) is found in mitochondria as compared to 95% of compound 10 (cationic). Photocytotoxicity was shown to be highly correlated with membrane affinity, which depends on the asymmetrical and amphiphilic characters of sens, as well as with sub-cellular localization.

Effects of a high fat diet on liver mitochondria: increased ATP-sensitive K(+) channel activity and reactive oxygen species generation

High fat diets are extensively associated with health complications within the spectrum of the metabolic syndrome. Some of the most prevalent of these pathologies, often observed early in the development of high-fat dietary complications, are non-alcoholic fatty liver diseases. Mitochondrial bioenergetics and redox state changes are also widely associated with alterations within the metabolic syndrome. We investigated the mitochondrial effects of a high fat diet leading to non-alcoholic fatty liver disease in mice. We found that the diet does not substantially alter respiratory rates, ADP/O ratios or membrane potentials of isolated liver mitochondria. However, H(2)O(2) release using different substrates and ATP-sensitive K(+) transport activities are increased in mitochondria from animals on high fat diets. The increase in H(2)O(2) release rates was observed with different respiratory substrates and was not altered by modulators of mitochondrial ATP-sensitive K(+) channels, indicating it was not related to an observed increase in K(+) transport. Altogether, we demonstrate that mitochondria from animals with diet-induced steatosis do not present significant bioenergetic changes, but display altered ion transport and increased oxidant generation. This is the first evidence, to our knowledge, that ATP-sensitive K(+) transport in mitochondria can be modulated by diet.

Cytotoxic and genotoxic effects of tambjamine D, an alkaloid isolated from the nudibranch Tambja eliora, on Chinese hamster lung fibroblasts

Marine organisms have been shown to be potential sources of bioactive compounds with pharmaceutical applications. Previous chemical investigation of the nudibranch Tambja eliora led to the isolation of the alkaloid tambjamine D. Tambjamines have been isolated from marine sources and belong to the family of 4-methoxypyrrolic-derived natural products, which display promising immunosuppressive and cytotoxic properties. Their ability to intercalate DNA and their pro-oxidant activity may be related to some of the biological effects of the 4-methoxypyrrolic alkaloids. The aim of the present investigation was to determine the cytotoxic, pro-oxidant and genotoxic properties of tambjamine D in V79 Chinese hamster lung fibroblast cells. Tambjamine D displayed a potent cytotoxic effect in V79 cells (IC50 1.2 mu g/mL) evaluated by the MTT assay. Based on the MTT result, V79 cells were treated with different concentrations of tambjamine D (0.6. 1.2. 2.4 and 4.8 mu g/mL). After 24 h, tambjamine D reduced the number of viable cells in a concentration-dependent way at all concentrations tested. assessed by the trypan blue dye exclusion test. The hemolytic assay showed that the cytotoxic activity of tambjamine D was not related to membrane disruption (EC50 > 100 mu g/mL). Tambjamine D increased the number of apoptotic cells in a concentration-dependent manner at all concentrations tested according to acridine orange/ethidium bromide staining, showing that the alkaloid cytotoxic effect was related to the induction of apoptosis. MTT reduction was stimulated by tambjamine D, which may indicate the generation of reactive oxygen species. Accordingly, treatment of cells with tambjamine D increased nitrite/nitrate at all concentrations and TBARS production starting at the concentration corresponding to the IC50. Tambjamine D, also, induced DNA strand breaks and increased the micronucleus cell frequency as evaluated by comet and micronucleus tests, respectively, at all concentrations evaluated. showing a genotoxic risk induced by tambjamine D. (C) 2008 Elsevier Ireland Ltd. All rights reserved.

Antiparasitic, antineuroinflammatory, and cytotoxic polyketides from the marine sponge Plakortis angulospiculatus collected in Brazil

Investigation of the bioactive crude extract from the sponge Plakortis angulospiculatus from Brazil led to the isolation of plakortenone (1) as a new polyketide, along with five known polyketides (2-6) previously isolated from other Plakortis sponges. The known polyketides were tested in antileishmanial, antitrypanosomal, antineuroinflammatory, and cytotoxicity assays. The results show that plakortide P (3) is a potent antiparasitic compound, against both Leishmania chagasi and Trypanosona cruzi, and exhibited antineuroinflammatory activity. The known polyketides 2-6 were tested for cytotoxicity against four human cancer cell lines, but displayed only moderate cytotoxic activity.