Repeated mapping of reefs constructed by Sabellaria spinulosa Leuckart 1849 at an offshore wind farm site

Sabellaria spinulosa reefs are considered to be sensitive and of high conservation status. This article evaluates the feasibility of using remote sensing technology to delineate S. spinulosa reefs. S. spinulosa reef habitats associated with the Thanet Offshore Windfarm site were mapped using high resolution sidescan sonar (410 kHz) and multibeam echo sounder (<1 m2) data in 2005 (baseline), 2007 (pre-construction baseline) and 2012 (post-construction). The S. spinulosa reefs were identified in the acoustic data as areas of distinct irregular texturing. Maps created using acoustic data were validated using quantitative measures of reef quality, namely tube density (as a proxy for the density of live S. spinulosa), percentage cover of S. spinulosa structures (both living and dead) and associated macrofauna derived from seabed images taken across the development site. Statistically significant differences were observed in all physical measures of S. spinulosa as well the number (S) and diversity (H׳) of associated species, derived from seabed images classified according to the presence or absence of reef, validating the use of high resolution sidescan sonar to map these important biogenic habitats. High precision mapping in the early stages allowed for the micro-siting of wind turbines in a way that caused minimal damage to S. spinulosa reefs during construction. These habitats have since recovered and expanded in extent. The surveys undertaken at the Thanet Offshore Windfarm site demonstrate the importance of repeat mapping for this emerging industry, allowing habitat enhancement to be attributed to the development whilst preventing background habitat degradation from being wrongly attributed to the development.

Caracterização dos padrões genéticos de populações invasoras e naturalizadas de schizolobium parahyba (Caesalpinioideae – Fabaceae) por restriction-site associated dna-sequencing

Pós-graduação em Ciência Florestal - FCA

Primary relapse site pattern in women with triple-negative breast cancer

Despite the remarkable improvements in breast cancer (BC) characterization, accurate prediction of BC clinical behavior is often still difficult to achieve. Some studies have investigated the association between the molecular subtype, namely the basal-like BC and the pattern of relapse, however only few investigated the association between relapse pattern and immunohistochemical defined triple-negative breast cancers (TNBCs). The aim of this study was to evaluate the pattern of relapse in patients with TNBC, namely the primary distant relapse site:One-hundred twenty nine (129) invasive breast carcinomas with follow-up information were classified according to the molecular subtype using immunohistochemistry for ER, PgR and Her2. The association between TNBC and distant relapse primary site was analyzed by logistic regression. Using multivariate logistic regression analysis patients with TNBC displayed only 0.09(95% CI: 0.00-0.74; p = 0.02) the odds of, the non-TNBC patients of developing bone primary relapse. Regarding visceral and lymph-node relapse, no differences between in this cohort were found.Though classically regarded as aggressive tumors, TNBCs rarely development primary relapse in bone when compared to non-TNBC, a clinical relevant fact when investigating a metastasis of an occult or non-sampled primary BC. (C) 2014 Elsevier GmbH. All rights reserved.

Proximity-accelerated chemical coupling reaction in the benzodiazepine-binding site of gamma-aminobutyric acid type A receptors: superposition of different allosteric modulators

Benzodiazepines are widely used drugs. They exert sedative/hypnotic, anxiolytic, muscle relaxant, and anticonvulsant effects and act through a specific high affinity binding site on the major inhibitory neurotransmitter receptor, the gamma-aminobutyric acid type A (GABA(A)) receptor. Ligands of the benzodiazepine-binding site are classified into three groups depending on their mode of action: positive and negative allosteric modulators and antagonists. To rationally design ligands of the benzodiazepine site in different isoforms of the GABA(A) receptor, we need to understand the relative positioning and overlap of modulators of different allosteric properties. To solve these questions, we used a proximity-accelerated irreversible chemical coupling reaction. GABA(A) receptor residues thought to reside in the benzodiazepine-binding site were individually mutated to cysteine and combined with a cysteine-reactive benzodiazepine site ligand. Direct apposition of reaction partners is expected to lead to a covalent reaction. We describe here such a reaction of predominantly alpha(1)H101C and also three other mutants (alpha(1)G157C, alpha(1)V202C, and alpha(1)V211C) with an Imid-NCS derivative in which a reactive isothiocyanate group (-NCS) replaces the azide group (-N(3)) in the partial negative allosteric modulator Ro15-4513. Our results show four contact points of imidazobenzodiazepines with the receptor, alpha(1)H101C being shared by classical benzodiazepines. Taken together with previous data, a similar orientation of these ligands within the benzodiazepine-binding pocket may be proposed.

Granulometry, mineralogy and geochemistry of sediments from ODP Hole 169-1037B and Site 169-1038

Central Hill is in the northern part of the Escanaba Trough, which is a sediment-filled rift of southern Gorda Ridge. Central Hill is oriented north-south and is associated with extensive sulfide deposits. Hydrothermal alteration of sediment from Site 1038 was studied through analyses of mineralogy and the chemistry and oxygen isotopic compositions of one nearly pure clay sample. In addition, Site 1037 was drilled to establish the character of the unaltered sedimentary sequence away from the hydrothermal centers of the Northern Escanaba Trough Study Area (NESCA). Mineralogy of the clay-size fraction of turbiditic and hemipelagic sediments of Hole 1037B are predominantly quartz, feldspar, pyroxene, illite, chlorite, and smectite, representing continental-derived material. Cores from Hole 1038I, located within the area of Central Hill but away from known active vent areas, recovered minor amounts of chlorite/smectite mixed-layer clay in the fine fraction, indicating a low-temperature hydrothermal alteration. The 137.4-m-thick sediment section of Hole 1038G is located in an area of low-temperature venting. The uppermost sample is classified as chlorite/smectite mixed layer, which is underlain by chlorite as the dominant mineral. The lowermost deposits of Hole 1038G are also characterized by chlorite/smectite mixed-layer clay. In comparison to Hole 1038I, the mineralogic sequence of Hole 1038G reflects increased chloritization. Intensely altered sediment is almost completely replaced by hydrothermal chlorite in subsurface sediments of Hole 1038H. Alteration to chlorite is characterized by depletion in Na, K, Ti, Ca, Sr, Cs, and Tl and enrichment in Ba. Further, Eu depletion reflects a high-temperature plagioclase alteration. A chlorite 18O value of 2.6 indicates formation at a temperature of ~190°C. It is concluded that the authigenic chlorite in Hole 1038H formed by an active high-temperature fluid flow in the shallow subsurface.

Chemistry of smectite and volcanic glass of ODP Site 159-959

The Ocean Drilling Program (ODP) Site 959 was drilled in the northern border of the Côte d'Ivoire-Ghana Ridge at a water depth of 2100 m. Pleistocene total thickness does not exceed 20 m. Winnowing processes resulted in a low accumulation rate and notable stratigraphic hiatuses. During the Late Pleistocene, bottom circulation was very active and controlled laminae deposition (contourites) which increased the concentration of glauconitic infillings of foraminifera, and of volcanic glass and blue-green grains more rarely, with one or several subordinate ferromagnesian silicates. Volcanic glass generally was X-ray amorphous and schematically classified as basic to intermediate (44-60% SiO2). Opal-A or opal-CT suggested the beginning of the palagonitisation process, and previous smectitic deposits may have been eroded mechanically. The blue-green grains presented two main types of mineralogic composition: (1) neoformed K, Fe-smectite associated with zeolite (like phillipsite) and unequal amounts of quartz and anorthite; (2) feldspathic grains dominated by albite but including quartz, volcanic glass and smectites as accessory components. They were more or less associated with the volcanic glass. On the basis of their chemical composition, the genetic relationship between the blue-green grains and the volcanic glass seemed to be obvious although some heterogeneous grains seemed to be primary ignimbrite and not the result of glass weathering. The most reasonable origin of these pyroclastic ejecta would be explosive events from the Cameroon Volcanic Ridge, especially from the Sao Thome and Principe Islands and Mount Cameroon area. This is supported both by grain geochemistry and the time of volcanic activity, i.e. Pleistocene. After westward wind transport (some 1200 km) and ash fall-out, the subsequent winnowing by bottom currents controlled the concentration of the volcanic grains previously disseminated inside the hemipelagic sediment. Palagonitisation, and especially phillipsite formation, may result from a relatively rapid reaction during burial diagenesis (<1 m.y.), in deep-sea deposits at relatively low sedimentation rate. However, it cannot be excluded that the weathering had begun widely on the Cameroon Ridge before the explosive event.

Geochemistry and provenance of basaltic clasts within volcaniclastic debris flows at DSDP Site 89-585

Pebble-sized basaltic and glassy clasts were extracted from seamount-derived volcaniclastic debris flows and analyzed for various trace elements, including the rare earths, to determine their genetic relationships and provenance. All the clasts were originally derived from relatively shallow submarine lava flows prior to sedimentary reworking, and have undergone minor low-grade alteration. They are classified into three petrographic groups (A, B, and C) characterized by different phenocryst assemblages and variable abundances and ratios of incompatible elements. Group A (clast from Hole 585) is a hyaloclastite fragment which is olivine-normative and distinct from the other clasts, with incompatibleelement ratios characteristic of transitional or alkali basalts. Groups B and C (clasts from Hole 585A) are quartz-normative, variably plagioclase-clinopyroxene-olivine phyric tholeiites, all with essentially similar ratios of highly incompatible elements and patterns of enrichment in light rare earth elements (chrondrite-normalized). Variation within Groups B and C was governed by low-pressure fractionation of the observed phenocryst phases, whereas the most primitive compositions of each group may be related by variable partial melting of a common source. The clasts have intraplate chemical characteristics, although relative to oceanic hot-spot-related volcanics (e.g., Hawaiian tholeiites) they are marginally depleted in most incompatible elements. The source region was enriched in all incompatible elements, compared with a depleted mid-ocean-ridge basalt source.

Palynology of ODP Site 108-658

Ocean Drilling Program Site 658 at 21°N off northwest Africa has a high sedimentation rate and a high concentration of pollen grains and is thus very suitable for detailed pollen analysis. The time scale for the upper 100 m (the last 670 k.y.) of Site 658 is based on biostratigraphic data and isotope stratigraphy. The pollen record has been divided into 34 zones. These are classified into 7 zone types covering a range from very arid to rather humid conditions. The sequence shows a long-term climatic decline: strong glacial stages were found only after 480 k.y. and strong interglacial stages only before 280 k.y. The Site 658 record correlates well with a terrestrial sequence from northern Greece, although both records differ in their response to global climatic change. Spectral analysis shows a 100- and a 42-k.y. period in the curves of pollen brought in by the northwest trade winds and only a 42-k.y. period in the curves of pollen mostly transported by the African Easterly Jet. A 31-k.y. period is found in the curves for Ephedra and Chenopodiaceae-Amaranthaceae. In addition, Ephedra shows a 54-k.y. period.

Field evaluation of a novel colorimetric method - Double-site enzyme-linked lactate dehydrogenase immunodetection assay - To determine drug susceptibilities of Plasmodium falciparum clinical isolates from northwestern Thailand

A double-site enzyme-linked lactate dehydrogenase enzyme inummodetection assay was tested against field isolates of Plasmodium falciparum for assessing in vitro drug susceptibilities to a wide range of antimalarial drugs. Its sensitivity allowed the use of parasite densities as low as 200 parasites/mul of blood. Being a nonisotopic, colorimetric assay, it lies within the capabilities of a modest laboratory at the district level.

Randomized, controlled trial of topical exit-site application of honey (Medihoney) versus Mupirocin for the prevention of catheter-associated infections in hemodialysis patients

The clinical usefulness of hemodialysis catheters is limited by increased infectious morbidity and mortality. Topical antiseptic agents, such as mupirocin, are effective at reducing this risk but have been reported to select for antibiotic-resistant strains. The aim of the present study was to determine the efficacy and the safety of exit-site application of a standardized antibacterial honey versus mupirocin in preventing catheter-associated infections. A randomized, controlled trial was performed comparing the effect of thrice-weekly exit-site application of Medihoney versus mupirocin on infection rates in patients who were receiving hemodialysis via tunneled, cuffed central venous catheters. A total of 101 patients were enrolled. The incidences of catheter-associated bacteremias in honey-treated (n = 51) and mupirocin-treated (n = 50) patients were comparable (0.97 versus 0.85 episodes per 1000 catheter-days, respectively; NS). On Cox proportional hazards model analysis, the use of honey was not significantly associated with bacteremia-free survival (unadjusted hazard ratio, 0.94; 95% confidence interval, 0.27 to 3.24; P = 0.92). No exit-site infections occurred. During the study period, 2% of staphylococcal isolates within the hospital were mupirocin resistant. Thrice-weekly application of standardized antibacterial honey to hemodialysis catheter exit sites was safe, cheap, and effective and resulted in a comparable rate of catheter-associated infection to that obtained with mupirocin (although the study was not adequately powered to assess therapeutic equivalence). The effectiveness of honey against antibiotic-resistant microorganisms and its low likelihood of selecting for further resistant strains suggest that this agent may represent a satisfactory alternative means of chemoprophylaxis in patients with central venous catheters.

Why H Atom Prefers the On-Top Site and Alkali Metals Favor the Middle Hollow Site on the Basal Plane of Graphite

In this work, the different adsorption properties of H and alkali metal atoms on the basal plane of graphite are studied and compared using a density functional method on the same model chemistry level. The results show that H prefers the on-top site while alkali metals favor the middle hollow site of graphite basal plane due to the unique electronic structures of H, alkali metals, and graphite. H has a higher electronegativity than carbon, preferring to form a covalent bond with C atoms, whereas alkaline metals have lower electronegativity, tending to adsorb on the highest electrostatic potential sites. During adsorption, there are more charges transferred from alkali metal to graphite than from H to graphite.

Molecular characterization and cancer risk associated with BRCA1 and BRCA2 splice site variants identified in multiple-case breast cancer families

Genetic screening of women from multiple-case breast cancer families and other research-based endeavors have identified an extensive collection of germline variations of BRCA1 and BRCA2 that can be classified as deleterious and have clinical relevance. For some variants, such as those in the conserved intronic splice site regions which are highly likely to alter splicing, it is not possible to classify them based on the identified DNA sequence variation alone. We studied 11 multiple-case breast cancer families carrying seven distinct splice site region genetic alterations in BRCA1 or BRCA2 (BRCA1, c.IVS6-2delA, c.IVS9-2A>C, c.IVS4-1G>T, c.IVS20+1G>A and BRCA2, c.IVS17-1G>C, c.IVS20+1G>A, c.IVS7-1G>A) and applied SpliceSiteFinder to predict possible changes in efficiency of splice donor and acceptor sites, characterized the transcripts, and estimated the average age-specific cumulative risk (penetrance) using a modified segregation analysis. SpliceSiteFinder predicted and we identified transcipts that illustrated that all variants caused exon skipping, and all but two led to frameshifts. The risks of breast cancer to age 70 yrs, averaged over all variants, over BRCA1 variants alone, and over BRCA2 variants alone, were 73% (95% confidence interval 47-93), 64% (95%CI 28-96) and 79% (95%CI 48-98) respectively (all P

Site-directed mutagenesis and kinetic studies of the West Nile virus NS3 protease identify key enzyme-substrate interactions

The flavivirus West Nile virus (WNV) has spread rapidly throughout the world in recent years causing fever, meningitis, encephalitis, and fatalities. Because the viral protease NS2B/NS3 is essential for replication, it is attracting attention as a potential therapeutic target, although there are currently no antiviral inhibitors for any flavivirus. This paper focuses on elucidating interactions between a hexapeptide substrate (Ae-KPGLKR-p-nitroanilide) and residues at S1 and S2 in the active site of WNV protease by comparing the catalytic activities of selected mutant recombinant proteases in vitro. Homology modeling enabled the predictions of key mutations in VWNV NS3 protease at S1 (V115A/F, D129A/ E/N, S135A, Y150A/F, S160A, and S163A) and S2 (N152A) that might influence substrate recognition and catalytic efficiency. Key conclusions are that the substrate P1 Arg strongly interacts with S1 residues Asp-129, Tyr-150, and Ser-163 and, to a lesser extent, Ser-160, and P2 Lys makes an essential interaction with Asn-152 at S2. The inferred substrate-enzyme interactions provide a basis for rational protease inhibitor design and optimization. High sequence conservation within flavivirus proteases means that this study may also be relevant to design of protease inhibitors for other flavivirus proteases.

Adsorption of carbon tetrachloride on graphitized thermal carbon black and in slit graphitic pores: Five-site versus one-site potential models

The performance of intermolecular potential models on the adsorption of carbon tetrachloride on graphitized thermal carbon black at various temperatures is investigated. This is made possible with the extensive experimental data of Machin and Ross(1), Avgul et al.,(2) and Pierce(3) that cover a wide range of temperatures. The description of all experimental data is only possible with the allowance for the surface mediation. If this were ignored, the grand canonical Monte Carlo (GCMC) simulation results would predict a two-dimensional (2D) transition even at high temperatures, while experimental data shows gradual change in adsorption density with pressure. In general, we find that the intermolecular interaction has to be reduced by 4% whenever particles are within the first layer close to the surface. We also find that this degree of surface mediation is independent of temperature. To understand the packing of carbon tetrachloride in slit pores, we compared the performance of the potential models that model carbon tetrachloride as either five interaction sites or one site. It was found that the five-site model performs better and describes the imperfect packing in small pores better. This is so because most of the strength of fluid-fluid interaction between two carbon tetrachloride molecules comes from the interactions among chlorine atoms. Methane, although having tetrahedral shape as carbon tetrachloride, can be effectively modeled as a pseudospherical particle because most of the interactions come from carbon-carbon interaction and hydrogen negligibly contributes to this.

Testing predictions of macroscopic binary diffusion coefficients using lattice models with site heterogeneity

Quantitatively predicting mass transport rates for chemical mixtures in porous materials is important in applications of materials such as adsorbents, membranes, and catalysts. Because directly assessing mixture transport experimentally is challenging, theoretical models that can predict mixture diffusion coefficients using Only single-component information would have many uses. One such model was proposed by Skoulidas, Sholl, and Krishna (Langmuir, 2003, 19, 7977), and applications of this model to a variety of chemical mixtures in nanoporous materials have yielded promising results. In this paper, the accuracy of this model for predicting mixture diffusion coefficients in materials that exhibit a heterogeneous distribution of local binding energies is examined. To examine this issue, single-component and binary mixture diffusion coefficients are computed using kinetic Monte Carlo for a two-dimensional lattice model over a wide range of lattice occupancies and compositions. The approach suggested by Skoulidas, Sholl, and Krishna is found to be accurate in situations where the spatial distribution of binding site energies is relatively homogeneous, but is considerably less accurate for strongly heterogeneous energy distributions.