H-induced platelet and crack formation in hydrogenated epitaxial Si/Si0.98 B0.02 /Si structures

An approach to transfer a high-quality Si layer for the fabrication of silicon-on-insulator wafers has been proposed based on the investigation of platelet and crack formation in hydrogenated epitaxialSi/Si0.98B0.02/Si structures grown by molecular-beam epitaxy. H-related defect formation during hydrogenation was found to be very sensitive to the thickness of the buried Si0.98B0.02 layer. For hydrogenated Si containing a 130nm thick Si0.98B0.02 layer, no platelets or cracking were observed in the B-doped region. Upon reducing the thickness of the buried Si0.98B0.02 layer to 3nm, localized continuous cracking was observed along the interface between the Si and the B-doped layers. In the latter case, the strains at the interface are believed to facilitate the (100)-oriented platelet formation and (100)-oriented crack propagation.

A preliminary evaluation of a novel method to monitor a triple antioxidant combination (vitamins E, C and alpha-lipoic acid) in diabetic volunteers using in vitro methaemoglobin formation

Eight otherwise healthy diabetic volunteers took a daily antioxidant supplement consisting of vitamin E (200 IU), vitamin C (250 mg) and α-lipoic acid (90 mg) for a period of 6 weeks. Diabetic dapsone hydroxylamine-mediated methaemoglobin formation and resistance to erythrocytic thiol depletion was compared with age and sex-matched non-diabetic subjects. At time zero, methaemoglobin formation in the non-diabetic subjects was greater at all four time points compared with that of the diabetic subjects. Resistance to glutathione depletion was initially greater in non-diabetic compared with diabetic samples. Half-way through the study (3 weeks), there were no differences between the two groups in methaemoglobin formation and thiol depletion in the diabetic samples was now lower than the non-diabetic samples at 10 and 20 min. At 6 weeks, diabetic erythrocytic thiol levels remained greater than those of non-diabetics. HbA1c values were significantly reduced in the diabetic subjects at 6 weeks compared with time zero values. At 10 weeks, 4 weeks after the end of supplementation, the diabetic HbA1c values significantly increased to the point where they were not significantly different from the time zero values. Total antioxidant status measurement (TAS) indicated that diabetic plasma antioxidant capacity was significantly improved during antioxidant supplementation. Conversion of α-lipoic acid to dihydrolipoic acid (DHLA) in vivo led to potent interference in a standard fructosamine assay kit, negating its use in this study. This report suggests that triple antioxidant therapy in diabetic volunteers attenuates the in vitro experimental oxidative stress of methaemoglobin formation and reduces haemoglobin glycation in vivo. © 2003 Elsevier Science B.V. All rights reserved.

A smart micro-drill for cochleostomy formation:a comparison of cochlear disturbances with manual drilling and a human trial

Background: Cochleostomy formation is a key stage of the cochlear implantation procedure. Minimizing the trauma sustained by the cochlea during this step is thought to be a critical feature in hearing preservation cochlear implantation. The aim of this paper is firstly, to assess the cochlea disturbances during manual and robotic cochleostomy formation. Secondly, to determine whether the use of a smart micro-drill is feasible during human cochlear implantation. Materials and methods: The disturbances within the cochlea during cochleostomy formation were analysed in a porcine specimen by creating a third window cochleostomy, preserving the underlying endosteal membrane, on the anterior aspect of the basal turn of the cochlea. A laser vibrometer was aimed at this third window, to assess its movement while a traditional cochleostomy was performed. Six cochleostomies were performed in total, three manually and three with a smart micro-drill. The mean and peak membrane movement was calculated for both manual and smart micro-drill arms, to represent the disturbances sustained within cochlea during cochleostomy formation. The smart micro-drill was further used to perform live human robotic cochleostomies on three adult patients who met the National Institute of Health and Clinical Excellence criteria for undergoing cochlear implantation. Results: In the porcine trial, the smart micro-drill preserved the endosteal membrane in all three cases. The velocity of movement of the endosteal membrane during manual cochleostomy is approximately 20 times higher on average and 100 times greater in peak velocity, than for robotic cochleostomy. The robot was safely utilized in theatre in all three cases and successfully created a bony cochleostomy while preserving the underlying endosteal membrane. Conclusions: Our experiments have revealed that controlling the force of drilling during cochleostomy formation and opening the endosteal membrane with a pick will minimize the trauma sustained by the cochlea by a factor of 20. Additionally, the smart micro-drill can safely perform a bony cochleostomy in humans under operative conditions and preserve the integrity of the underlying endosteal membrane. © W. S. Maney & Son Ltd 2013.

Role of Pseudomonas aeruginosa mifSR Two-Component System in Antibiotic Resistance and Biofilm Formation

Pseudomonas aeruginosa is an opportunistic pathogen found in a wide variety of environments. It is one of the leading causes of morbidity and mortality in cystic fibrosis patients, and one of the main sources of nosocomial infections in the United States. One of the most prominent features of this pathogen is its wide resistance to antibiotics. P. aeruginosa employs a variety of mechanisms including efflux pumps and the expression of B-lactamases to overcome antibiotic treatment. Two chromosomally encoded lactamases, ampC and poxB, have been identified in P. aeruginosa. Sequence analyses have shown the presence of a two-component system (TCS) called MifSR (MifS-Sensor and MifR-Response Regulator), immediately upstream of the poxAB operon. It is hypothesized that the MifSR TCS is involved in B-lactam resistance via the regulation of poxB. Recently, the response regulator MifR has been reported to play a crucial role in biofilm formation, a major characteristic of chronic infections and increased antibiotic resistance. In this study, mifR and mifSR deletion mutants were constructed, and compared to the wild type parent strain PAOl for differences in growth and B-lactam sensitivity. Results obtained thus far indicate that mifR and mifSR are not essential for growth, and do not confer B-lactam resistance under the conditions tested. This study is significant because biofilm formation and antibiotic resistance are two hallmarks of P. aeruginosa infections, and finding a link between these two may lead to the development of improved treatment strategies.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Role of metalliferous mudstones and graphitic shales in the location, genesis, and paleoenvironment

The Cambrian Tally Pond volcanic belt in central Newfoundland contains numerous volcanogenic massive sulphide (VMS) deposits, prospects, and showings that are locally associated with metalliferous mudstones and/or graphitic shales. Deposits in the belt are bimodal felsic-type VMS that are both base metal- (e.g., Duck Pond, Boundary) and precious metal-enriched (e.g., Lemarchant). At the Lemarchant deposit metalliferous mudstones are genetically and spatially associated with mineralization, whereas the relationship of other mudstones and shales to massive sulphide mineralization is more intricate and remains not fully understood. Metalliferous mudstones represent a hiatus in the volcanic activity where the deposition of hydrothermal products dominated over the abiogenic background sedimentation and/or dilution by volcaniclastic-epiclastic material. Lithogeochemical signatures allow one to distinguish between predominantly hydrothermally or detritally (i.e., non-hydrothermal) derived material. Metalliferous mudstones with a significant hydrothermal component, like those at Lemarchant, have elevated Fe/Al and base-metal contents, compared to detrital shales, and shale-normalized negative Ce and positive Eu anomalies, indicative of deposition from high temperature (>250°C) hydrothermal fluids within an oxygenated water column. Mudstones and shales sampled from other locations in the Tally Pond volcanic belt have more variable signatures ranging from hydrothermal (signatures as above) to non-hydrothermal (no positive Eu-anomalies, flat REE patterns), with some that have mixed (hydrothermal and detrital) signatures. Both S and Pb isotopic compositions indicate that proximal sulphides hosted in mudstones immediately associated with massive sulphide mineralization within the Lemarchant deposit contain a higher proportion of sulphur derived from hydrothermal sources and processes, and have more juvenile lead contributions, when compared to sulphides distal (not associated with massive sulphides) from mineralization. Lead and Nd isotopic compositions of both whole rock and minerals in the Lemarchant mudstones indicate involvement of underlying crustal basement during massive sulphide formation and throughout the evolution of the Tally Pond belt. Metalliferous mudstones precipitated early in the massive sulphide depositional history, but also have undergone syn- and post-ore-forming processes and have a larger lateral extent than the mineralization. Using lithogeochemistry, whole rock and in situ stable and radiogenic isotopes it is possible to distinguish prospective vent proximal (immediately associated with massive sulphide mineralization) from less prospective distal (not associated with massive sulphides) depositional environments and to reconstruct the paleotectonic setting on a deposit- to regional-scale for the Lemarchant deposit and other mudstone-associated prospects in the Tally Pond volcanic belt.

X-ray diffraction analysis, binocular component analysis and radiocarbon dating of sediment cores from the NW Iberian shelf system

Based on a well-established stratigraphic framework and 47 AMS-14C dated sediment cores, the distribution of facies types on the NW Iberian margin is analysed in response to the last deglacial sea-level rise, thus providing a case study on the sedimentary evolution of a high-energy, low-accumulation shelf system. Altogether, four main types of sedimentary facies are defined. (1) A gravel-dominated facies occurs mostly as time-transgressive ravinement beds, which initially developed as shoreface and storm deposits in shallow waters on the outer shelf during the last sea-level lowstand; (2) A widespread, time-transgressive mixed siliceous/biogenic-carbonaceous sand facies indicates areas of moderate hydrodynamic regimes, high contribution of reworked shelf material, and fluvial supply to the shelf; (3) A glaucony-containing sand facies in a stationary position on the outer shelf formed mostly during the last-glacial sea-level rise by reworking of older deposits as well as authigenic mineral formation; and (4) A mud facies is mostly restricted to confined Holocene fine-grained depocentres, which are located in mid-shelf position. The observed spatial and temporal distribution of these facies types on the high-energy, low-accumulation NW Iberian shelf was essentially controlled by the local interplay of sediment supply, shelf morphology, and strength of the hydrodynamic system. These patterns are in contrast to high-accumulation systems where extensive sediment supply is the dominant factor on the facies distribution. This study emphasises the importance of large-scale erosion and material recycling on the sedimentary buildup during the deglacial drowning of the shelf. The presence of a homogenous and up to 15-m thick transgressive cover above a lag horizon contradicts the common assumption of sparse and laterally confined sediment accumulation on high-energy shelf systems during deglacial sea-level rise. In contrast to this extensive sand cover, laterally very confined and maximal 4-m thin mud depocentres developed during the Holocene sea-level highstand. This restricted formation of fine-grained depocentres was related to the combination of: (1) frequently occurring high-energy hydrodynamic conditions; (2) low overall terrigenous input by the adjacent rivers; and (3) the large distance of the Galicia Mud Belt to its main sediment supplier.

Seismic reflection data, calcium/iron ratios, stable istopes, and magnetic susceptibility of sediment cores from the Pen Duick Escarpment, Gulf of Cadiz

Here we present a case study of three cold-water coral mounds in a juvenile growth stage on top of the Pen Duick Escarpment in the Gulf of Cadiz; Alpha, Beta and Gamma mounds. Although cold-water corals are a common feature on the adjacent cliffs, mud volcanoes and open slope, no actual living cold-water coral has been observed. This multidisciplinary and integrated study comprises geophysical, sedimentological and (bio)geochemical data and aims to present a holistic view on the interaction of both environmental and geological drivers in cold-water coral mound development in the Gulf of Cadiz. Coring data evidences (past or present) methane seepage near the Pen Duick Escarpment. Several sources and pathways are proposed, among which a stratigraphic migration through uplifted Miocene series underneath the escarpment. The dominant morphology of the escarpment has influenced the local hydrodynamics within the course of the Pliocene, as documented by the emplacement of a sediment drift. Predominantly during post-Middle Pleistocene glacial episodes, favourable conditions were present for mound growth. An additional advantage for mound formation near the top of Pen Duick Escarpment is presented by seepage-related carbonate crusts which might have offered a suitable substrate for coral settling. The spatially and temporally variable character and burial stage of the observed open reef frameworks, formed by cold-water coral rubble, provides a possible model for the transition from cold-water coral reef patches towards juvenile mound. These rubble "graveyards" not only act as sediment trap but also as micro-habitat for a wide range of organisms. The presence of a fluctuating Sulphate-Methane Transition Zone has an important effect on early diagenetic processes, affecting both geochemical and physical characteristics, transforming the buried reef into a solid mound. Nevertheless, the responsible seepage fluxes seem to be locally variable. As such, the origin and evolution of the cold-water coral mounds on top of the Pen Duick Escarpment is, probably more than any other NE Atlantic cold-water coral mound province, located on the crossroads of environmental (hydrodynamic) and geological (seepage) pathways.

Dinocyst-derived sea-surface characteristics, palynomorph abundances, ice-rafted debris, and planktonic foraminifera abundances and d18O of the 35-41 ka BP interval of core MD99-2285

The last glacial millennial climatic events (i.e. Dansgaard-Oeschger and Heinrich events) constitute outstanding case studies of coupled atmosphere-ocean-cryosphere interactions. Here, we investigate the evolution of sea-surface and subsurface conditions, in terms of temperature, salinity and sea ice cover, at very high-resolution (mean resolution between 55 and 155 years depending on proxies) during the 35-41 ka cal BP interval covering three Dansgaard-Oeschger cycles and including Heinrich event 4, in a new unpublished marine record, i.e. the MD99-2285 core (62.69°N; -3.57s°E). We use a large panel of complementary tools, which notably includes dinocyst-derived sea-ice cover duration quantifications. The high temporal resolution and multiproxy approach of this work allows us to identify the sequence of processes and to assess ocean-cryosphere interactions occurring during these periodic ice-sheet collapse events. Our results evidence a paradoxical hydrological scheme where (i) Greenland interstadials are marked by a homogeneous and cold upper water column, with intensive winter sea ice formation and summer sea ice melting, and (ii) Greenland and Heinrich stadials are characterized by a very warm and low saline surface layer with iceberg calving and reduced sea ice formation, separated by a strong halocline from a less warm and saltier subsurface layer. Our work also suggests that this stadial surface/subsurface warming started before massive iceberg release, in relation with warm Atlantic water advection. These findings thus support the theory that upper ocean warming might have triggered European ice-sheet destabilization. Besides, previous paleoceanographic studies conducted along the Atlantic inflow pathways close to the edge of European ice-sheets suggest that such a feature might have occurred in this whole area. Nonetheless, additional high resolution paleoreconstructions are required to confirm such a regional scheme.

Substitutions in the glycogenin-1 gene are associated with the evolution of endothermy in sharks and tunas

We thank Sean Tracey and Jaime McAllister for supplying albacore and southern bluefin tuna samples, Eva Giacomello for collecting the skipjack tuna sample, Elena Sarropoulou for providing the Atlantic bonito assembly, Helen Hipperson for assistance in the lab, Barbara Block and Ziheng Yang for advice, the editors and reviewers for comments, and the Leverhulme Trust and BBSRC for funding

(Table T1) Geochemistry of calcium carbonate veins from ODP Holes 206-1256C and 206-1256D

Drilling a complete deep crustal section has been a primary yet elusive goal since the inception of scientific ocean drilling. In situ ocean crustal sections would contribute enormously to our understanding of the formation and subsequent evolution of the ocean crust, in particular the interplay between magmatic, hydrothermal, and tectonic processes. Ocean Drilling Program (ODP) Leg 206 was the first of a multileg project to drill an in situ crustal section that penetrated the gabbroic rocks of the Cocos plate (6°44.2'N, 91°56.1'W), which formed ~15 m.y. ago on the East Pacific Rise during a period of superfast spreading (>200 mm/yr) (Wilson, Teagle, Acton, et al., 2003, doi:10.2973/odp.proc.ir.206.2003). During Leg 206, the upper 500 m of basement was cored in Holes 1256C and 1256D with moderate to high recovery rates. The igneous rocks recovered are predominantly thin (10 cm to 3 m) basalt flows separated by chilled margins. There are also several massive flows (>3 m thick), although their abundance decreases with depth in Hole 1256D, as well as minor pillow basalts, hyaloclastites, and rare dikes. The lavas have been slightly (<10%) altered by low-temperature hydrothermal fluids, which resulted in pervasive dark gray background alteration and precipitation of saponite, pyrite, silica, celadonite, and calcium carbonate veins. Here we present a geochemical analysis of the CaCO3 recovered from cores. The compositions of ridge flank fluids within superfast spreading crust will be determined from these data, following the approach of Hart et al. (1994, doi:10.1029/93JB02035), Yatabe et al. (2000, doi:10.2973/odp.proc.sr.168.003.2000), and Coggon et al. (2004, doi:10.1016/S0012-821X(03)00697-6).

Chlorine concentrations and stable isotope ratios in Izu Bonin tephra

d37Cl values were determined for Izu Bonin arc magmas erupted 0-44 Ma in order to better understand the time-dependent processing of volatiles in subduction zones. Pristine ash-sized particles (glass, pumice, scoria, and rock fragments) were handpicked from tephra drilled at ODP Site 782. d37Cl values for these particles span a large range from -2.1 to +1.7 per mil (error = ± 0.3 per mil) vs. SMOC (Standard Mean Ocean Chloride, defined as 0 per mil). The temporal data extend the previously reported range of d37Cl values of -2.6 to 0.4 per mil (bulk ash) and -5.4 to -0.1 per mil (volcanic gases) from the Quaternary Izu Bonin-Mariana volcanic front to more positive values. Overall, the temporal data indicate a time-progressive evolution, from isotopically negative Eocene and Oligocene magmas (-0.7 ± 1.1 per mil, n = 10) to Neogene magmas that have higher ?37Cl values on average (+0.3 ± 1.1 per mil; n = 13). The increase is due to the emergence of positive d37Cl values in the Neogene, while minimum d37Cl values are similar through time. The range in d37Cl values cannot be attributed to fractionation during melt formation and differentiation, and must reflect the diversity of Cl present in the arc magma sources. Cl clearly derives from the slab (> 96% Cl in arc magmas), but d37Cl values do not correlate with isotope tracers (e.g. 207Pb/204Pb and 87Sr/86Sr) that are indicative of the flux from subducting sedimentary and igneous crust. Given the steady, high Cl flux since at least 42 Ma, the temporal variability of d37Cl values is best explained by a flux from subducting isotopically positive and negative serpentinite formed in the ocean basins that mingles with and possibly overprints the isotopically negative flux from sediment and igneous crust at arc front depths. The change in the d37Cl values before and after backarc spreading may reflect either a tectonically induced change in the mechanism of serpentinite formation on the oceanic plate, or possibly the integration of isotopically positive wedge serpentinite as arc fluid source during the Neogene. Our study suggests that serpentinites are important fluid sources at arc front depth, and implies the return of isotopically positive and negative Cl from the Earth surface to the mantle.

Fossil associations from the middle and upper Eocene strata of the Pamplona Basin and surrounding areas (Navarre, western Pyrenees)

Fossil associations from the middle and upper Eocene (Bartonian and Priabonian) sedimentary succession of the Pamplona Basin are described. This succession was accumulated in the western part of the South Pyrenean peripheral foreland basin and extends from deep-marine turbiditic (Ezkaba Sandstone Formation) to deltaic (Pamplona Marl, Ardanatz Sandstone and Ilundain Marl formations) and marginal marine deposits (Gendulain Formation). The micropalaeontological content is high. It is dominated by foraminifera, and common ostracods and other microfossils are also present. The fossil ichnoasssemblages include at least 23 ichnogenera and 28 ichnospecies indicative of Nereites, Cruziana, Glossifungites and ?Scoyenia-Mermia ichnofacies. Body macrofossils of 78 taxa corresponding to macroforaminifera, sponges, corals, bryozoans, brachiopods, annelids, molluscs, arthropods, echinoderms and vertebrates have been identified. Both the number of ichnotaxa and of species (e. g. bryozoans, molluscs and condrichthyans) may be considerably higher. Body fossil assemblages are comparable to those from the Eocene of the Nord Pyrenean area (Basque Coast), and also to those from the Eocene of the west-central and eastern part of South Pyrenean area (Aragon and Catalonia). At the European scale, the molluscs assemblages seem endemic from the Pyrenean area, although several Tethyan (Italy and Alps) and Northern elements (Paris basin and Normandy) have been recorded. Palaeontological data of studied sedimentary units fit well with the shallowing process that throughout the middle and late Eocene occurs in the area, according to the sedimentological and stratigraphical data.

Evolution of the diatoms: major steps in their evolution and a review of the supporting molecular and morphological evidence.

Over the years, many reviews of different aspects of diatom biology, ecology and evolution have appeared. Since 1993 many molecular trees have been produced to infer diatom phylogeny. In 2004, Medlin & Kaczmarska revised the systematics of the diatoms based on more than 20 years of consistent recovery of two major clades of diatoms that did not correspond to a traditional concept of centrics and pennates and established three classes of diatoms: Clade 1 = Coscinodiscophyceae (radial centrics) and Clade 2 = Mediophyceae (polar centrics + radial Thalassiosirales) and Bacillariophyceae (pennates). However, under certain analytical conditions, an alternative view of diatom evolution, a grades of clades, has been recovered that suggests a gradual evolution from centric to pennate symmetry. These two schemes of diatom evolution are evaluated in terms of whether or not the criteria advocated by Medlin & Kaczmarska that should be met to recover monophyletic classes have been used. The monophyly of the three diatom classes can only be achieved if (1) a secondary structure of the small subunit (SSU) rRNA gene was used to construct the alignment and not an alignment based on primary structure and (2) multiple outgroups were used. These requirements have not been met in each study of diatom evolution; hence, the grade of clades, which is useful in reconstructing the sequence of evolution, is not useful for accepting the new classification of the diatoms. Evidence for how these two factors affect the recovery of the three monophyletic classes is reviewed here. The three classes have been defined by clear morphological differences primarily based on gametangia and auxospore ontogeny and envelope structure, the presence or absence of a structure (tube process or sternum) associated with the annulus and the location of the cribrum in those genera with loculate areolae. New evidence supporting the three clades is reviewed. Other features of the cell are examined to determine whether they can also be used to support the monophyly of the three classes.

Evolution of the diatoms: major steps in their evolution and a review of the supporting molecular and morphological evidence.

Over the years, many reviews of different aspects of diatom biology, ecology and evolution have appeared. Since 1993 many molecular trees have been produced to infer diatom phylogeny. In 2004, Medlin & Kaczmarska revised the systematics of the diatoms based on more than 20 years of consistent recovery of two major clades of diatoms that did not correspond to a traditional concept of centrics and pennates and established three classes of diatoms: Clade 1 = Coscinodiscophyceae (radial centrics) and Clade 2 = Mediophyceae (polar centrics + radial Thalassiosirales) and Bacillariophyceae (pennates). However, under certain analytical conditions, an alternative view of diatom evolution, a grades of clades, has been recovered that suggests a gradual evolution from centric to pennate symmetry. These two schemes of diatom evolution are evaluated in terms of whether or not the criteria advocated by Medlin & Kaczmarska that should be met to recover monophyletic classes have been used. The monophyly of the three diatom classes can only be achieved if (1) a secondary structure of the small subunit (SSU) rRNA gene was used to construct the alignment and not an alignment based on primary structure and (2) multiple outgroups were used. These requirements have not been met in each study of diatom evolution; hence, the grade of clades, which is useful in reconstructing the sequence of evolution, is not useful for accepting the new classification of the diatoms. Evidence for how these two factors affect the recovery of the three monophyletic classes is reviewed here. The three classes have been defined by clear morphological differences primarily based on gametangia and auxospore ontogeny and envelope structure, the presence or absence of a structure (tube process or sternum) associated with the annulus and the location of the cribrum in those genera with loculate areolae. New evidence supporting the three clades is reviewed. Other features of the cell are examined to determine whether they can also be used to support the monophyly of the three classes.