Phocine distemper virus (PDV) seroprevalence as predictor for future outbreaks in harbour seals.

PubMed

Ludes-Wehrmeister, Eva; Dupke, Claudia; Harder, Timm C; Baumgärtner, Wolfgang; Haas, Ludwig; Teilmann, Jonas; Dietz, Rune; Jensen, Lasse F; Siebert, Ursula

2016-02-01

Phocine distemper virus (PDV) infections caused the two most pronounced mass mortalities in marine mammals documented in the past century. During the two outbreaks, 23,000 and 30,000 harbour seals (Phoca vitulina), died in 1988/1989 and 2002 across populations in the Wadden Sea and adjacent waters, respectively. To follow the mechanism and development of disease spreading, the dynamics of Morbillivirus-specific antibodies in harbour seal populations in German and Danish waters were examined. 522 serum samples of free-ranging harbour seals of different ages were sampled between 1990 and 2014. By standard neutralisation assays, Morbillivirus-specific antibodies were detected, using either the PDV isolate 2558/Han 88 or the related canine distemper virus (CDV) strain Onderstepoort. A total of 159 (30.5%) of the harbour seals were seropositive. Annual seroprevalence rates showed an undulating course: Peaks were seen in the post-epidemic years 1990/1991 and 2002/2003. Following each PDV outbreak, seroprevalence decreased and six to eight years after the epidemics samples were tested seronegative, indicating that the populations are now again susceptible to new PDV outbreak. After the last outbreak in 2002, the populations grew steadily to an estimated maximum (since 1975) of about 39,100 individuals in the Wadden Sea in 2014 and about 23,540 harbour seals in the Kattegat area in 2013. A re-appearence of PDV would presumably result in another epizootic with high mortality rates as encountered in the previous outbreaks. The current high population density renders harbour seals vulnerable to rapid spread of infectious agents including PDV and the recently detected influenza A virus. Copyright © 2015 Elsevier B.V. All rights reserved.

Deciphering natural to anthropogenic control on sedimentation: the Late Holocene Magdala (Kinneret Lake, Israel) harbour hystory

NASA Astrophysics Data System (ADS)

Sarti, G.; Rossi, V.; Amorosi, A.; Bertoni, D.; Ribolini, A.; Sammartino, I.; Zanchetta, G.

2012-04-01

Using a multidisciplinary approach involving geologists, geomorphologists and archeologists, the late Holocene sedimentary succession buried beneath the ancient Magdala harbour area (Kinneret Lake, Israel) was studied, in order to highlight the strict relationships among harbour evolutive phases (e.g. foundation, siltation, abandonment), natural events (e.g. sea-level variations, climatic changes and earthquakes among the most important) and, obviously, archaeological history. Recent excavations performed within the "Magdala Project" have discovered a harbour structure with late Hellenistic-Roman mooring stones at altitudes of 208.100 m and 208.320 m bsl respectively, suggestive of a higher lake-level (about 212 m bsl) than previously hypothesized. Along the most representative sections of trenches, integrated sedimentological, micropalaeontological (benthic meiofauna and pollen) and geochemical analyses were carried out on sedimentary deposits underlying and overlying the harbour structures, to define the main depositional facies and evolution phases that took place during the last millennia. Spatial variability of coeval palaeoenvironments across the archaeological site allowed to reconstruct a comprehensive picture of the harbour complex, evidencing the occurrence of three main evolution phases, similar to those reported from several Mediterranean Sea harbour systems: 1) a pre-harbor foundation phase; 2) a sin-harbor activity phase and 3) an harbor-abandonment phase. The first phase corresponds to the development of a natural lacustrine sandy beach barren in archaeological remains and containing an ostracod fauna very similar to the one observed within the present-day lake basin at ca. 5 m water depth. The second phase was characterized by the formation of an early Hellenistic sheltered lacustrine basin, recording the first anthropogenic control exerted on coastal sedimentation by the construction of harbour structures ("anthropogenically forced sheltered basin

Detection and effects of harmful algal toxins in Scottish harbour seals and potential links to population decline.

PubMed

Jensen, Silje-Kristin; Lacaze, Jean-Pierre; Hermann, Guillaume; Kershaw, Joanna; Brownlow, Andrew; Turner, Andrew; Hall, Ailsa

2015-04-01

Over the past 15 years or so, several Scottish harbour seal (Phoca vitulina) populations have declined in abundance and several factors have been considered as possible causes, including toxins from harmful algae. Here we explore whether a link could be established between two groups of toxins, domoic acid (DA) and saxitoxins (STXs), and the decline in the harbour seal populations in Scotland. We document the first evidence that harbour seals are exposed to both DA and STXs from consuming contaminated fish. Both groups of toxins were found in urine and faeces sampled from live captured (n = 162) and stranded animals (n = 23) and in faecal samples collected from seal haul-out sites (n = 214) between 2008 and 2013. The proportion of positive samples and the toxins levels measured in the excreta were significantly higher in areas where harbour seal abundance is in decline. There is also evidence that DA has immunomodulatory effects in harbour seals, including lymphocytopenia and monocytosis. Scottish harbour seals are exposed to DA and STXs through contaminated prey at potentially lethal levels and with this evidence we suggest that exposure to these toxins are likely to be important factors driving the harbour seal decline in some regions of Scotland. Copyright © 2015 Elsevier Ltd. All rights reserved.

Stereotypical rapid source level regulation in the harbour porpoise biosonar

NASA Astrophysics Data System (ADS)

Linnenschmidt, Meike; Kloepper, Laura N.; Wahlberg, Magnus; Nachtigall, Paul E.

2012-09-01

Some odontocetes and bats vary both click intensity and receiver sensitivity during echolocation, depending on target range. It is not known how this so-called automatic gain control is regulated by the animal. The source level of consecutive echolocation clicks from a harbour porpoise was measured with a hydrophone array while the animal detected an aluminium cylinder at 2, 4 or 8 m distance in a go/no-go paradigm. On-axis clicks had source levels of 145-174 dB re 1 μPa peak-to-peak. During target-present trials the click trains reached comparable source levels independent of the range to the target after three clicks. After an additional click, the source level was reduced for the 2 and 4 m trials until it equalled the one-way transmission loss. During target-absent trials, the source level remained high throughout the entire click train. Given typical values of harbour porpoise inter-click intervals, the source level reduction commenced within a few 100 ms from the first click in the click train. This may indicate a sub-cortically regulated source level regulation in the harbour porpoise.

Stereotypical rapid source level regulation in the harbour porpoise biosonar.

PubMed

Linnenschmidt, Meike; Kloepper, Laura N; Wahlberg, Magnus; Nachtigall, Paul E

2012-09-01

Some odontocetes and bats vary both click intensity and receiver sensitivity during echolocation, depending on target range. It is not known how this so-called automatic gain control is regulated by the animal. The source level of consecutive echolocation clicks from a harbour porpoise was measured with a hydrophone array while the animal detected an aluminium cylinder at 2, 4 or 8 m distance in a go/no-go paradigm. On-axis clicks had source levels of 145-174 dB re 1 μPa peak-to-peak. During target-present trials the click trains reached comparable source levels independent of the range to the target after three clicks. After an additional click, the source level was reduced for the 2 and 4 m trials until it equalled the one-way transmission loss. During target-absent trials, the source level remained high throughout the entire click train. Given typical values of harbour porpoise inter-click intervals, the source level reduction commenced within a few 100 ms from the first click in the click train. This may indicate a sub-cortically regulated source level regulation in the harbour porpoise.

Understanding coastal processes to assist with coastal erosion management in Darwin Harbour, Northern Territory, Australia

NASA Astrophysics Data System (ADS)

Tonyes, S. G.; Wasson, R. J.; Munksgaard, N. C.; Evans, K. G.; Brinkman, R.; Williams, D. K.

2017-02-01

Sand transport pathways in Darwin Harbour, Northern Territory, Australia, are being investigated to assist with coastal management. Coastal erosion, which threatens public and private infrastructure, is one of the major problems along the harbour beaches. A study of sediment transport is essential to identify the challenges encountered by the stakeholders in coastal management. Darwin Harbour, located in the tropical, cyclone prone area of Australia, was, until recently, considered a near pristine estuary. A semi-diurnal macro-tidal embayment, the tidal variation in the harbour reaches up to 8 m with a mean tidal range of 3.7 m. The beach morphology consists of sandy pocket beaches between coastal cliffs, sandbars, rocky shore platforms, tidal flats and mangrove fringes. A two-dimensional depth averaged finite-element hydrodynamic model (RMA-2), coupled with a sediment transport model (RMA-11) from Resource Modelling Associates, has been used to infer the sources and the depositional areas of sand in the harbour. Grain size distributions and geochemical analysis are also used to characterize the sand and its source(s). Initial results show that the beach sand is mostly of offshore origin with small sand input from the rivers. Potential supplementary sand sources are the eroded materials from the shore platforms and the rocky cliffs. Due to the rapid development in Darwin Harbour, this study is fundamental in understanding coastal processes to support decision making in coastal management, particularly in a macro-tidal, tropical estuary.

Macro- and meiofaunal community features in the critical environmental system of a tourist harbour (Rapallo, Ligurian Sea, NW Mediterranean).

PubMed

Harriague, Anabella Covazzi; Albertelli, Giancarlo; Misic, Cristina

2012-03-01

Two samplings were carried out in a tourist harbour, during low and high touristic activity periods, to study the macro- and meiofaunal communities in relation to the environmental features. A multivariate analysis showed close relationships: the maritime traffic disturbance and the food quality and availability drive the spatial differences of the assemblages, dividing the area into three sub-areas: the area near the Boate torrent that empties into the harbour, the harbour proper, and the external area (just outside the harbour). Macro- and meiofauna showed notably different temporal trends, indicating competition for the resources and the higher sensitivity of the macrofauna to environmental pressures. The macrofauna strongly decreased as a response to heavier harbour activities, with increasing turbidity also affecting the external station outside the harbour. Finally, comparing the macrofaunal communities to those sampled in the same area 10 years before, we found that their abundance, richness and biomass had notably decreased, highlighting the worsening of the harbour environment due to the increased organic load and turbidity. Copyright © 2011 Elsevier Ltd. All rights reserved.

Year-round spatiotemporal distribution of harbour porpoises within and around the Maryland wind energy area

PubMed Central

O’Brien, Michael; Lyubchich, Vyacheslav; Roberts, Jason J.; Halpin, Patrick N.; Rice, Aaron N.; Bailey, Helen

2017-01-01

Offshore windfarms provide renewable energy, but activities during the construction phase can affect marine mammals. To understand how the construction of an offshore windfarm in the Maryland Wind Energy Area (WEA) off Maryland, USA, might impact harbour porpoises (Phocoena phocoena), it is essential to determine their poorly understood year-round distribution. Although habitat-based models can help predict the occurrence of species in areas with limited or no sampling, they require validation to determine the accuracy of the predictions. Incorporating more than 18 months of harbour porpoise detection data from passive acoustic monitoring, generalized auto-regressive moving average and generalized additive models were used to investigate harbour porpoise occurrence within and around the Maryland WEA in relation to temporal and environmental variables. Acoustic detection metrics were compared to habitat-based density estimates derived from aerial and boat-based sightings to validate the model predictions. Harbour porpoises occurred significantly more frequently during January to May, and foraged significantly more often in the evenings to early mornings at sites within and outside the Maryland WEA. Harbour porpoise occurrence peaked at sea surface temperatures of 5°C and chlorophyll a concentrations of 4.5 to 7.4 mg m-3. The acoustic detections were significantly correlated with the predicted densities, except at the most inshore site. This study provides insight into previously unknown fine-scale spatial and temporal patterns in distribution of harbour porpoises offshore of Maryland. The results can be used to help inform future monitoring and mitigate the impacts of windfarm construction and other human activities. PMID:28467455

Year-round spatiotemporal distribution of harbour porpoises within and around the Maryland wind energy area.

PubMed

Wingfield, Jessica E; O'Brien, Michael; Lyubchich, Vyacheslav; Roberts, Jason J; Halpin, Patrick N; Rice, Aaron N; Bailey, Helen

2017-01-01

Offshore windfarms provide renewable energy, but activities during the construction phase can affect marine mammals. To understand how the construction of an offshore windfarm in the Maryland Wind Energy Area (WEA) off Maryland, USA, might impact harbour porpoises (Phocoena phocoena), it is essential to determine their poorly understood year-round distribution. Although habitat-based models can help predict the occurrence of species in areas with limited or no sampling, they require validation to determine the accuracy of the predictions. Incorporating more than 18 months of harbour porpoise detection data from passive acoustic monitoring, generalized auto-regressive moving average and generalized additive models were used to investigate harbour porpoise occurrence within and around the Maryland WEA in relation to temporal and environmental variables. Acoustic detection metrics were compared to habitat-based density estimates derived from aerial and boat-based sightings to validate the model predictions. Harbour porpoises occurred significantly more frequently during January to May, and foraged significantly more often in the evenings to early mornings at sites within and outside the Maryland WEA. Harbour porpoise occurrence peaked at sea surface temperatures of 5°C and chlorophyll a concentrations of 4.5 to 7.4 mg m-3. The acoustic detections were significantly correlated with the predicted densities, except at the most inshore site. This study provides insight into previously unknown fine-scale spatial and temporal patterns in distribution of harbour porpoises offshore of Maryland. The results can be used to help inform future monitoring and mitigate the impacts of windfarm construction and other human activities.

Why do seals have cones? Behavioural evidence for colour-blindness in harbour seals.

PubMed

Scholtyssek, Christine; Kelber, Almut; Dehnhardt, Guido

2015-03-01

All seals and cetaceans have lost at least one of two ancestral cone classes and should therefore be colour-blind. Nevertheless, earlier studies showed that these marine mammals can discriminate colours and a colour vision mechanism has been proposed which contrasts signals from cones and rods. However, these earlier studies underestimated the brightness discrimination abilities of these animals, so that they could have discriminated colours using brightness only. Using a psychophysical discrimination experiment, we showed that a harbour seal can solve a colour discrimination task by means of brightness discrimination alone. Performing a series of experiments in which two harbour seals had to discriminate the brightness of colours, we also found strong evidence for purely scotopic (rod-based) vision at light levels that lead to mesopic (rod-cone-based) vision in other mammals. This finding speaks against rod-cone-based colour vision in harbour seals. To test for colour-blindness, we used a cognitive approach involving a harbour seal trained to use a concept of same and different. We tested this seal with pairs of isoluminant stimuli that were either same or different in colour. If the seal had perceived colour, it would have responded to colour differences between stimuli. However, the seal responded with "same", providing strong evidence for colour-blindness.

Modelling the tsunami threat to Sydney Harbour, Australia, with comparisons to historical events.

NASA Astrophysics Data System (ADS)

Wilson, O.; Power, H.

2016-12-01

Sydney Harbour is an iconic location with a dense population and low-lying development. On the east coast of Australia, facing the Pacific Ocean it is exposed to several tsunamigenic trenches. To date, this is the most detailed assessment of the potential for earthquake-generated tsunami impact on Sydney Harbour. The tsunami wave trains modelled include tsunami modelled from earthquakes of magnitude 7.5, 8.0, 8.5 and 9.0 MW from the Puysegur and New Hebrides trenches. Historical events from Chile in 1960 and Japan in 2011 are also modelled for comparison. Using the hydrodynamic model ANUGA, results show that the events modelled have the potential to cause high current speeds, hazardous waves and rapid changes in water level. These effects are most dramatic at pinch points such as Spit Bridge and Anzac Bridge, particularly with regard to current speeds. Large waves are shown to be a particular threat at the mouth of the harbour, where the bathymetry causes the tsunami wave train to shoal. Inundation is less of a hazard for the tsunami events modlled, although some inundation is evident at several low-lying embayments in the south of the harbour. These results will provide an evidence base for tsunami threat emergency management.

Wave and tidal level analysis, maritime climate change, navigation's strategy and impact on the costal defences - Study case of São Paulo State Coastline Harbour Areas (Brazil)

NASA Astrophysics Data System (ADS)

Alfredini, P.; Pezzoli, A.; Cristofori, E. I.; Dovetta, A.; Arasaki, E.

2012-04-01

São Paulo State Coastline Harbour Area concentrates around of 40% of Brazilian GNP, Santos Harbour is the America South Atlantic Hub Port and São Sebastião Oil Maritime Terminal is the most important oil and gas facility of PETROBRAS, the Brazilian National Petroleum Company. Santos Harbour had in the last decade increased rapidly the container handling rate, being the first in Latin America. In the last decade important oil and gas reserves were discovered in the Santos Oceanic Basin and São Paulo Coastline received a big demand for supplier ships harbours for the petroleum industry. Santos Metropolitan Region is one of the most important of Brazilian Coastline, also considering the turism. For that great economic growth scenario it is very important to have the main maritime hydrodynamics forcing processes, wave climate and tidal levels, well known, considering the sea hazards influence in ship operations. Since the hindcast just represents the deep water wave climate, to make time-series of the waves parameters in coastal waters, for evaluation of sea hazards and ship operations, it is necessary to take into acount the variations of those parameters in shallow waters with coastal instrumental data. Analysis of long term wave data-base (1957-2002) generated by a comparison between wave's data modeled by a "deep water model" (ERA40-ECMWF) and measured wave's data in the years 1982-1984 by a coastal buoy in Santos littoral (São Paulo State, Brazil) was made. Calibration coefficients according to angular sectors of wave's direction were obtained by the comparison of the instrument data with the modeled ones, and applied to the original scenarios. Validation checking procedures with instrumental measurements of storm surges made in other years than 1982-1984 shows high level of confidence. The analysis of the wave climate change on the extreme storm surge wave's conditions, selecting cases of Hs > 3,0 m, using that virtual data-base shows an increase in the Hs

Colistin-resistant Escherichia coli clinical isolate harbouring the mcr-1 gene in Ecuador.

PubMed

Ortega-Paredes, D; Barba, P; Zurita, J

2016-10-01

Colistin resistance mediated by the mcr-1 gene has been reported worldwide, but to date not from the Andean region, South America. We report the first clinical isolate of Escherichia coli harbouring the mcr-1 gene in Ecuador. The strain was isolated from peritoneal fluid from a 14-year-old male with acute appendicitis, and subjected to molecular analysis. The minimum inhibitory concentration of colistin for the strain was 8 mg/ml and it was susceptible to carbapenems but resistant to tigecycline. The strain harboured mcr-1 and bla CTX-M-55 genes and was of sequence type 609. The recognition of an apparently commensal strain of E. coli harbouring mcr-1 serves as an alert to the presence in the region of this recently described resistance mechanism to one of the last line of drugs available for the treatment of multi-resistant Gram-negative infections.

Detection and direction discrimination of single vortex rings by harbour seals (Phoca vitulina).

PubMed

Krüger, Yvonne; Hanke, Wolf; Miersch, Lars; Dehnhardt, Guido

2018-04-25

Harbour seals possess highly sensitive vibrissae that enable them to track hydrodynamic trails left behind by a swimming fish. Most of these trails contain vortex rings as a main hydrodynamic component. They may reveal information about their generator as the trails differ depending on the fish species, the fish's body shape, size and swimming style. In addition, fish generate single vortex rings in diverse natural situations. In this study, the ability of blindfolded stationary harbour seals to detect and analyse single vortex rings regarding directional information has been investigated. In three different behavioural experiments, the animals were trained to respond to single artificially generated vortex rings. The results show that harbour seals are able to respond to a variety of different vortex rings upon vibrissal stimulation. The investigation of the minimum hydrodynamically perceivable angle revealed that it is at least as small as 5.7 deg, which was the smallest adjustable angle. Moreover, harbour seals are capable of analysing the travel direction of a vortex ring perceived by the mystacial vibrissae irrespective of whether the vibrissae were stimulated ipsilaterally or contralaterally. In situations in which no complex hydrodynamic trail is available, it is advantageous for a hunting seal to be able to extract information from a single vortex ring. © 2018. Published by The Company of Biologists Ltd.

Geodetic infrastructure at the Barcelona harbour for sea level monitoring

NASA Astrophysics Data System (ADS)

Martinez-Benjamin, Juan Jose; Gili, Josep; Lopez, Rogelio; Tapia, Ana; Pros, Francesc; Palau, Vicenc; Perez, Begona

2015-04-01

The presentation is directed to the description of the actual geodetic infrastructure of Barcelona harbour with three tide gauges of different technologies for sea level determination and contribution to regional sea level rise and understanding past and present sea level rise in the Barcelona harbour. It is intended that the overall system will constitute a CGPS Station of the ESEAS (European Sea Level) and TIGA (GPS Tide Gauge Benchmark Monitoring) networks. At Barcelona harbour there is a MIROS radar tide gauge belonging to Puertos del Estado (Spanish Harbours).The radar sensor is over the water surface, on a L-shaped structure which elevates it a few meters above the quay shelf. 1-min data are transmitted to the ENAGAS Control Center by cable and then sent each 1 min to Puertos del Estado by e-mail. The information includes wave forescast (mean period, significant wave height, sea level, etc.This sensor also measures agitation and sends wave parameters each 20 min. There is a GPS station Leica Geosystems GRX1200 GG Pro and antenna AX 1202 GG. The Control Tower of the Port of Barcelona is situated in the North dike of the so-called Energy Pier in the Barcelona harbor (Spain). This tower has different kind of antennas for navigation monitoring and a GNSS permanent station. As the tower is founded in reclaimed land, and because its metallic structure, the 50 m building is subjected to diverse movements, including periodic fluctuations due to temperature changes. In this contribution the 2009, 2011, 2012, 2013 and 2014 the necessary monitoring campaigns are described. In the framework of a Spanish Space Project, the instrumentation of sea level measurements has been improved by providing the Barcelona site with a radar tide gauge Datamar 2000C from Geonica S.L. in June 2014 near an acoustic tide gauge from the Barcelona Harbour installed in 2013. Precision levelling has been made several times in the last two years because the tower is founded in reclaimed land and

Deep Biosphere Secrets of the Mediterranean Salt Giant

NASA Astrophysics Data System (ADS)

Aloisi, Giovanni; Lugli, Stefano; McGenity, Terry; Kuroda, Junichiro; Takai, Ken; Treude, Tina; Camerlenghi, Angelo

2015-04-01

One component of the IODP multi-platform drilling proposal called DREAM (Deep-Sea Record of Mediterranean Messisnian Events), plans to investigate the deep biosphere associated to the Messinian Salinity Crisis (MSC) Salt Giant. We propose that the MSC Salt Giant, because of the variety of chemical environments it produces, has the potential to harbour an unprecedented diversity of microbial life with exceptional metabolic activity. Gypsum and anhydrite deposits provide a virtually unlimited source of sulphate at depths where oxidants are a rarity in other sedimentary environments. When reduced organic carbon comes into contact with these minerals there is the potential for a dynamic deep biosphere community of sulphate reducers to develop, with implications for sedimentary biogeochemical cycles and the souring of cruide oil. But the thickness of the Messinian evaporites and the range of chemical environments it harbours poses fundamental questions: will the interaction of several extreme conditions of temperature, salinity, pressure and chemical composition limit the ability of microbes to take advantage of such favourable thermodynamic conditions? And has such a diverse set of physical and chemical environments fostered microbal diversity, rather than phylogenetic specialization, as recent research into deep Mediterranean brine systems seems to indicate ? Over three kilometres in thickness, approaching the known temperature limits of life and with fluids precipitating carbonate, sulphate, halite and potash salts, microbes living within and around the MSC Salt Giant will be subject to the most exotic combinations of extremes, and have likely evolved yet unknown adaptations. Gypsum and Halite crystals contain fluid inclusions that are a micro-habitat in which microbes survive for tens of thousands, to possibly millions, of years, posing the fundamental question of cells devoting nearly all of their energy flow to somatic maintenance needs, rather than growth and

Chemical tracers of shipping emissions in a Mediterranean harbour

NASA Astrophysics Data System (ADS)

Viana, M.; Amato, F.; Alastuey, A.; Querol, X.; Román, A.; García, M.

2009-04-01

Particle emissions from transport-related activities are known as one of the most important sources contributing to the PM mass concentrations in urban environments. However, only limited information is currently available in the literature on the contribution to PM levels by specific transport related sources such as shipping emissions, even though according to the latest IPCC report (Ribeiro et al., 2007), shipping emissions are receiving increased scrutiny by international and regional regulatory agencies because of their potential impact on air quality and human health in communities downwind from major shipping lanes and ports (Dominguez et al., 2008). One of the main reasons for this lack of information is the complexity in the detection of shipping emissions, given that no specific emission tracers have so far been identified as a consequence of the vast variability of combustion fuels burnt by vessels. The city of Melilla was selected for the study of shipping emissions due to its location on the South-Western sector of the Mediterranean basin, on the Northern coast of Morocco and less than 200 km from the Gibraltar Strait (35°17´40" N, 2°56´30" W). The city covers an extension of 13.4 km2, with a population of 70000 inhabitants. The monitoring station selected for the present study is representative of urban background levels, and it is located at approximately 150 m from the Melilla harbour. The harbour is mainly characterised by commercial traffic (passanger and container), although minerals and other loose materials are also stocked on the docks located farthest away from the monitoring site. PM10, PM2.5 and PM1 levels were determined on an hourly basis between 12/01/2008 and 19/12/2008 using a GRIMM laser spectrometer, which produced more than 8000 data points for each size fraction (24000 data points in total). In addition, PM10 and PM2.5 levels were sampled on quartz fibre filter substrates (Munktell) by means of high-volume samplers (PM1025 MCV

17. MARINA WAY, HARBOUR WAY, AND MARITIME CHILD DEVELOPMENT CENTER ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

17. MARINA WAY, HARBOUR WAY, AND MARITIME CHILD DEVELOPMENT CENTER (SEE ALSO HABS No. CA-2718), WITH RICHMOND SHIPYARD NO. 3. S. - Rosie the Riveter National Historical Park, 1401 Marina Way South, Richmond, Contra Costa County, CA

SITE DEMONSTRATION OF THE TORONTO HARBOUR COMMISSIONERS SOIL RECYCLING PROJECT

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA), in cooperation with the Toronto Harbour Commissioners (THC), conducted a Superfund InnovativeTechnology Evaluation (SITE) demonstration of the THC Soil Recycle Treatment Train. The treatment train consists of three technologies op...

Ancient harbour infrastructure in the Levant: tracking the birth and rise of new forms of anthropogenic pressure.

PubMed

Marriner, Nick; Morhange, Christophe; Kaniewski, David; Carayon, Nicolas

2014-07-03

Beirut, Sidon and Tyre were major centres of maritime trade from the Bronze Age onwards. This economic prosperity generated increased pressures on the local environment, through urbanization and harbour development. Until now, however, the impact of expanding seaport infrastructure has largely been neglected and there is a paucity of data concerning the environmental stresses caused by these new forms of anthropogenic impacts. Sediment archives from Beirut, Sidon and Tyre are key to understanding human impacts in harbour areas because: (i) they lie at the heart of ancient trade networks; (ii) they encompass the emergence of early maritime infrastructure; and (iii) they enable human alterations of coastal areas to be characterized over long timescales. Here we report multivariate analyses of litho- and biostratigraphic data to probe human stressors in the context of their evolving seaport technologies. The statistical outcomes show a notable break between natural and artificial sedimentation that began during the Iron Age. Three anchorage phases can be distinguished: (i) Bronze Age proto-harbours that correspond to natural anchorages, with minor human impacts; (ii) semi-artificial Iron Age harbours, with stratigraphic evidence for artificial reinforcement of the natural endowments; and (iii) heavy human impacts leading to completely artificial Roman and Byzantine harbours.

Ancient harbour infrastructure in the Levant: tracking the birth and rise of new forms of anthropogenic pressure

PubMed Central

Marriner, Nick; Morhange, Christophe; Kaniewski, David; Carayon, Nicolas

2014-01-01

Beirut, Sidon and Tyre were major centres of maritime trade from the Bronze Age onwards. This economic prosperity generated increased pressures on the local environment, through urbanization and harbour development. Until now, however, the impact of expanding seaport infrastructure has largely been neglected and there is a paucity of data concerning the environmental stresses caused by these new forms of anthropogenic impacts. Sediment archives from Beirut, Sidon and Tyre are key to understanding human impacts in harbour areas because: (i) they lie at the heart of ancient trade networks; (ii) they encompass the emergence of early maritime infrastructure; and (iii) they enable human alterations of coastal areas to be characterized over long timescales. Here we report multivariate analyses of litho- and biostratigraphic data to probe human stressors in the context of their evolving seaport technologies. The statistical outcomes show a notable break between natural and artificial sedimentation that began during the Iron Age. Three anchorage phases can be distinguished: (i) Bronze Age proto-harbours that correspond to natural anchorages, with minor human impacts; (ii) semi-artificial Iron Age harbours, with stratigraphic evidence for artificial reinforcement of the natural endowments; and (iii) heavy human impacts leading to completely artificial Roman and Byzantine harbours. PMID:24989979

Ancient harbour infrastructure in the Levant: tracking the birth and rise of new forms of anthropogenic pressure

NASA Astrophysics Data System (ADS)

Marriner, Nick; Morhange, Christophe; Kaniewski, David; Carayon, Nicolas

2014-07-01

Beirut, Sidon and Tyre were major centres of maritime trade from the Bronze Age onwards. This economic prosperity generated increased pressures on the local environment, through urbanization and harbour development. Until now, however, the impact of expanding seaport infrastructure has largely been neglected and there is a paucity of data concerning the environmental stresses caused by these new forms of anthropogenic impacts. Sediment archives from Beirut, Sidon and Tyre are key to understanding human impacts in harbour areas because: (i) they lie at the heart of ancient trade networks; (ii) they encompass the emergence of early maritime infrastructure; and (iii) they enable human alterations of coastal areas to be characterized over long timescales. Here we report multivariate analyses of litho- and biostratigraphic data to probe human stressors in the context of their evolving seaport technologies. The statistical outcomes show a notable break between natural and artificial sedimentation that began during the Iron Age. Three anchorage phases can be distinguished: (i) Bronze Age proto-harbours that correspond to natural anchorages, with minor human impacts; (ii) semi-artificial Iron Age harbours, with stratigraphic evidence for artificial reinforcement of the natural endowments; and (iii) heavy human impacts leading to completely artificial Roman and Byzantine harbours.

Towards ecosystem based management and monitoring of the deep Mediterranean, North-East Atlantic and Beyond

NASA Astrophysics Data System (ADS)

Grehan, Anthony J.; Arnaud-Haond, Sophie; D'Onghia, Gianfranco; Savini, Alessandra; Yesson, Chris

2017-11-01

The deep sea covers 65% of the earth's surface and 95% of the biosphere but only a very small fraction (less than 0.0001%) of this has been explored (Rogers et al., 2015; Taylor and Roterman, 2017). However, current knowledge indicates that the deep ocean is characterized by a high level of biodiversity and by the presence of important biological and non-renewable resources. As well as vast flat and muddy plains, the topography of the deep ocean contains a variety of complex and heterogeneous seafloor features, such as canyons, seamounts, cold seeps, hydrothermal vents and biogenic (deep-water coral) reefs and sponge bioherms that harbour an unquantified and diverse array of organisms. The deep sea, despite its remoteness, provides a variety of supporting, provisioning, regulating and cultural, ecosystem goods and services (Thurber et al., 2014). The recent push for 'Blue Growth', to unlock the potential of seas and oceans (European Commission, 2017) has increased the focus on the potential to exploit resources in the deep-sea and consequently the need for improved management (Thurber et al., 2014).

Comparing Distribution of Harbour Porpoises (Phocoena phocoena) Derived from Satellite Telemetry and Passive Acoustic Monitoring

PubMed Central

Rigét, Frank F.; Kyhn, Line A.; Sveegaard, Signe; Dietz, Rune; Tougaard, Jakob; Carlström, Julia A. K.; Carlén, Ida; Koblitz, Jens C.; Teilmann, Jonas

2016-01-01

Cetacean monitoring is essential in determining the status of a population. Different monitoring methods should reflect the real trends in abundance and patterns in distribution, and results should therefore ideally be independent of the selected method. Here, we compare two independent methods of describing harbour porpoise (Phocoena phocoena) relative distribution pattern in the western Baltic Sea. Satellite locations from 13 tagged harbour porpoises were used to build a Maximum Entropy (MaxEnt) model of suitable habitats. The data set was subsampled to one location every second day, which were sufficient to make reliable models over the summer (Jun-Aug) and autumn (Sep-Nov) seasons. The modelled results were compared to harbour porpoise acoustic activity obtained from 36 static acoustic monitoring stations (C-PODs) covering the same area. The C-POD data was expressed as the percentage of porpoise positive days/hours (the number of days/hours per day with porpoise detections) by season. The MaxEnt model and C-POD data showed a significant linear relationship with a strong decline in porpoise occurrence from west to east. This study shows that two very different methods provide comparable information on relative distribution patterns of harbour porpoises even in a low density area. PMID:27463509

Patterns of Occurrence of Sharks in Sydney Harbour, a Large Urbanised Estuary.

PubMed

Smoothey, Amy F; Gray, Charles A; Kennelly, Steve J; Masens, Oliver J; Peddemors, Victor M; Robinson, Wayne A

2016-01-01

Information about spatial and temporal variability in the distribution and abundance of shark-populations are required for their conservation, management and to update measures designed to mitigate human-shark interactions. However, because some species of sharks are mobile, migratory and occur in relatively small numbers, estimating their patterns of distribution and abundance can be very difficult. In this study, we used a hierarchical sampling design to examine differences in the composition of species, size- and sex-structures of sharks sampled with bottom-set longlines in three different areas with increasing distance from the entrance of Sydney Harbour, a large urbanised estuary. During two years of sampling, we obtained data for four species of sharks (Port Jackson, Heterodontus portusjacksoni; wobbegong, Orectolobus maculatus; dusky whaler, Carcharhinus obscurus and bull shark, Carcharhinus leucas). Only a few O. maculatus and C. obscurus were caught, all in the area closest to the entrance of the Harbour. O. maculatus were caught in all seasons, except summer, while C. obscurus was only caught in summer. Heterodontus portusjacksoni were the most abundant species, caught in the entrance location mostly between July to November, when water temperature was below 21.5°C. This pattern was consistent across both years. C. leucas, the second most abundant species, were captured in all areas of Sydney Harbour but only in summer and autumn when water temperatures were above 23°C. This study quantified, for this first time, how different species utilise different areas of Sydney Harbour, at different times of the year. This information has implications for the management of human-shark interactions, by enabling creation of education programs to modify human behaviour in times of increased risk of potentially dangerous sharks.

Patterns of Occurrence of Sharks in Sydney Harbour, a Large Urbanised Estuary

PubMed Central

Smoothey, Amy F.; Gray, Charles A.; Kennelly, Steve J.; Masens, Oliver J.; Peddemors, Victor M.; Robinson, Wayne A.

2016-01-01

Information about spatial and temporal variability in the distribution and abundance of shark-populations are required for their conservation, management and to update measures designed to mitigate human-shark interactions. However, because some species of sharks are mobile, migratory and occur in relatively small numbers, estimating their patterns of distribution and abundance can be very difficult. In this study, we used a hierarchical sampling design to examine differences in the composition of species, size- and sex-structures of sharks sampled with bottom-set longlines in three different areas with increasing distance from the entrance of Sydney Harbour, a large urbanised estuary. During two years of sampling, we obtained data for four species of sharks (Port Jackson, Heterodontus portusjacksoni; wobbegong, Orectolobus maculatus; dusky whaler, Carcharhinus obscurus and bull shark, Carcharhinus leucas). Only a few O. maculatus and C. obscurus were caught, all in the area closest to the entrance of the Harbour. O. maculatus were caught in all seasons, except summer, while C. obscurus was only caught in summer. Heterodontus portusjacksoni were the most abundant species, caught in the entrance location mostly between July to November, when water temperature was below 21.5°C. This pattern was consistent across both years. C. leucas, the second most abundant species, were captured in all areas of Sydney Harbour but only in summer and autumn when water temperatures were above 23°C. This study quantified, for this first time, how different species utilise different areas of Sydney Harbour, at different times of the year. This information has implications for the management of human-shark interactions, by enabling creation of education programs to modify human behaviour in times of increased risk of potentially dangerous sharks. PMID:26824349

Selective habituation shapes acoustic predator recognition in harbour seals.

PubMed

Deecke, Volker B; Slater, Peter J B; Ford, John K B

2002-11-14

Predation is a major force in shaping the behaviour of animals, so that precise identification of predators will confer substantial selective advantages on animals that serve as food to others. Because experience with a predator can be lethal, early researchers studying birds suggested that predator recognition does not require learning. However, a predator image that can be modified by learning and experience will be advantageous in situations where cues associated with the predator are highly variable or change over time. In this study, we investigated the response of harbour seals (Phoca vitulina) to the underwater calls of different populations of killer whales (Orcinus orca). We found that the seals responded strongly to the calls of mammal-eating killer whales and unfamiliar fish-eating killer whales but not to the familiar calls of the local fish-eating population. This demonstrates that wild harbour seals are capable of complex acoustic discrimination and that they modify their predator image by selectively habituating to the calls of harmless killer whales. Fear in these animals is therefore focused on local threats by learning and experience.

Recolonization of macrofauna in unpolluted sands placed in a polluted yachting harbour: A field approach using experimental trays

NASA Astrophysics Data System (ADS)

Guerra-García, J. M.; García-Gómez, J. C.

2009-01-01

A field experiment using trays was conducted at Ceuta's yachting harbour, North Africa, to study the effect in recolonization of placing trays with unpolluted defaunate sediments (fine and gross sands with low contents of organic matter) inside an enclosed yachting harbour characterized by high percentages of silt and clay and high concentrations of organic matter. Sediment recolonization in the trays was mainly undertaken by the species living naturally at the yachting harbour, which recolonized both uncontaminated gross and fine sand trays (such as the crustaceans Corophium runcicorne, Corophium sextonae and Nebalia bipes, the mollusc Parvicardium exiguum and the polychaete Pseudomalacoceros tridentata). However, other species like the polychaetes Cirriformia tentaculata and Platynereis dumerilii, although also abundant in the yachting harbour, were unable to colonize the trays through transport of larvae and/or adults in the water column. The recolonization was very quick, and after the first month, the values of abundance, species richness, diversity and evenness were similar in the experimental trays and in the reference area (yachting harbour). Although the multivariate analysis showed that the species composition differed between the trays and the reference area, there were no significant differences in recolonization of gross and fine sands, indicating that other factors different from the granulometry are modulating the recolonization patterns.

The ancient harbour system of Terracina (Latium, Italy) obtained by gravity survey.

NASA Astrophysics Data System (ADS)

di Nezza, M.; di Filippo, M.

2009-04-01

Historical research has shown that Terracina (Latina, Latium) played a fundamental role in the maritime and land traffic since before the foundation of the colony. The settlement was established where the organized system of maritime, land, coastal, and fluvial transport had the most ideal conditions to constitute an important commercial crossroads, apparently since the beginning of recorded history. In order to reconstruction the buried archaeological structures attributed to the ancient Roman port, traditionally attributed to Traiano, in the current area of the harbour of Terracina, it was carried out a gravity survey, more than 380 gravity stations. This method enables to recognize the cavity and the structures of the buildings underground through the results of variations density in the subsoil. In the residual gravity anomaly map a series of positive anomalies are visible which confirm the round structures and the pier of the buried foundations of the Imperial harbour. Unfortunately, little remains of the functioning facilities of the harbour's activities. The modern construction of the harbour, in fact, has to be developed around the new inhabitable commercial area, know today as Terracina Bassa or Borgo alla Marina. It had to be developed with a modern infrastructure of a harbor area, as in the construction of the rooms for storage of goods, warehouses, as well as for the thermal baths, hotels and amphitheatre. Furthermore, there are always the positive anomalies that characterize the area to the north-east of "Montone" hill where archaeological remains are easily visible near Via Lungolinea Pio VI. A large negative anomaly is situated in correspondence with "Montone". Gravity information shows an average density of the hill approximately 1.10 g/cm3, notably less than the recorded data relative to dry sand, approximately 1.6 g/cm3. The low value founds hits at the possibility of an "emptiness" in the subsoil of "Montone" hill, attribuiting to the possible

Early detection of potentially invasive invertebrate species in Mytilus galloprovincialis Lamarck, 1819 dominated communities in harbours

NASA Astrophysics Data System (ADS)

Preda, Cristina; Memedemin, Daniyar; Skolka, Marius; Cogălniceanu, Dan

2012-12-01

Constanţa harbour is a major port on the western coast of the semi-enclosed Black Sea. Its brackish waters and low species richness make it vulnerable to invasions. The intensive maritime traffic through Constanţa harbour facilitates the arrival of alien species. We investigated the species composition of the mussel beds on vertical artificial concrete substrate inside the harbour. We selected this habitat for study because it is frequently affected by fluctuating levels of temperature, salinity and dissolved oxygen, and by accidental pollution episodes. The shallow communities inhabiting it are thus unstable and often restructured, prone to accept alien species. Monthly samples were collected from three locations from the upper layer of hard artificial substrata (maximum depth 2 m) during two consecutive years. Ten alien macro-invertebrate species were inventoried, representing 13.5% of the total number of species. Two of these alien species were sampled starting the end of summer 2010, following a period of high temperatures that triggered hypoxia, causing mass mortalities of benthic organisms. Based on the species accumulation curve, we estimated that we have detected all benthic alien species on artificial substrate from Constanţa harbour, but additional effort is required to detect all the native species. Our results suggest that monitoring of benthic communities at small depths in harbours is a simple and useful tool in early detection of potentially invasive alien species. The selected habitat is easily accessible, the method is low-cost, and the samples represent reliable indicators of alien species establishment.

Assessing the importance of alien macro-Crustacea (Malacostraca) within macroinvertebrate assemblages in Belgian coastal harbours

NASA Astrophysics Data System (ADS)

Boets, Pieter; Lock, Koen; Goethals, Peter L. M.

2012-06-01

Harbours, which are often characterised by anthropogenic stress in combination with intensive international ship traffic, tend to be very susceptible to aquatic invasions. Since alien macrocrustaceans are known to be very successful across many European waters, a study was made on their distribution and impact in the four Belgian coastal harbours (Nieuwpoort, Ostend, Blankenberge and Zeebrugge). Biological and physical-chemical data were gathered at 43 sampling sites distributed along a salinity gradient in the four harbours. One-fourth of all crustacean species recorded were alien and represented on average 30% of the total macrocrustacean abundance and 65% of the total macrocrustacean biomass. The large share of alien crustaceans in the total macrocrustacean biomass was mainly due to several large alien crab species. Most alien species were found in the oligohaline zone, whereas the number of indigenous species slightly increased with increasing salinity. The low number of indigenous species present at low salinities was probably not only caused by salinity, but also by the lower water quality in this salinity range. Based on the site-specific biocontamination index (SBCI), which was used to assess the ecological water quality, the harbour of Nieuwpoort and Ostend scored best and were classified as good, indicating the limited abundance and the low number of alien macrocrustaceans. Sampling locations situated more inland generally had a higher SBCI and a lower ecological water quality. Zeebrugge and Blankenberge were characterised by a severe biocontamination. For Zeebrugge, this is probably related to the intensive transcontinental commercial ship traffic, whereas for Blankenberge, this could be due to introduction of alien species via recreational crafts or due to its geographical location in the proximity of Zeebrugge. Consistent monitoring of estuarine regions and harbours, which are seen as hotspots for introductions, could help in understanding and

Sustainable management of harbours : a numerical approach for the assessment of waters quality

NASA Astrophysics Data System (ADS)

Bonamano, Simone; Madonia, Alice; Piazzolla, Daniele; Paladini de Mendoza, Francesco; Piermattei, Viviana; Scanu, Sergio; Melchiorri, Cristiano; Marcelli, Marco

2017-04-01

Within the Water Framework Directive (WFD), harbours must reach or maintain the good ecological potential, being classified as heavily modified water bodies. To fulfill this task and to comply the Marine Spatial Planning (MSP) principles, port managers have to monitor the water quality that can be compromised by the numerous activities including the realization of new infrastructures. The port of Civitavecchia, located on the central west coast of Italy, is undergoing to major structural changes to become one of the first ports of the Mediterranean in terms of passenger traffic and goods, thus requiring the development of management tools for the predictive assessment of harbour water quality. This study focused on the evaluation of water degradation within Civitavecchia port trough the calculation of Flushing time (FT) and the development of the new Flushing Efficiency Index (FEI). FT was calculated through the use of a numerical model under different scenarios selected combining different weather conditions with the new port configurations. FT values was then used to estimate the FEI for the evaluation of the improvement (positive values) or the deterioration (negative values) of water quality in the different zones of the port. The increase in the harbour basin size due to the embankment extension results in high values of FT, particularly in the inner part of the port, in accordance with the highest values of the Enrichment Factor (EF) of the trace metals found in the sediment. The correlation between FT and EF confirms that renewal time can be used as a proxy to evaluate the water quality conditions in the harbour basin, as also stated by the WFD guidelines. Also the results of FEI calculation indicate the potential occurrence of water degradation due to the embankment extension. Otherwise, the realization of a second entrance in the southern part of Civitavecchia port produces FEI positive values, highlighting a drastic improvement in harbour water renewal

Biodiversity loss in seagrass meadows due to local invertebrate fisheries and harbour activities

NASA Astrophysics Data System (ADS)

Nordlund, Lina Mtwana; Gullström, Martin

2013-12-01

Seagrass meadows provide a wide variety of ecosystem services, but their distribution and health are adversely affected by man. In the present study, we examined the influence of coastal exploitation in terms of invertebrate harvesting and harbour activity on invertebrate community composition in subtropical seagrass meadows at Inhaca Island, Mozambique, in the Western Indian Ocean. There was a fivefold higher invertebrate density and biomass, and clearly higher invertebrate species richness, in the protected (control) site compared to the two exploited sites. The causes for the clear differences between protected and exploited sites were probably a result of (1) the directional outtake of large edible or saleable invertebrates (mostly molluscs) and the absence of boat traffic in the harvested site, and (2) harbour activities. Invertebrate community composition in the two exploited sites also differed (although less clear), which was likely due to inherent distinction in type of disturbance. Our findings revealed that protection of seagrass habitat is necessary and that disturbances of different origin might require different forms of management and conservation. Designing protected areas is however a complex process due to competition for use and space with activities such as invertebrate harvesting and harbours.

Sediment transport modelling based on grain size trend analysis in Augusta Harbour (Sicily)

NASA Astrophysics Data System (ADS)

Barbera, Giuseppe; Feo, Roberto; Freni, Gabriele

2015-12-01

To support marine civil engineer in pollutant studies, sediment management or dredging operations, is useful to know how the sediments move in accumulation basin. This paper investigates the dynamic of the sediment path using a two-dimensional numeric model: the Grain Size Trend Analysis (GSTA). The GSTA was applied using GiSedTrend plugin, under GIS software. The case study is the Augusta Harbour, which is one of the most polluted Italian harbours. It is the marine part of the Site of National Interest (SNI) of Priolo Gargallo (Siracusa, Italy) and it can be hydrodynamically considered as a lagoon. Two scenarios were obtained by using different geostatistical criteria.

Heartworm (Acanthocheilonema spirocauda) and seal louse (Echinophthirius horridus) infections in harbour seals (Phoca vitulina) from the North and Baltic Seas

NASA Astrophysics Data System (ADS)

Lehnert, Kristina; Schwanke, Eva; Hahn, Kerstin; Wohlsein, Peter; Siebert, Ursula

2016-07-01

The seal louse (Echinophthirius [E.] horridus) and the heartworm (Acanthocheilonema [A.] spirocauda) are parasites of harbour seal (Phoca vitulina). Little is known about the role of the seal louse as a potential vector and its role for the development and transmission of heartworm larvae to their final host, the harbour seal. The life-cycle of the heartworm is still not fully understood. For the presented study, findings of 1191 stranded harbour seals collected along the North- and Baltic Sea coast between 1996 and 2013 were examined. 4.4% (n = 53) of these harbour seals were infected with adult heartworms and 3.4% (n = 40) harbour seals carried seal lice. The highest prevalence and level of infection with adult heartworms (A. spirocauda) (9.3%) and seal lice (E. horridus) (8.9%) were found on yearling harbour seals (7-18 months) compared to neonate and adult seals. Investigating seal lice (n = 35) for larval heartworm stages one larvae was encountered in an ethanol-fixated seal louse. During a health monitoring survey of live harbour seals, 109 animals were captured and examined during spring and autumn between 2008 and 2014. Blood samples were taken and microfilariae were discovered in blood smears in 41% (n = 45) of the examined harbour seals. Yearling seals (n = 21) showed higher prevalence (86%) and level of infection with microfilariae than adults. Microfilariae were identified as A. spirocauda by sequencing the species-specific COI gene in 24 blood samples. The high prevalence of microfilariae of A. spirocauda in blood samples (41%) is in contrast to the low prevalence of mature infections/adult specimens in stranded seals (4.4%) investigated. Although rare parasites of seals, the recent increase in prevalence of heartworm and seal lice in stranded seals and the relatively high occurrence of microfilaria in the free-ranging population underscore the importance of further studies investigating the immunology of infections and their transmission pathways, as

Mitochondrial DNA reveals secondary contact in Japanese harbour seals, the southernmost population in the western Pacific

PubMed Central

Sasaki, Takeshi; Kobayashi, Mari; Haneda, Takayuki; Masubuchi, Takahito

2018-01-01

In this study, we used relatively large number of samples (n = 178) and control region of mtDNA (454bp) to clearify the divergence history of Japanese harbour seals (Phoca vitulina stejnegeri) and phylogenetic relationship between the seals in Japan and other countries. Our results suggested that Japanese harbour seals possibly consisted of more than two lineages and secondary contact of populations after a long isolation. Furthermore, one of the lineage was made only by Japanese harbour seals (Group P1). The proportion of Group P1 was the highest at the South West and gradually decreased towards the North East of Hokkaido, Japan. On the other hand, the haplotypes do not belonged to Group P1 showed close relationship to the seals in the North Pacific. Based on the fossil record of harbour seal in Japan and the range of sea ice during the Last Glacial Maximum (LGM), Group P1 might have entered Japan before the LGM and became isolated due to the geographical boundary, and gradually extended its range from the South West towards the North East of Hokkaido after the disappearance of the sea ice, while the seals which are not in Group P1 immigrated into Japan from the North Pacific. PMID:29385193

TORONTO HARBOUR COMMISSIONERS (THC) SOIL RECYCLE TREATMENT TRAIN - APPLICATIONS ANALYSIS REPORT

EPA Science Inventory

The Toronto Harbour Commissioners (THC) have developed a soil treatment train designed to treat inorganic and organic contaminants in soils. THC has conducted a large-scale demonstration of these technologies in an attempt to establish that contaminated soils at the Toronto Port ...

SITE DEMONSTRATION BULLETIN: SOIL RECYCLING TREATMENT TRAIN - THE TORONTO HARBOUR COMMISSIONERS

EPA Science Inventory

The Toronto Harbour Commissioners (THC) have developed a soil treatment train designed to treat inorganic and organic contaminants in soils. THC has conducted a large-scale demonstration of these technologies in an attempt to establish that contaminated soils at the Toronto Port...

The use of sequential extraction to evaluate the remediation potential of heavy metals from contaminated harbour sediment

NASA Astrophysics Data System (ADS)

Nystrøm, G. M.; Ottosen, L. M.; Villumsen, A.

2003-05-01

In this work sequential extraction is performed with harbour sediment in order to evaluate the electrodialytic remediation potential for harbour sediments. Sequential extraction was performed on a sample of Norwegian harbour sediment; with the original sediment and after the sediment was treated with acid. The results from the sequential extraction show that 75% Zn and Pb and about 50% Cu are found in the most mobile phases in the original sediment and more than 90% Zn and Pb and 75% Cu are found in the most mobile phase in the sediment treated with acid. Electrodialytic remediation experiments were made. The method uses a low direct current as cleaning agent, removing the heavy metals towards the anode and cathode according to the charge of the heavy metals in the electric field. The electrodialytic experiments show that up to 50% Cu, 85% Zn and 60% Pb can be removed after 20 days. Thus, there is still a potential for a higher removal, with some changes in the experimental set-up and longer remediation time. The experiments show that thc use of sequential extraction can be used to predict the electrodialytic remediation potential for harbour sediments.

Mortality and histopathological effects in harbour-transplanted snails with different exposure histories.

PubMed

Bighiu, Maria Alexandra; Watermann, Burkard; Guo, Xueli; Almroth, Bethanie Carney; Eriksson-Wiklund, Ann-Kristin

2017-09-01

Contaminants are important stressors in the aquatic environment and may exert selective pressures on organisms. We hypothesized that snails originating from a metal-contaminated habitat (B) would have increased tolerance to harbour contaminants (e.g. metals from antifouling paints), compared to snails originating from a relatively clean habitat (A). We assessed tolerance to metals in terms of survival and histopathological alterations after 2, 4 and 8 weeks of in situ exposure in three Baltic Sea boat harbours and three reference sites. We also hypothesized that any potential tolerance to contaminants would be associated with differences in genetic diversity between the two snail populations (evaluated as mitochondrial cytochrome c oxidase subunit I, COI). The results show that snails from population A survived to a higher extent compared to population B, possibly indicating either a lack of adaptation to metals in snails B or impaired health condition due to contaminant pre-exposure or a higher resilience of snails A. Moreover, the genetic diversity of COI was low within each population and did not differ between populations. In general, 83% of all the types of histopathological alterations (e.g. lysis and necrosis of gonads and digestive gland or granulocytoma and phagocytosis in the storage tissue, among others) had a higher probability of occurrence among harbour-exposed snails compared to reference-exposed snails, regardless of snail population origin. The only significant difference in histological effects between the two populations was in the frequency of parasite infestations and shell fouling, both being larger for population A than B. Interestingly, the rate of parasite infestations was higher for males than females from population A, whereas no sexual dichotomy was observed for population B. Our results show that exposure to harbour contaminants causes both lethal and sublethal toxicity to snails, and the association between many of the toxic responses

Implementation of CGPS at Estartit, Ibiza and Barcelona harbours for sea level monitoring

NASA Astrophysics Data System (ADS)

Martinez-Benjamin, J. J.; Ortiz Castellon, M.; Martinez-Garcia, M.; Perez, B.; Bosch, E.; Termens, A.; Martinez de Oses, X.

2009-12-01

The determination of global and regional mean sea level variations with accura-cies better than 1 mm/yr is a critical problem, the resolution of which is central to the current debate on climate change and its impact on the environment. Highly accurate time series from both satellite altimetry and tide gauges are needed. Measuring the sea surface height with in-situ tide gauges and GPS receivers pro-vides an efficient way to control the long term stability of the radar altimeters and other applications as the vertical land motion and studies of sea level change. L’Estartit tide gauge is a classical floating tide gauge set up in l’Estartit harbour (NE Spain) in 1990. Data are taken in graphics registers from which each two hours the mean value is recorded in an electronic support and delivered to the Permanent Service for Mean Sea level (PSMSL). Periodic surveying campaigns along the year are carried out for monitoring possible vertical movement of the geodetic benchmark adjacent to the tide gauge. Puertos del Estado (Spanish Harbours) installed the tide gauge station at Ibiza har-bour in January 2003 and a near GPS reference station. The station belongs to the REDMAR network, composed at this moment by 21 stations distributed along the whole Spanish waters, including also the Canary islands (http://www.puertos.es). The tide gauge also belongs to the ESEAS (European Sea Level) network. A description of the actual infrastructure at Ibiza, Barcelona and l’Estartit har-bours is presented.The main objective is the implementation of these harbours as a precise geodetic areas for sea level monitoring and altimeter calibration. Actually is a CGPS with a radar tide gauge from Puertos del Estado and a GPS belonging to Puerto de Barcelona. A precise levelling has been made by the Cartographic Insti-tute of Catalonia, ICC. The instrumentation of sea level measurements has been improved by providing the Barcelona site with a radar tide gauge Datamar 3000C device and a

A Method for Identifying Pollution Sources of Heavy Metals and PAH for a Risk-Based Management of a Mediterranean Harbour

PubMed Central

Moranda, Arianna

2017-01-01

A procedure for assessing harbour pollution by heavy metals and PAH and the possible sources of contamination is proposed. The procedure is based on a ratio-matching method applied to the results of principal component analysis (PCA), and it allows discrimination between point and nonpoint sources. The approach can be adopted when many sources of pollution can contribute in a very narrow coastal ecosystem, both internal and outside but close to the harbour, and was used to identify the possible point sources of contamination in a Mediterranean Harbour (Port of Vado, Savona, Italy). 235 sediment samples were collected in 81 sampling points during four monitoring campaigns and 28 chemicals were searched for within the collected samples. PCA of total samples allowed the assessment of 8 main possible point sources, while the refining ratio-matching identified 1 sampling point as a possible PAH source, 2 sampling points as Cd point sources, and 3 sampling points as C > 12 point sources. By a map analysis it was possible to assess two internal sources of pollution directly related to terminals activity. The study is the prosecution of a previous work aimed at assessing Savona-Vado Harbour pollution levels and suggested strategies to regulate the harbour activities. PMID:29270328

A Method for Identifying Pollution Sources of Heavy Metals and PAH for a Risk-Based Management of a Mediterranean Harbour.

PubMed

Paladino, Ombretta; Moranda, Arianna; Seyedsalehi, Mahdi

2017-01-01

A procedure for assessing harbour pollution by heavy metals and PAH and the possible sources of contamination is proposed. The procedure is based on a ratio-matching method applied to the results of principal component analysis (PCA), and it allows discrimination between point and nonpoint sources. The approach can be adopted when many sources of pollution can contribute in a very narrow coastal ecosystem, both internal and outside but close to the harbour, and was used to identify the possible point sources of contamination in a Mediterranean Harbour (Port of Vado, Savona, Italy). 235 sediment samples were collected in 81 sampling points during four monitoring campaigns and 28 chemicals were searched for within the collected samples. PCA of total samples allowed the assessment of 8 main possible point sources, while the refining ratio-matching identified 1 sampling point as a possible PAH source, 2 sampling points as Cd point sources, and 3 sampling points as C > 12 point sources. By a map analysis it was possible to assess two internal sources of pollution directly related to terminals activity. The study is the prosecution of a previous work aimed at assessing Savona-Vado Harbour pollution levels and suggested strategies to regulate the harbour activities.

Airborne emissions in the harbour and port of Cork.

PubMed

Sodeau, John R; Hellebust, Stig; Allanic, Arnaud; O'Connor, Ian; Healy, David A; Healy, Robert; Wenger, John

2009-07-01

It is now accepted that the transport sector is responsible for a large and growing share of global emissions affecting both health and climate. The quantification of these effects requires, as an essential first step, a comprehensive analysis and characterization of the contributing subsectors, i.e. road transport, shipping, aviation and rail. The shipping contribution in dock/harbour areas is of particular interest because many vessels use old engines powered with old technology giving rise to high levels of particulate emissions mainly because the fuel employed contains high levels of sulphur, up to 4.5%. Large amounts of polyaromatic hydrocarbons and varying contents of transition metals are also detected. Few studies on the physicochemical composition of direct emissions from ship fuels have been performed; none have been compared to actual contents in local harbour or port atmospheres. The transformation of these ship-related materials to toxicologically active species may be much more efficient than corresponding road emission or domestic sources because of the expected highly acidic nature of the particulates. Surface, toxic material may therefore become readily bioavailable under such conditions but such studies have not been performed hitherto. This mini-review outlines in detail the issues raised above in the context of measurements made in Cork, Ireland.

Identification of a novel gammaherpesvirus associated with (muco)cutaneous lesions in harbour porpoises (Phocoena phocoena).

PubMed

van Beurden, Steven J; IJsseldijk, Lonneke L; Ordonez, Soledad R; Förster, Christine; de Vrieze, Geert; Gröne, Andrea; Verheije, M Hélène; Kik, Marja

2015-12-01

Herpesviruses infect a wide range of vertebrates, including toothed whales of the order Cetacea. One of the smallest toothed whales is the harbour porpoise (Phocoena phocoena), which is widespread in the coastal waters of the northern hemisphere, including the North Sea. Here, we describe the detection and phylogenetic analysis of a novel gammaherpesvirus associated with mucocutaneous and skin lesions in stranded harbour porpoises along the Dutch coast, tentatively designated phocoenid herpesvirus 1 (PhoHV1). Phylogenetically, PhoHV1 forms a monophyletic clade with all other gammaherpesviruses described in toothed whales (Odontoceti) to date, suggesting a common evolutionary origin.

Removal of Historic Low-Level Radioactive Sediment from the Port Hope Harbour - 13314

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolberg, Mark; Case, Glenn; Ferguson Jones, Andrea

2013-07-01

At the Port Hope Harbour, located on the north shore of Lake Ontario, the presence of low-level radioactive sediment, resulting from a former radium and uranium refinery that operated alongside the Harbour, currently limits redevelopment and revitalization opportunities. These waste materials contain radium-226, uranium, arsenic and other contaminants. Several other on-land locations within the community of Port Hope are also affected by the low-level radioactive waste management practices of the past. The Port Hope Project is a community initiated undertaking that will result in the consolidation of an estimated 1.2 million cubic metres of the low-level radioactive waste from themore » various sites in Port Hope into a new engineered above ground long-term waste management facility. The remediation of the estimated 120,000 m{sup 3} of contaminated sediments from the Port Hope Harbour is one of the more challenging components of the Port Hope Project. Following a thorough review of various options, the proposed method of contaminated sediment removal is by dredging. The sediment from the dredge will then be pumped as a sediment-water slurry mixture into geo-synthetic containment tubes for dewatering. Due to the hard substrate below the contaminated sediment, the challenge has been to set performance standards in terms of low residual surface concentrations that are attainable in an operationally efficient manner. (authors)« less

A comparison of eutrophication impacts in two harbours in Hong Kong with different hydrodynamics

NASA Astrophysics Data System (ADS)

Xu, J.; Yin, K.; Liu, H.; Lee, J. H. W.; Anderson, D. M.; Ho, A. Y. T.; Harrison, P. J.

2010-11-01

Eutrophication impacts may vary spatially and temporally due to different physical processes. Using a 22-year time series data set (1986-2007), a comparison was made of eutrophication impacts between the two harbours with very different hydrodynamic conditions. Victoria Harbour (Victoria) receives sewage effluent and therefore nutrients are abundant. In the highly-flushed Victoria, the highest monthly average Chl a (13 μg L -1) occurred during the period of strongest stratification in summer as a result of rainfall, runoff and the input of the nutrient-rich Pearl River estuarine waters, but the high flushing rate restricted nutrient utilization and further accumulation of algal biomass. In other seasons, vertical mixing induced light limitation and horizontal dilution led to low Chl a (< 2 μg L -1) and no spring bloom. Few hypoxic events (DO < 2 mg L -1) occurred due to re-aeration and limited accumulation at depth due to flushing and vertical mixing. Therefore, Victoria is resilient to nutrient enrichment. In contrast, in the weakly-flushed Tolo Harbour (Tolo), year long stratification, long residence times and weak tidal currents favored algal growth, resulting in a spring diatom bloom and high Chl a (10-30 μg L -1) all year and frequent hypoxic events in summer. Hence, Tolo is susceptible to nutrient enrichment and responded to nutrient reduction after sewage diversion in 1997. Sewage diversion from Tolo resulted in a 32-38% decrease in algal biomass in Tolo, but not in Victoria. There has been a significant increase (11-22%) in bottom DO in both harbours. Our findings demonstrate that an understanding of the role of physical processes is critical in order to predict the effectiveness of sewage management strategies in reducing eutrophication impacts.

Pathology of finfish and mud crabs Scylla serrata during a mortality event associated with a harbour development project in Port Curtis, Australia.

PubMed

Dennis, M M; Diggles, B K; Faulder, R; Olyott, L; Pyecroft, S B; Gilbert, G E; Landos, M

2016-10-27

The objective of this study was to assess the extent and describe the nature of a multi-species marine finfish and crustacean disease event that occurred in Gladstone Harbour, Australia, 2011-2012. Finfish were examined for this study in January to April 2012 from sites where diseased animals were previously observed by the public. Gross abnormalities, including excessive skin and gill mucus, erythema, heavy ecto-parasitism, cutaneous ulceration, corneal opacity, and exophthalmos, were higher (25.5%) in finfish from Gladstone Harbour (n = 435) than in those from an undeveloped reference site, 250 km to the north (5.5%, n = 146, p < 0.0001). Microscopic abnormalities, especially non-infectious erosive to ulcerative dermatitis and internal parasitism, were more prevalent in fish from Gladstone Harbour (n = 34 of 36, prevalence = 94.4%) than in fish from the reference site (3 of 23, prevalence = 13.0% p < 0.0001). The prevalence of shell lesions was higher in mud crabs Scylla serrata sampled from Gladstone Harbour (270 of 718, prevalence = 37.5%) than from the reference site (21 of 153, prevalence = 13.7%; p < 0.0001). The significantly higher prevalence of ulcerative skin disease and parasitism in a range of species suggests affected animals were subjected to influences in Gladstone Harbour that were not present in the control sites. The disease epidemic coincided temporally and spatially with water quality changes caused by a harbour development project. The unique hydrology, geology, and industrial history of the harbour, the scope of the development of the project, and the failure of a bund wall built to retain dredge spoil sediment were important factors contributing to this epidemic.

Geodetic Infrastructure in the Ibiza and Barcelona Harbours for Sea Level Monitoring

NASA Astrophysics Data System (ADS)

Martinez-Benjamin, J. J.; Gili, J.; Lopez, R.; Tapia, A.; Perez, B.; Pros, F.

2013-12-01

The presentation is directed to the description of the actual situation and relevant information of the geodetic infrastructure of Ibiza and Barcelona sites for sea level determination and contribution to regional sea level rise. Time series are being analysed for mean sea level variations www.puertos.es. .In the framework of a Spanish Space Project, the instrumentation of sea level measurements has been improved by providing the Barcelona site with a radar tide gauge Datamar 2000C from Geonica s.l. near an acoustic tide gauge. Puertos del Estado installed in 2007 a MIROS radar tide gauge and the Barcelona Harbour Authority a GPS referente station in the roof of the new Control Tower situated in the Energy Pier. The radar sensor is over the water surface, on a L-shaped structure which elevates it a few meters above the quay shelf. 1-min data are transmitted to the ENAGAS Control Center by cable and then sent each 1 min to Puertos del Estado by e-mail. There is a GPS station Leica Geosystems GRX1200 GG Pro and antenna 1202. Precision levelling has been made several times in the last two years because the tower is founded in reclaimed land. The measured settlement rate is about 1cm/year that may be could mask the values registered by the tide gauge. A description of the actual infrastructure at Ibiza harbour at Marina de Botafoch, is presented and its applications to sea level monitoring and altimeter calibration in support of the main CGPS at Ibiza harbour. It is described the geometrical precision levelling made in June 2013 between the radar tide gauge and the GPS station. In particular, the CGPS located at Ibiza harbour is essential for its application to the marine campaign Baleares 2013, near Ibiza island. The main objective is to determine the altimeter bias for Jason-2, about 9:09 UTC September 15, 2013, and Saral/AltiKa, about 05:30 UTC September 16, UTC. These activities has been received funding of the Ministerio de Ciencia e Innovacion under Spanish

Charting the Development of Portsmouth Harbour, Dockyard and Town in the Tudor Period

NASA Astrophysics Data System (ADS)

Fontana, Dominic

2013-12-01

Portsmouth was crucial to the defence of Tudor England and consequently it was mapped for military planning purposes throughout the Tudor period from 1545. The resulting sequence of maps records much of the town and harbour. The maps offer opportunities for furthering our understanding of Tudor Portsmouth and its population Additionally, images of the urban landscape provided by the "Cowdray Engraving", which depicts the loss of Henry VIII's warship Mary Rose on the 19th July 1545, may also be considered and compared with those presented in the early maps of the town. This paper considers the Portsmouth maps of 1545, 1552, 1584 and the chart of Portsmouth Harbour dating from between 1586 and 1620. These are examined in relation to one another and compared with evidence from the Cowdray Engraving.

The Development and Characteristics of Ancient Harbours-Applying the PADM Chart to the Case Studies of Ostia and Portus.

PubMed

Salomon, Ferreol; Keay, Simon; Carayon, Nicolas; Goiran, Jean-Philippe

2016-01-01

Over the last 20 years, the geoarchaeology of ancient harbours has been a very active area of research around the Mediterranean basin, generating much palaeoenvironmental data from many sites, including estimations of sedimentation rates, the height of the ancient sea-level at different dates and palaeo-geographical reconstructions. Combining this information has proved a major challenge. This article proposes a new chart called the Palaeoenvironmental Age-Depth Model (PADM chart), that allows the researchers to combine all relevant indicators in order to estimate harbour potential of a given ancient port, and to generate comparable data between harbours in terms of degree of closure and water depth available against a synchronised chronology. This new approach, developed in the context of the ERC-funded RoMP Portuslimen project, takes into account estimations of water depths relating to differing Roman ship draughts at different periods. It is tested against the palaeoenvironmental evidence published over 10 years from two Roman harbours located at the mouth of the river Tiber: Ostia and Portus. This reveals that: (1) there has been an underestimate of the real sedimentation rates due to the margins of error of the radiocarbon dates; (2) there was effective control of the water column by dredging; (3) there were different periods of control of the sedimentation. We suggest that the navigability of the Ostia harbour by ships with shallower draughts was maintained until sometime between the 2nd c. BC and 1st c. AD, while at Portus it was retained until the 6th-7th c. AD.

Identification of potential fish carcinogens in sediment from Hamilton Harbour, Ontario, Canada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balch, G.C.; Metcalfe, C.D.; Huestis, S.Y.

1995-01-01

A carcinogenicity- and mutagenicity-directed fractionation approach was used to identify the carcinogenic compounds in contaminated sediments that are putatively responsible for the high prevalence of tumors in bottom-dwelling fish from Hamilton Harbour, Ontario. Mutagenic activity was detected with Ames tester strains (TA98, TA100) in relatively nonpolar fractions of sediment extract containing PAHs and nitrogen-containing aromatic compounds (NCACs). These fractions were also carcinogenic in an in vivo carcinogenicity bioassay with rainbow trout (Oncorhynchus mykiss). When a more polar extract fraction was tested for mutagenicity and carcinogenicity, weak mutagenic activity was detected with an O-acetyltransferase-enriched Ames tester strain (YG1024), and weak carcinogenicmore » activity was detected in the rainbow trout assay. These data indicate that PAHs in contaminated Hamilton Harbour sediments are potent fish carcinogens, but it is also evident that other organic compounds in the sediment, such as NCACs and nitroarenes, may contribute to carcinogenicity.« less

Seal dynamics on the Swedish west coast: Scenarios of competition as Baltic grey seal intrude on harbour seal territory

NASA Astrophysics Data System (ADS)

Svensson, Carl Johan

2012-07-01

The Kattegat-Skagerrak region on the Swedish west coast is home to an abundant harbour seal population (Phoca vitulina) and a small scattered grey seal population (Halichoerus grypus). In addition, grey seal from the growing population in the Baltic Sea frequently migrate into the Kattegat-Skagerrak. Harbour seals on the west coast of Sweden show relatively high population growth (approximately 9%) compared to the Baltic grey seal in ice-free habitats (approximately 6%), which, in theory, makes harbour seal the stronger competitor of the two in this region. However, incidents of disease in harbour seals that lower population growth are becoming more frequent. These epidemics are primarily caused by the Phocine Distemper Virus (PDV), and may reduce population size with up to 70%. This study models the average development under potential scenarios of competing harbour- and Baltic grey seal populations using Leslie matrices and the Lotka-Volterra model of inter-specific competition. The model is parameterised with previously published data, and resource overlap is incorporated through density dependent pup survival. Using numerical methods short- and long-term abundances are simulated under weak, moderate and strong competition and for different frequencies of PDV epidemics. Results show that the harbour seals are resilient to competition while exerting a negative effect on grey seal abundance under moderate to strong competition. Hence Baltic grey seal benefit from weaker levels of competition. Under moderate and strong competition grey seal abundance is a direct function of the PDV frequency as this reduces the competitive strength of harbour seals. Theoretically this means that higher frequencies of PDV or other pathogens epidemics could facilitate an expansion of Baltic grey seal into Kattegat-Skagerrak. Independent of interaction strength and frequency of epidemics the projected changes to abundances are slow (50-100 years), and even in exceedingly stable

TECHNOLOGY EVALUATION REPORT: TORONTO HARBOUR COMMISSIONERS (THC) SOIL RECYCLE TREATMENT TRAIN. Project Summary

EPA Science Inventory

A demonstration of the Toronto Harbour Commissioners' (THC) Soil Recycle Treatment Train was performed under the Superfund Innovative Technology Evaluation (SITE) Program at a pilot plant facility in Toronto, Ontario, Canada. The Soil Recycle Treatment Train, which consists of s...

Monitoring Sea Level by Tide Gauges and GPS at Barcelona and Estartit Harbours

NASA Astrophysics Data System (ADS)

Martinez Benjamin, J. J.; Gili, J.; Lopez, R.; Tapia, A.; Bosch, E.; Perez, B.; Pros, F.

2012-04-01

Sea level is an environmental variable which is widely recognised as being important in many scientific disciplines as a control parameter for coastal dynamical processes or climate processes in the coupled atmosphere-ocean systems, as well as engineering applications. A major source of sea-level data are the national networks of coastal tide gauges, in Spain belonging to different institutions as the Instituto Geográfico Nacional (IGN), Puertos del Estado (PE), Instituto Hidrográfico de la Marina (IHM), etc. The tide gauge of l'Estartit is a traditional floating gauge placed 21 years ago and has an accuracy of ± 2 mm. Since 1996, l'Estartit tide gauge has been co-located with geodetic techniques (GPS measurements of XU, Utilitary Network, and XdA, Levelling Network,) and it is tied to the SPGIC (Integrated Geodetic Positioning System of Catalonia) project of the Cartographic Institute of Catalunya (ICC). In 2006, due to the work for the expansion of the harbour, the tide gauge had to be moved. Before the work started, appropiate GPS measurements were carried out in order to ensure the connection of the tide gauge data. During October 2006 and May 2008, the tide gauge was inactive and it has been moved on to a new location inside the harbour. In June 2008, new GPS and levelling measures have been done in order to tie the new location into SPGIC project and to co-locate old data respect the new one. Although l'Estartit does not have a GPS permanent station, it is possible to build a virtual one from the service "CATNET web" of the ICC. "CATNET web" is a data distribution system of a virtual GPS permanent station via web. From the coordinates where you want to place the virtual station, the time interval and the measurement rate, the system generates a RINEX file under the requested conditions. At Barcelona harbour there is one MIROS radar tide gauge belonging to Puertos del Estado (Spanish Harbours). It is placed at the dock 140 of the ENAGAS Building.The radar

Applicability of market-based instruments for safeguarding water quality in coastal waterways: Case study for Darwin Harbour, Australia

NASA Astrophysics Data System (ADS)

Greiner, Romy

2014-02-01

Water pollution of coastal waterways is a complex problem due to the cocktail of pollutants and multiplicity of polluters involved and pollution characteristics. Pollution control therefore requires a combination of policy instruments. This paper examines the applicability of market-based instruments to achieve effective and efficient water quality management in Darwin Harbour, Northern Territory, Australia. Potential applicability of instruments is examined in the context of biophysical and economic pollution characteristics, and experience with instruments elsewhere. The paper concludes that there is potential for inclusion of market-based instruments as part of an instrument mix to safeguard water quality in Darwin Harbour. It recommends, in particular, expanding the existing licencing system to include quantitative pollution limits for all significant point polluters; comprehensive and independent pollution monitoring across Darwin Harbour; public disclosure of water quality and emissions data; positive incentives for landholders in the Darwin Harbour catchment to improve land management practices; a stormwater offset program for greenfield urban developments; adoption of performance bonds for developments and operations which pose a substantial risk to water quality, including port expansion and dredging; and detailed consideration of a bubble licensing scheme for nutrient pollution. The paper offers an analytical framework for policy makers and resource managers tasked with water quality management in coastal waterways elsewhere in Australia and globally, and helps to scan for MBIs suitable in any given environmental management situation.

Contribution of harbour activities to atmospheric aerosol in the Brindisi area

NASA Astrophysics Data System (ADS)

Donateo, Antonio; Cesari, Daniela; Nocioni, Alessandra; Grasso, Fabio M.; Merico, Eva; Giua, Roberto; Contini, Daniele

2013-04-01

The port areas are economic centres and transport hubs, that bring together different transport modes (sea, road, railway transport) and also industrial activities. Ship emissions when docked and during port manoeuvring can have a substantial negative effect on local air quality. The Fagerli and Tarrason (2001) simulation results indicated that ship traffic emissions contribute to 5% and 10% of PM10 concentrations in large parts of Great Britain, Portugal and Italy; similarly to what was obtained by Dalsoren et al. (2009). At the beginning of 2012 it was started the research project CESAPO (Contribution of Emission Sources on the Air quality of the POrt-cities in Greece and Italy), funded within the framework of Interreg Italy-Greece (2007/2013), having as objective the quantification of the contribution to atmospheric particles of emission sources in two important Mediterranean port-cities, namely Patra (Greece) and Brindisi (Italy). In this work the first results of the CESAPO project will be presented giving more emphasis on the analysis of the maritime transport and the activities within the harbour of Brindisi that is characterized by several emission sources operating concurrently. In 2010 and 2011, in the port of Brindisi freight traffic and total goods movement accounted for more than 9.5 million tons, with over 520,000 passengers. To recognize the contribution of harbour activities to PM2.5 and to the total number concentration of particles with respect to other emission sources (urban traffic and industrial pollution) it has been performed an intensive observation period (IOP) of 5 months (June 1 to October 31, 2012). During the IOP the data of 10 fixed monitoring stations (of the regional network managed by ARPA Puglia) and those from two additional stations specifically installed during the project inside the harbour area. A station was used to characterize the chemical composition of PM2.5 and PAHs (in the gaseous and aerosol phases) and the other was

Endoparasitic helminths of the harbour seal, Phoca vitulina, in the Netherlands

NASA Astrophysics Data System (ADS)

Borgsteede, F. H. M.; Bus, H. G. J.; Verplanke, J. A. W.; van Burg, W. P. J.

The endoparasitic helminth fauna of harbour seals which had died during the epidemic of the phocine distemper virus in 1988 was studied. Lungs, heart and gastrointestinal tracts of 94 animals collected along the Dutch coast were available for investigation. The following parasites and infection percentages were found: Nematoda: Dipetalonema spirocauda (24.5%), Otostrongylus circumlitus (6.4%), Parafilaroides gymnurus (24.5%), Ascaridoidea spec. (58.5%); Trematoda: Phagicola septentrionalis (66.0%), Cryptocotyle lingua (74.5%); Cestoda: Diphyllobothrium spec. (8.5%); Acanthocephala: Corynosoma strumosum (70.2%). The presence of worm species was not evenly distributed over the age classes. Seals younger than one year harboured fewer parasites. The highest percentages were found in 1 to 2 year old seals. The number of worms per seal varied greatly. The highest burden for ascarids was 253, for P. septentrionalis 123 000, for C. lingua 112 000 and for C. strumosum 251. A comparison of the present results with those described in the literature shows that in Dutch seals the same species were present and that numbers of worms were not higher than before the 1988 mass mortality. It is therefore concluded that helminth parasites did not cause the mass mortality.

[Asbestos import in Italy: the transit through Livorno harbour from 1957 to 1995].

PubMed

Nemo, Alessandro; Boccuzzi, Maria Teresa; Silvestri, Stefano

2009-01-01

This work aims to describe quantities, type of packaging and geographical area of origin of the asbestos fibres unloaded in Livorno harbour between 1957 and 1995. Historical data, available for this period, were collected from Il Messaggero Marittimo, a periodical journal dealing with Livorno harbour activities. Collaboration between the local Health and Safety Unit (ASL 6) and the Institute for Study and Prevention of Cancer (ISPO), both Regional Institutions of the National Health Service, made it possible to carry out this work. The computation of the collected data for the whole period allows the description of the quantities, year by year and the assessment of the percentage imported through Livorno on the total tonnage imported in Italy during the same period. The detection of the geographical areas of origin allowed to estimate the quantities subdivided by type of fibre (serpentine/amphiboles). These results will help the historical assessment of occupational asbestos exposure of the Livorno dockers.

Environmental impacts of iron ore tailings—The case of Tolo Harbour, Hong Kong

NASA Astrophysics Data System (ADS)

Wong, M. H.

1981-03-01

Disposal of iron ore tailings along the shore of Tolo Harbour, Hong Kong has altered the adjacent environment. Due to the ever-expanding population, the vast development of various industries, and the lack of sanitary control, the existing pollution problem of Tolo Harbour is serious. The iron ore tailings consist of a moderate amount of various heavy metals, e.g., copper, iron, manganese, lead, zinc, and a lower level of macronutrients. A few living organisms have been found colonizing this manmade habitat. Higher metal contents were also found in the tissue of Paphia sp. (clam); Scopimera intermedia (crab); Chaetomorpha brychagona (green alga); Enteromorpha crinita (green alga); and Neyraudia reynaudiana (grass). The area can be reclaimed by surface amelioration using inert materials, soils, or organic substrates, and by direct seeding, using nontolerant and tolerant plant materials. Reclamation of the tailings would improve the amenity of the adjacent environment and also mitigate pollution escaping to the sea.

Man and the Last Great Wilderness: Human Impact on the Deep Sea

PubMed Central

Ramirez-Llodra, Eva; Tyler, Paul A.; Baker, Maria C.; Bergstad, Odd Aksel; Clark, Malcolm R.; Escobar, Elva; Levin, Lisa A.; Menot, Lenaick; Rowden, Ashley A.; Smith, Craig R.; Van Dover, Cindy L.

2011-01-01

The deep sea, the largest ecosystem on Earth and one of the least studied, harbours high biodiversity and provides a wealth of resources. Although humans have used the oceans for millennia, technological developments now allow exploitation of fisheries resources, hydrocarbons and minerals below 2000 m depth. The remoteness of the deep seafloor has promoted the disposal of residues and litter. Ocean acidification and climate change now bring a new dimension of global effects. Thus the challenges facing the deep sea are large and accelerating, providing a new imperative for the science community, industry and national and international organizations to work together to develop successful exploitation management and conservation of the deep-sea ecosystem. This paper provides scientific expert judgement and a semi-quantitative analysis of past, present and future impacts of human-related activities on global deep-sea habitats within three categories: disposal, exploitation and climate change. The analysis is the result of a Census of Marine Life – SYNDEEP workshop (September 2008). A detailed review of known impacts and their effects is provided. The analysis shows how, in recent decades, the most significant anthropogenic activities that affect the deep sea have evolved from mainly disposal (past) to exploitation (present). We predict that from now and into the future, increases in atmospheric CO2 and facets and consequences of climate change will have the most impact on deep-sea habitats and their fauna. Synergies between different anthropogenic pressures and associated effects are discussed, indicating that most synergies are related to increased atmospheric CO2 and climate change effects. We identify deep-sea ecosystems we believe are at higher risk from human impacts in the near future: benthic communities on sedimentary upper slopes, cold-water corals, canyon benthic communities and seamount pelagic and benthic communities. We finalise this review with a short

Wave simulation for the design of an innovative quay wall: the case of Vlorë Harbour

NASA Astrophysics Data System (ADS)

Antonini, Alessandro; Archetti, Renata; Lamberti, Alberto

2017-01-01

Sea states and environmental conditions are basic data for the design of marine structures. Hindcasted wave data have been applied here with the aim of identifying the proper design conditions for an innovative quay wall concept. In this paper, the results of a computational fluid dynamics model are used to optimise the new absorbing quay wall of Vlorë Harbour (Republic of Albania) and define the design loads under extreme wave conditions. The design wave states at the harbour entrance have been estimated analysing 31 years of hindcasted wave data simulated through the application of WaveWatch III. Due to the particular geography and topography of the Bay of Vlorë, wave conditions generated from the north-west are transferred to the harbour entrance with the application of a 2-D spectral wave module, whereas southern wave states, which are also the most critical for the port structures, are defined by means of a wave generation model, according to the available wind measurements. Finally, the identified extreme events have been used, through the NewWave approach, as boundary conditions for the numerical analysis of the interaction between the quay wall and the extreme events. The results show that the proposed method, based on numerical modelling at different scales from macro to meso and to micro, allows for the identification of the best site-specific solutions, also for a location devoid of any wave measurement. In this light, the objectives of the paper are two-fold. First, they show the application of sea condition estimations through the use of wave hindcasted data in order to properly define the design wave conditions for a new harbour structure. Second, they present a new approach for investigating an innovative absorbing quay wall based on CFD modelling and the NewWave theory.

The harbour of Elaia: A palynological archive for human environmental interactions during the last 7500 years

NASA Astrophysics Data System (ADS)

Shumilovskikh, Lyudmila S.; Seeliger, Martin; Feuser, Stefan; Novenko, Elena; Schlütz, Frank; Pint, Anna; Pirson, Felix; Brückner, Helmut

2016-10-01

Elaia, the harbour city for ancient Pergamon (western Turkey), was investigated using geoarchaeological methods. The rise and fall of Elaia were closely linked to the flourishing period of Pergamon, which ruled wide parts of today's western Turkey in Hellenistic times. In the framework of this research, the palynological analysis of a 9 m sediment core, Ela-70, retrieved from the enclosed harbour of the city, was carried out to reconstruct the vegetation and environmental history of the wider Gulf of Elaia region. An age-depth model, based on 11 calibrated radiocarbon ages, starting from 7.5 ka BP, provides the basis for the high resolution study of sediments from the Hellenistic period, as well as before and after. The lower part of the pollen diagram is characterised by high percentages of deciduous oaks and pines, suggesting the dominance of open forests close to the coring site. The change from oak forests to a cultural landscape, with olive, pistachio, walnut, and grape, started around 850 BC, reaching a maximum ca. 250 BC, and continuing to ca. AD 800. This period is characterised by increase of fire activity, soil erosion intensity, and pastoral farming. Such long-lasting intensive land use likely led to the climax ecosystem turnover from open deciduous oak forests to pine stands, while salt marshes developed around the coring site. The discovery of the dinoflagellate cysts of Peridinium ponticum, a Black Sea endemic species, in the harbour of Elaia evidences maritime trade between the Aegean Sea and the Black Sea; its first occurrence coincides with the time of the Mithridatic Wars (1st century BC). In conclusion, palynological data, in addition to historical and archaeological records, provide a deeper insight into human environmental interactions, as derived from the geoarchaeological archive of the harbour of Elaia.

Hydrodynamic sensory threshold in harbour seals (Phoca vitulina) for artificial flatfish breathing currents.

PubMed

Niesterok, Benedikt; Dehnhardt, Guido; Hanke, Wolf

2017-07-01

Harbour seals have the ability to detect benthic fish such as flatfish using the water currents these fish emit through their gills (breathing currents). We investigated the sensory threshold in harbour seals for this specific hydrodynamic stimulus under conditions which are realistic for seals hunting in the wild. We used an experimental platform where an artificial breathing current was emitted through one of eight different nozzles. Two seals were trained to search for the active nozzle. Each experimental session consisted of eight test trials of a particular stimulus intensity and 16 supra-threshold trials of high stimulus intensity. Test trials were conducted with the animals blindfolded. To determine the threshold, a series of breathing currents differing in intensity was used. For each intensity, three sessions were run. The threshold in terms of maximum water velocity within the breathing current was 4.2 cm s -1 for one seal and 3.7 cm s -1 for the other. We measured background flow velocities from 1.8 to 3.4 cm s -1 Typical swimming speeds for both animals were around 0.5 m s -1 Swimming speed differed between successful and unsuccessful trials. It appears that swimming speed is restricted for the successful detection of a breathing current close to the threshold. Our study is the first to assess a sensory threshold of the vibrissal system for a moving harbour seal under near-natural conditions. Furthermore, this threshold was defined for a natural type of stimulus differing from classical dipole stimuli which have been widely used in threshold determination so far. © 2017. Published by The Company of Biologists Ltd.

Nematode assemblages in the deep-sea benthos of the Norwegian Sea

NASA Astrophysics Data System (ADS)

Jensen, Preben

1988-07-01

The deep-sea benthos of the Norwegian Sea contains 20-204 nematodes per 10 cm 2 down to 3 cm depth at seven stations sampled between 970 and 3294 m water depth. The majority of nematodes occur in the uppermost cm. Biomass varies from 3 to 73 μg C per 10 cm 2. Individual adult weight of the most dominant species differs by a factor of almost 1000, i.e. from 3-4 ng C to 3400 ng C; however, the majority of the nematodes is small-sized. Species diversity and evenness are high at all stations and each station harbours its specific fauna with little overlap between stations. Analysis of trophic group composition suggests that microbial feeding types (deposit and epistrate feeders) prevail in the deep-sea benthos; predators and scavengers are scarce. It is concluded that the nematode assemblage at each station consists of a mosaic of many microhabitats. The small nematode body weight probably results from limited food supply and/or poor food quality.

Do syntopic host species harbour similar symbiotic communities? The case of Chaetopterus spp. (Annelida: Chaetopteridae).

PubMed

Britayev, Temir A; Mekhova, Elena; Deart, Yury; Martin, Daniel

2017-01-01

To assess whether closely related host species harbour similar symbiotic communities, we studied two polychaetes, Chaetopterus sp. ( n  = 11) and Chaetopterus cf. appendiculatus ( n  = 83) living in soft sediments of Nhatrang Bay (South China Sea, Vietnam). The former harboured the porcellanid crabs Polyonyx cf. heok and Polyonyx sp., the pinnotherid crab Tetrias sp. and the tergipedid nudibranch Phestilla sp. The latter harboured the polynoid polychaete Ophthalmonoe pettiboneae , the carapid fish Onuxodon fowleri and the porcellanid crab Eulenaios cometes , all of which, except O. fowleri , seemed to be specialized symbionts. The species richness and mean intensity of the symbionts were higher in Chaetopterus sp. than in C. cf. appendiculatus (1.8 and 1.02 species and 3.0 and 1.05 individuals per host respectively). We suggest that the lower density of Chaetopterus sp. may explain the higher number of associated symbionts observed, as well as the 100% prevalence (69.5% in C. cf. appenciculatus ). Most Chaetopterus sp. harboured two symbiotic species, which was extremely rare in C. cf. appendiculatus , suggesting lower interspecific interactions in the former. The crab and nudibranch symbionts of Chaetopterus sp. often shared a host and lived in pairs, thus partitioning resources. This led to the species coexisting in the tubes of Chaetopterus sp., establishing a tightly packed community, indicating high species richness and mean intensity, together with a low species dominance. In contrast, the aggressive, strictly territorial species associated with C. cf. appendiculatus established a symbiotic community strongly dominated by single species and, thus, low species richness and mean intensity. Therefore, we suggest that interspecific interactions are determining species richness, intensity and dominance, while intraspecific interactions are influencing only intensity and abundance. It is possible that species composition may have influenced the differences in

Do syntopic host species harbour similar symbiotic communities? The case of Chaetopterus spp. (Annelida: Chaetopteridae)

PubMed Central

Britayev, Temir A.; Mekhova, Elena; Deart, Yury

2017-01-01

To assess whether closely related host species harbour similar symbiotic communities, we studied two polychaetes, Chaetopterus sp. (n = 11) and Chaetopterus cf. appendiculatus (n = 83) living in soft sediments of Nhatrang Bay (South China Sea, Vietnam). The former harboured the porcellanid crabs Polyonyx cf. heok and Polyonyx sp., the pinnotherid crab Tetrias sp. and the tergipedid nudibranch Phestilla sp. The latter harboured the polynoid polychaete Ophthalmonoe pettiboneae, the carapid fish Onuxodon fowleri and the porcellanid crab Eulenaios cometes, all of which, except O. fowleri, seemed to be specialized symbionts. The species richness and mean intensity of the symbionts were higher in Chaetopterus sp. than in C. cf. appendiculatus (1.8 and 1.02 species and 3.0 and 1.05 individuals per host respectively). We suggest that the lower density of Chaetopterus sp. may explain the higher number of associated symbionts observed, as well as the 100% prevalence (69.5% in C. cf. appenciculatus). Most Chaetopterus sp. harboured two symbiotic species, which was extremely rare in C. cf. appendiculatus, suggesting lower interspecific interactions in the former. The crab and nudibranch symbionts of Chaetopterus sp. often shared a host and lived in pairs, thus partitioning resources. This led to the species coexisting in the tubes of Chaetopterus sp., establishing a tightly packed community, indicating high species richness and mean intensity, together with a low species dominance. In contrast, the aggressive, strictly territorial species associated with C. cf. appendiculatus established a symbiotic community strongly dominated by single species and, thus, low species richness and mean intensity. Therefore, we suggest that interspecific interactions are determining species richness, intensity and dominance, while intraspecific interactions are influencing only intensity and abundance. It is possible that species composition may have influenced the differences in community

Echoes from the past: Regional variations in recovery within a harbour seal population

PubMed Central

Reijnders, Peter J. H.; Cremer, Jenny; Meesters, Erik; Kirkwood, Roger; Jensen, Lasse Fast; Jeβ, Armin; Galatius, Anders; Teilmann, Jonas; Aarts, Geert

2018-01-01

Terrestrial and marine wildlife populations have been severely reduced by hunting, fishing and habitat destruction, especially in the last centuries. Although management regulations have led to the recovery of some populations, the underlying processes are not always well understood. This study uses a 40-year time series of counts of harbour seals (Phoca vitulina) in the Wadden Sea to study these processes, and demonstrates the influence of historical regional differences in management regimes on the recovery of this population. While the Wadden Sea is considered one ecologically coupled zone, with a distinct harbour seal population, the area is divided into four geo-political regions i.e. the Netherlands, Lower Saxony including Hamburg, Schleswig-Holstein and Denmark. Gradually, seal hunting was banned between 1962 and 1977 in the different regions. Counts of moulting harbour seals and pup counts, obtained during aerial surveys between 1974 and 2014, show a population growth from approximately 4500 to 39,000 individuals. Population growth models were developed to assess if population growth differed between regions, taking into account two Phocine Distemper Virus (PDV) epizootics, in 1988 and 2002 which seriously affected the population. After a slow start prior to the first epizootic, the overall population grew exponentially at rates close to assumed maximum rates of increase in a harbour seal population. Recently, growth slowed down, potentially indicative of approaching carrying capacity. Regional differences in growth rates were demonstrated, with the highest recovery in Netherlands after the first PDV epizootic (i.e. 17.9%), suggesting that growth was fuelled by migration from the other regions, where growth remained at or below the intrinsic growth rate (13%). The seals’ distribution changed, and although the proportion of seals counted in the German regions declined, they remained by far the most important pupping region, with approximately 70% of all

Echoes from the past: Regional variations in recovery within a harbour seal population.

PubMed

Brasseur, Sophie M J M; Reijnders, Peter J H; Cremer, Jenny; Meesters, Erik; Kirkwood, Roger; Jensen, Lasse Fast; Jeβ, Armin; Galatius, Anders; Teilmann, Jonas; Aarts, Geert

2018-01-01

Terrestrial and marine wildlife populations have been severely reduced by hunting, fishing and habitat destruction, especially in the last centuries. Although management regulations have led to the recovery of some populations, the underlying processes are not always well understood. This study uses a 40-year time series of counts of harbour seals (Phoca vitulina) in the Wadden Sea to study these processes, and demonstrates the influence of historical regional differences in management regimes on the recovery of this population. While the Wadden Sea is considered one ecologically coupled zone, with a distinct harbour seal population, the area is divided into four geo-political regions i.e. the Netherlands, Lower Saxony including Hamburg, Schleswig-Holstein and Denmark. Gradually, seal hunting was banned between 1962 and 1977 in the different regions. Counts of moulting harbour seals and pup counts, obtained during aerial surveys between 1974 and 2014, show a population growth from approximately 4500 to 39,000 individuals. Population growth models were developed to assess if population growth differed between regions, taking into account two Phocine Distemper Virus (PDV) epizootics, in 1988 and 2002 which seriously affected the population. After a slow start prior to the first epizootic, the overall population grew exponentially at rates close to assumed maximum rates of increase in a harbour seal population. Recently, growth slowed down, potentially indicative of approaching carrying capacity. Regional differences in growth rates were demonstrated, with the highest recovery in Netherlands after the first PDV epizootic (i.e. 17.9%), suggesting that growth was fuelled by migration from the other regions, where growth remained at or below the intrinsic growth rate (13%). The seals' distribution changed, and although the proportion of seals counted in the German regions declined, they remained by far the most important pupping region, with approximately 70% of all pups

Hepatic CYP1A levels and EROD activity in English sole: biomonitoring of marine contaminants in Vancouver Harbour.

PubMed

Miller, K A; Addison, R F; Bandiera, S M

2004-01-01

To assess chemical contaminant stress in the marine environment, ethoxyresorufin-O-deethylase (EROD) activity and cytochrome P450 1A (CYP1A) expression were measured in 88 English Sole (Pleuronectes vetulus) collected during May and June 1999 from four sites in Vancouver Harbour and at an expected reference site outside the harbour. Hepatic microsomes were prepared from the fish and analyzed for total CYP content, EROD activity, and CYP1A protein levels. Hepatic EROD activity and CYP1A protein levels were elevated in fish from two sites in the inner harbour. A comparison with sediment chemistry data showed that fish with increased EROD activity and CYP1A levels came from sites containing relatively high levels of polycyclic aromatic hydrocarbons and polychlorinated biphenyls. Unexpectedly high levels of EROD activity and CYP1A protein were also found in fish from a reference site near Gibsons, in Howe Sound. The elevated EROD activity and CYP1A expression in fish from this site cannot be explained by the chemical analysis data collected.

Serratia marcescens harbouring SME-type class A carbapenemases in Canada and the presence of blaSME on a novel genomic island, SmarGI1-1.

PubMed

Mataseje, L F; Boyd, D A; Delport, J; Hoang, L; Imperial, M; Lefebvre, B; Kuhn, M; Van Caeseele, P; Willey, B M; Mulvey, M R

2014-07-01

An increasing prevalence since 2010 of Serratia marcescens harbouring the Ambler class A carbapenemase SME prompted us to further characterize these isolates. Isolates harbouring bla(SME) were identified by PCR and sequencing. Phenotypic analysis for carbapenemase activity was carried out by a modified Hodge test and a modified Carba NP test. Antimicrobial susceptibilities were determined by Etest and Vitek 2. Typing was by PFGE of macrorestriction digests. Whole-genome sequencing of three isolates was carried out to characterize the genomic region harbouring the bla(SME)-type genes. All S. marcescens harbouring SME-type enzymes could be detected using a modified Carba NP test. Isolates harbouring bla(SME) were resistant to penicillins and carbapenems, but remained susceptible to third-generation cephalosporins, as well as fluoroquinolones and trimethoprim/sulfamethoxazole. Isolates exhibited diverse genetic backgrounds, though 57% of isolates were found in three clusters. Analysis of whole-genome sequence data from three isolates revealed that the bla(SME) gene occurred in a novel cryptic prophage genomic island, SmarGI1-1. There has been an increasing occurrence of S. marcescens harbouring bla(SME) in Canada since 2010. The bla(SME) gene was found on a genomic island, SmarGI1-1, that can be excised and circularized, which probably contributes to its dissemination amongst S. marcescens. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Characterization of contaminants in snapping turtles (Chelydra serpentina) from Canadian Lake Erie Areas of Concern: St. Clair River, Detroit River, and Wheatley Harbour.

PubMed

de Solla, Shane R; Fernie, Kimberly J

2004-11-01

PCBs, organochlorine pesticides and dioxins/furans in snapping turtle eggs and plasma (Chelydra serpentina) were evaluated at three Areas of Concern (AOCs) on Lake Erie and its connecting channels (St. Clair River, Detroit River, and Wheatley Harbour), as well as two inland reference sites (Algonquin Provincial Park and Tiny Marsh) in 2001-2002. Eggs from the Detroit River and Wheatley Harbour AOCs had the highest levels of p,p'-DDE (24.4 and 57.9 ng/g) and sum PCBs (928.6 and 491.0 ng/g) wet weight, respectively. Contaminant levels in eggs from St. Clair River AOC were generally higher than those from Algonquin Park, but similar to those from Tiny Marsh. Dioxins appeared highest from the Detroit River. The PCB congener pattern in eggs suggested that turtles from the Detroit River and Wheatley Harbour AOCs were exposed to Aroclor 1260. TEQs of sum PCBs in eggs from all AOCs and p,p'-DDE levels in eggs from the Wheatley Harbour and the Detroit River AOCs exceeded the Canadian Environmental Quality Guidelines. Furthermore, sum PCBs in eggs from Detroit River and Wheatley Harbour exceeded partial restriction guidelines for consumption. Although estimated PCB body burdens in muscle tissue of females were well below consumption guidelines, estimated residues in liver and adipose were above guidelines for most sites.

Evaluation of immune and stress status in harbour porpoises (Phocoena phocoena): can hormones and mRNA expression levels serve as indicators to assess stress?

PubMed Central

2013-01-01

Background The harbour porpoise is exposed to increasing pressure caused by anthropogenic activities in its marine environment. Numerous offshore wind farms are planned or under construction in the North and Baltic Seas, which will increase underwater noise during both construction and operation. A better understanding of how anthropogenic impacts affect the behaviour, health, endocrinology, immunology and physiology of the animals is thus needed. The present study compares levels of stress hormones and mRNA expression of cytokines and acute-phase proteins in blood samples of harbour porpoises exposed to different levels of stress during handling, in rehabilitation or permanent human care. Free-ranging harbour porpoises, incidentally caught in pound nets in Denmark, were compared to harbour porpoises in rehabilitation at SOS Dolfijn in Harderwijk, the Netherlands, and individuals permanently kept in human care in the Dolfinarium Harderwijk and Fjord & Belt Kerteminde, Denmark. Blood samples were investigated for catecholamines, adrenaline, noradrenaline and dopamine, as well as for adrenocorticotropic hormone (ACTH), cortisol, metanephrine and normetanephrine. mRNA expression levels of relevant cell mediators (cytokines IL-10 and TNFα, acute-phase proteins haptoglobin and C-reactive protein and the heat shock protein HSP70) were measured using real-time PCR. Results Biomarker expression levels varied between free-ranging animals and porpoises in human care. Hormone and cytokine ranges showed correlations to each other and to the health status of investigated harbour porpoises. Hormone concentrations were higher in free-ranging harbour porpoises than in animals in human care. Adrenaline can be used as a parameter for the initial reaction to acute stress situations; noradrenaline, dopamine, ACTH and cortisol are more likely indicators for the following minutes of acute stress. There is evidence for different correlations between production of normetanephrine

Fatal Disseminated Toxoplasma gondii Infection in a Captive Harbour Porpoise (Phocoena phocoena).

PubMed

Herder, V; van de Velde, N; Højer Kristensen, J; van Elk, C; Peters, M; Kilwinski, J; Schares, G; Siebert, U; Wohlsein, P

2015-11-01

A 7-year-old female harbour porpoise (Phocoena phocoena), born and held in captivity, suffered from reduced consciousness, imprecise and circling swimming movements and long phases of immobility over a period of 3 weeks. The animal died during treatment in a Danish open sea facility. Pathological examination revealed multifocal pyogranulomatous to necrotizing meningoencephalomyelitis, ganglioneuritis, plexus chorioiditis, myocarditis, hepatitis and adrenalitis with few intralesional protozoal tachyzoites and bradyzoites within cysts. Immunohistochemistry was positive for Toxoplasma gondii antigen within the lesions. Using polymerase chain reaction (PCR), the presence of T. gondii-specific genome fragments was confirmed. A multilocus PCR-restriction fragment length polymorphism analysis using nine unlinked marker regions (nSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) resulted in the identification of T. gondii type II (variant Apico Type I), which is the T. gondii genotype dominating in Germany. This is the first description of disseminated fatal toxoplasmosis in a captive harbour porpoise that lived in an open sea basin. Surface water contaminated with toxoplasma oocysts is regarded as the most likely source of infection. Copyright © 2015 Elsevier Ltd. All rights reserved.

DDTs and other chlorinated organic pesticides and polychlorinated biphenyls pollution in the surface sediments of Keratsini harbour, Saronikos gulf, Greece.

PubMed

Galanopoulou, Stavroula; Vgenopoulos, Andreas; Conispoliatis, Nikolaos

2005-05-01

Sediment samples were collected from Keratsini harbour, Saronikos gulf, Greece and were analysed for chlorinated organic pesticides (DDTs, HCB, Lindane) and polychlorinated biphenyls (PCBs). High total DDTs values were detected in all the sediments samples ranging from 9.1 to 75.6 mug/g, dry weight. PCBs concentrations range from 47.8 to 351.8 ng/g. The results and especially the high concentrations of DDTs reflect the influence of the industrial and urban wastes in the pollution for the Keratsini harbour environment.

The ancient harbour system of Terracina (Latium, Italy) obtained by gravity and seismic surveys.

NASA Astrophysics Data System (ADS)

di Nezza, Maria; di Filippo, Michele

2010-05-01

Historical research has shown that Terracina (Latina, Latium) played a fundamental role in the maritime and land traffic since before the foundation of the colony. The settlement was established where the organized system of maritime, land, coastal, and fluvial transport had the most ideal conditions to constitute an important commercial crossroads, apparently since the beginning of recorded history. In order to reconstruction the buried archaeological structures attributed to the ancient Roman port, traditionally attributed to Traiano, in the current area of the harbour of Terracina, it was carried out a gravity survey, more than 380 gravity stations. The gravity method enables to recognize the cavity and the structures of the buildings underground through the results of variations density in the subsoil. Seismic tomography treats the problem of identifying a buried structure as a wave propagation process by inverting the linearized wave equation to compute the spatial distribution of the slowness of the velocity. The purpose of our tomographic study is to further test the method and to guide archaeologists in their future excavations by locating and identifying buried structures. In the residual gravity anomaly map a series of positive anomalies are visible which confirm the round structures and the pier of the buried foundations of the Imperial harbour. Unfortunately, little remains of the functioning facilities of the harbour's activities. The modern construction of the harbour, in fact, has to be developed around the new inhabitable commercial area, know today as Terracina Bassa or Borgo alla Marina. It had to be developed with a modern infrastructure of a harbor area, as in the construction of the rooms for storage of goods, warehouses, as well as for the thermal baths, hotels and amphitheatre. Furthermore, there are always the positive anomalies that characterize the area to the north-east of "Montone" hill where archaeological remains are easily visible

Hydrodynamic detection and localization of artificial flatfish breathing currents by harbour seals (Phoca vitulina).

PubMed

Niesterok, Benedikt; Krüger, Yvonne; Wieskotten, Sven; Dehnhardt, Guido; Hanke, Wolf

2017-01-15

Harbour seals are known to be opportunistic feeders, whose diet consists mainly of pelagic and benthic fish, such as flatfish. As flatfish are often cryptic and do not produce noise, we hypothesized that harbour seals are able to detect and localize flatfish using their hydrodynamic sensory system (vibrissae), as fish emit water currents through their gill openings (breathing currents). To test this hypothesis, we created an experimental platform where an artificial breathing current was emitted through one of eight different openings. Three seals were trained to search for the active opening and station there for 5 s. Half of the trials were conducted with the seal blindfolded with an eye mask. In blindfolded and non-blindfolded trials, all seals performed significantly better than chance. The seals crossed the artificial breathing current (being emitted into the water column at an angle of 45 deg to the ground) from different directions. There was no difference in performance when the seals approached from in front, from behind or from the side. All seals responded to the artificial breathing currents by directly moving their snout towards the opening from which the hydrodynamic stimulus was emitted. Thus, they were also able to extract directional information from the hydrodynamic stimulus. Hydrodynamic background noise and the swimming speed of the seals were also considered in this study as these are aggravating factors that seals in the wild have to face during foraging. By creating near-natural conditions, we show that harbour seals have the ability to detect a so-far overlooked type of stimulus. © 2017. Published by The Company of Biologists Ltd.

Pup Mortality in a Rapidly Declining Harbour Seal (Phoca vitulina) Population

PubMed Central

Hanson, Nora; Thompson, Dave; Duck, Callan; Moss, Simon; Lonergan, Mike

2013-01-01

The harbour seal population in Orkney, off the north coast of Scotland, has reduced by 65% between 2001 and 2010. The cause(s) of this decline are unknown but must affect the demographic parameters of the population. Here, satellite telemetry data were used to test the hypothesis that increased pup mortality could be a primary driver of the decline in Orkney. Pup mortality and tag failure parameters were estimated from the duration of operation of satellite tags deployed on harbour seal pups from the Orkney population (n = 24) and from another population on the west coast of Scotland (n = 24) where abundance was stable. Survival probabilities from both populations were best represented by a common gamma distribution and were not different from one another, suggesting that increased pup mortality is unlikely to be the primary agent in the Orkney population decline. The estimated probability of surviving to 6 months was 0.390 (95% CI 0.297 – 0.648) and tag failure was represented by a Gaussian distribution, with estimated mean 270 (95% CI = 198 – 288) and s.d. 21 (95% CI = 1 – 66) days. These results suggest that adult survival is the most likely proximate cause of the decline. They also demonstrate a novel technique for attaining age-specific mortality rates from telemetry data. PMID:24312239

Humpback whales harbour a combination of specific and variable skin bacteria.

PubMed

Apprill, Amy; Mooney, T Aran; Lyman, Edward; Stimpert, Alison K; Rappé, Michael S

2011-04-01

Investigations of marine mammal skin-associated microbiota are limited to cultivation-based studies of lesioned individuals, resulting in a lack of understanding about the composition of 'normal' skin-associated microbial communities, their variation among individuals, and whether or not the microbial communities change with host health or environmental exposures. In this study, bacterial communities associated with the skin of 19 North Pacific humpback whales (Megaptera novaeangliae), including skin from three health-compromised individuals, were examined using small subunit ribosomal RNA gene-based culture-independent techniques. These analyses revealed that the skin-associated bacteria were significantly different from free-living bacterial communities in the surrounding seawater. Two novel groups within the Flavobacteriaceae family of the Bacteroidetes phylum were found to be associated with multiple whales, including a species within the Tenacibaculum genus that associated with 95% of the individuals. Statistical analyses revealed that a group of eight 'healthy' whales harboured similar microbial communities, while the health-compromised and other 'healthy' animals harboured communities that were unique to the specific animal. These results describe two components of the whale skin bacterial community: a specific and potentially co-evolved fraction, and a more variable microbial community fraction that may offer a diagnostic-type tool for investigating the health and life-related events of these endangered animals. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

Modelling the distribution of hard seabed using calibrated multibeam acoustic backscatter data in a tropical, macrotidal embayment: Darwin Harbour, Australia

NASA Astrophysics Data System (ADS)

Siwabessy, P. Justy W.; Tran, Maggie; Picard, Kim; Brooke, Brendan P.; Huang, Zhi; Smit, Neil; Williams, David K.; Nicholas, William A.; Nichol, Scott L.; Atkinson, Ian

2018-06-01

Spatial information on the distribution of seabed substrate types in high use coastal areas is essential to support their effective management and environmental monitoring. For Darwin Harbour, a rapidly developing port in northern Australia, the distribution of hard substrate is poorly documented but known to influence the location and composition of important benthic biological communities (corals, sponges). In this study, we use angular backscatter response curves to model the distribution of hard seabed in the subtidal areas of Darwin Harbour. The angular backscatter response curve data were extracted from multibeam sonar data and analysed against backscatter intensity for sites observed from seabed video to be representative of "hard" seabed. Data from these sites were consolidated into an "average curve", which became a reference curve that was in turn compared to all other angular backscatter response curves using the Kolmogorov-Smirnov goodness-of-fit. The output was used to generate interpolated spatial predictions of the probability of hard seabed ( p-hard) and derived hard seabed parameters for the mapped area of Darwin Harbour. The results agree well with the ground truth data with an overall classification accuracy of 75% and an area under curve measure of 0.79, and with modelled bed shear stress for the Harbour. Limitations of this technique are discussed with attention to discrepancies between the video and acoustic results, such as in areas where sediment forms a veneer over hard substrate.

Environmental implications and spatial distribution of natural radionuclides and heavy metals in sediments from four harbours in the Egyptian Red Sea coast.

PubMed

El-Taher, Atef; Zakaly, Hesham M H; Elsaman, Reda

2018-01-01

Measurements of natural radionuclides concentrations ( 226 Ra, 232 Th and 40 K) in sediments collected from sea, rivers or ocean is significant to protect the sea water ecosystem and to human health from radiation. Thirty-three sample of sediment have been collected from four ports in the Red Sea coast, Egypt for investigation by gamma-ray spectrometer using NaI(Tl) detector. The average and range activity concentrations of 226 Ra, 232 Th and 40 K were 26(5-58), 19(4-33) and 458(16-2665)Bqkg -1 in Quseir Harbour, 30(14-53), 20(14-34) and 430(378-511)Bqkg -1 in Abu-Tartour Harbour. However, the average and range activity concentrations were 23(14-35), 21(15-32), and 602(327-821)Bqkg -1 in Touristic Harbour and 14(5-26), 13(2-23) and 489(36-950)Bqkg -1 in Hurghada harbour. These results were compared with reported ranges in the literature from other location in the world. The radiation hazard parameters; radium equivalent activity annual dose, external hazard were also calculated and compared with the recommended levels by UNSCEAR reports. Eight heavy metals (Fe, Mn, Ni, Co, Zn, Cu, Pb and Cd) have been measured and analyzed by atomic absorption spectrometer. The concentration for the investigated heavy metals overtakes the allowable limits recommended by the Canadian Environmental Quality Guidelines. Because there are no existing databases for the natural radioactivity in the sediment samples from Egyptian Red Sea ports, our results are a start to establishing a database for Red Sea harbours environment. Copyright © 2017 Elsevier Ltd. All rights reserved.

A system shift in tidal choking due to the construction of Yangshan Harbour, Shanghai, China

NASA Astrophysics Data System (ADS)

Guo, Wenyun; Wang, Xiao Hua; Ding, Pingxing; Ge, Jianzhong; Song, Dehai

2018-06-01

Tidal choking is a geometric feature caused by a narrowed channel. Construction of the Yangshan Harbour, Shanghai, China obstructed three key channels and intensively changed the local geometry and topography. In this study nine numerical experiments based on the Finite-Volume Community Ocean Model are conducted to study the project's influence on tidal characteristics. Results show that stronger tidal choking happened at the East Entrance after project, mainly due to the jet induced water-level drop forced by Bernoulli law and the longer and narrower geometry. The stronger tidal choking forces a faster flow and larger tidal energy flux at the choked channel while reducing the tidal amplitude in the Inner Harbour Area (IHA). The scouring on this channel reduces the choking effect but further enlarges tidal energy flux. Moreover, damming the channels decrease the tidal amplitude at the lee side of tidal propagating direction while increasing the amplitude on the stoss side. The dams also decrease the tidal current on both sides, and meanwhile develop two patches with stronger current aside the dam. The project induced changes in tidal characteristics are complex in space, and perturbations in bathymetry increase this complexity. Yangshan Harbour's construction induces little changes in the total tidal energy density in the IHA, but induces obvious changes in the spatial distribution of tidal energy. Although this study is site-specific, the findings may be applicable to tidal dynamics in land reclamation close to open seas, such as the dramatic reclamation of islands in the South China Sea.

Clicking in a killer whale habitat: narrow-band, high-frequency biosonar clicks of harbour porpoise (Phocoena phocoena) and Dall's porpoise (Phocoenoides dalli).

PubMed

Kyhn, Line A; Tougaard, Jakob; Beedholm, Kristian; Jensen, Frants H; Ashe, Erin; Williams, Rob; Madsen, Peter T

2013-01-01

Odontocetes produce a range of different echolocation clicks but four groups in different families have converged on producing the same stereotyped narrow band high frequency (NBHF) click. In microchiropteran bats, sympatric species have evolved the use of different acoustic niches and subtly different echolocation signals to avoid competition among species. In this study, we examined whether similar adaptations are at play among sympatric porpoise species that use NBHF echolocation clicks. We used a six-element hydrophone array to record harbour and Dall's porpoises in British Columbia (BC), Canada, and harbour porpoises in Denmark. The click source properties of all porpoise groups were remarkably similar and had an average directivity index of 25 dB. Yet there was a small, but consistent and significant 4 kHz difference in centroid frequency between sympatric Dall's (137±3 kHz) and Canadian harbour porpoises (141±2 kHz). Danish harbour porpoise clicks (136±3 kHz) were more similar to Dall's porpoise than to their conspecifics in Canada. We suggest that the spectral differences in echolocation clicks between the sympatric porpoises are consistent with evolution of a prezygotic isolating barrier (i.e., character displacement) to avoid hybridization of sympatric species. In practical terms, these spectral differences have immediate application to passive acoustic monitoring.

Microzooplankton grazing and selective feeding during bloom periods in the Tolo Harbour area as revealed by HPLC pigment analysis

NASA Astrophysics Data System (ADS)

Liu, Xiangjiang; Tang, Chi Hung; Wong, Chong Kim

2014-07-01

Dilution experiments were conducted to investigate microzooplankton grazing impact on phytoplankton of different taxonomic groups and size fractions (< 5, 5-20, 20-200 μm) during spring and summer bloom periods at two different sites (inner Tolo Harbour and Tolo Channel) in the Tolo Harbour area, the northeastern coastal area of Hong Kong. Experiments combined with HPLC pigment analysis in three phytoplankton size fractions measured pigment and size specific phytoplankton growth rates and microzooplankton grazing rates. Pigment-specific phytoplankton growth rates ranged between 0.08 and 3.53 d- 1, while specific grazing rates of microzooplankton ranged between 0.07 and 2.82 d- 1. Highest specific rates of phytoplankton growth and microzooplankton grazing were both measured in fucoxanthin in 5-20 μm size fraction in inner Tolo Harbour in summer, which coincided with the occurrence of diatom bloom. Results showed significant correlations between phytoplankton growth and microzooplankton grazing rates. Microzooplankton placed high grazing pressure on phytoplankton community. High microzooplankton grazing impact on alloxanthin (2.63-5.13) suggested strong selection toward cryptophytes. Our results provided no evidence for size selective grazing on phytoplankton by microzooplankton.

CO2 emissions from a temperate drowned river valley estuary adjacent to an emerging megacity (Sydney Harbour)

NASA Astrophysics Data System (ADS)

Tanner, E. L.; Mulhearn, P. J.; Eyre, B. D.

2017-06-01

The Sydney Harbour Estuary is a large drowned river valley adjacent to Sydney, a large urban metropolis on track to become a megacity; estimated to reach a population of 10 million by 2100. Monthly underway surveys of surface water pCO2 were undertaken along the main channel and tributaries, from January to December 2013. pCO2 showed substantial spatio-temporal variability in the narrow high residence time upper and mid sections of the estuary, with values reaching a maximum of 5650 μatm in the upper reaches and as low as 173 μatm in the mid estuary section, dominated by respiration and photosynthesis respectively. The large lower estuary displayed less variability in pCO2 with values ranging from 343 to 544 μatm controlled mainly by tidal pumping and temperature. Air-water CO2 emissions reached a maximum of 181 mmol C m-2 d-1 during spring in the eutrophic upper estuary. After a summer high rainfall event nutrient-stimulated biological pumping promoted a large uptake of CO2 transitioning the Sydney Harbour Estuary into a CO2 sink with a maximum uptake of rate of -10.6 mmol C m-2 d-1 in the mid-section of the estuary. Annually the Sydney Harbour Estuary was heterotrophic and a weak source of CO2 with an air-water emission rate of 1.2-5 mmol C m-2 d-1 (0.4-1.8 mol C m-2 y-1) resulting in a total carbon emission of around 930 tonnes per annum. CO2 emissions (weighted m3 s-1 of discharge per km2 of estuary surface area) from Sydney Harbour were an order of magnitude lower than other temperate large tectonic deltas, lagoons and engineered systems of China, India, Taiwan and Europe but were similar to other natural drowned river valley systems in the USA. Discharge per unit area appears to be a good predictor of CO2 emissions from estuaries of a similar climate and geomorphic class.

Sensor and Video Monitoring of Water Quality at Bristol Floating Harbour

NASA Astrophysics Data System (ADS)

Chen, Yiheng; Han, Dawei

2017-04-01

Water system is an essential component in a smart city for its sustainability and resilience. The harbourside is a focal area of​ ​Bristol with new buildings and features redeveloped in the last ten years, attracting numerous visitors by the diversity of attractions and beautiful views. There is a strong​ ​relationship between the satisfactory of the visitors and local people with the water quality in the Harbour. The freshness and beauty of the water body would please people as well as benefit the aquatic ecosystems. As we are entering a data-rich era, this pilot project aims to explore the concept of using​ ​ video cameras and smart sensors to collect and monitor water quality condition at the Bristol harbourside. The video cameras and smart sensors are connected to the Bristol Is Open network, an open programmable city platform. This will be the​ first​ attempt to collect water quality data in real time in the​ ​Bristol urban area with the wireless network. The videos and images of the water body collected by the cameras will be correlated with the in-situ water quality parameters for research​ ​purposes. The successful implementation of the sensors can attract more academic researchers and industrial partners to expand the sensor network to multiple locations​ ​around the city covering the other parts of the Harbour and River Avon, leading to a new generation of urban system infrastructure model.

Harbour porpoises respond to climate change.

PubMed

Heide-Jørgensen, Mads Peter; Iversen, Maria; Nielsen, Nynne Hjort; Lockyer, Christina; Stern, Harry; Ribergaard, Mads Hvid

2011-12-01

The effects of climate change on marine ecosystems and in particular on marine top predators are difficult to assess due to, among other things, spatial variability, and lack of clear delineation of marine habitats. The banks of West Greenland are located in a climate sensitive area and are likely to elicit pronounced responses to oceanographic changes in the North Atlantic. The recent increase in sea temperatures on the banks of West Greenland has had cascading effects on sea ice coverage, residency of top predators, and abundance of important prey species like Atlantic cod (Gadus morhua). Here, we report on the response of one of the top predators in West Greenland; the harbour porpoise (Phocoena phocoena). The porpoises depend on locating high densities of prey species with high nutritive value and they have apparently responded to the general warming on the banks of West Greenland by longer residence times, increased consumption of Atlantic cod resulting in improved body condition in the form of larger fat deposits in blubber, compared to the situation during a cold period in the 1990s. This is one of the few examples of a measurable effect of climate change on a marine mammal population.

Testing deep-sea biodiversity paradigms on abyssal nematode genera and Acantholaimus species

NASA Astrophysics Data System (ADS)

Lins, Lidia; da Silva, Maria Cristina; Neres, Patrícia; Esteves, André Morgado; Vanreusel, Ann

2018-02-01

Biodiversity patterns in the deep sea have been extensively studied in the last decades. In this study, we investigated whether reputable concepts in deep-sea ecology also explain diversity and distribution patterns of nematode genera and species in the abyss. Among them, three paradigms were tackled: (1) the deep sea is a highly diverse environment at a local scale, while on a regional and even larger geographical scale, species and genus turnover is limited; (2) the biodiversity of deep-sea nematode communities changes with the nature and amount of organic matter input from the surface; and (3) patch-mosaic dynamics of the deep-sea environment drive local diversity. To test these hypotheses, diversity and density of nematode assemblages and of species of the genus Acantholaimus were studied along two abyssal E-W transects. These two transects were situated in the Southern Ocean ( 50°S) and the North Atlantic ( 10°N). Four different hierarchical scales were used to compare biodiversity: at the scale of cores, between stations from the same region, and between regions. Results revealed that the deep sea harbours a high diversity at a local scale (alpha diversity), but that turnover can be shaped by different environmental drivers. Therefore, these results question the second part of the paradigm about limited species turnover in the deep sea. Higher surface primary productivity was correlated with greater nematode densities, whereas diversity responses to the augmentation of surface productivity showed no trend. Areas subjected to a constant and low food input revealed similar nematode communities to other oligotrophic abyssal areas, while stations under high productivity were characterized by different dominant genera and Acantholaimus species, and by a generally low local diversity. Our results corroborate the species-energy hypothesis, where productivity can set a limit to the richness of an ecosystem. Finally, we observed no correlation between sediment

Occurrence and characterization of mcr-1-harbouring Escherichia coli isolated from pigs in Great Britain from 2013 to 2015.

PubMed

Duggett, Nicholas A; Sayers, Ellie; AbuOun, Manal; Ellis, Richard J; Nunez-Garcia, Javier; Randall, Luke; Horton, Robert; Rogers, Jon; Martelli, Francesca; Smith, Richard P; Brena, Camilla; Williamson, Susanna; Kirchner, Miranda; Davies, Robert; Crook, Derrick; Evans, Sarah; Teale, Chris; Anjum, Muna F

2017-03-01

To determine the occurrence of mcr-1 -harbouring Escherichia coli in archived pig material originating in Great Britain (GB) from 2013 to 2015 and characterize mcr-1 plasmids. Enrichment and selective culture of 387 archived porcine caecal contents and recovery from archive of 1109 E. coli isolates to identify colistin-resistant bacteria by testing for the presence of mcr-1 by PCR and RT-PCR. mcr-1 -harbouring E. coli were characterized by WGS and compared with other available mcr-1 WGS. Using selective isolation following enrichment, the occurrence of mcr-1 E. coli in caeca from healthy pigs at slaughter from unique farms in GB was 0.6% (95% CI 0%-1.5%) in 2015. mcr-1 E. coli were also detected in isolates from two porcine veterinary diagnostic submissions in 2015. All isolates prior to 2015 were negative. WGS analysis of the four mcr-1 -positive E. coli indicated no other antimicrobial resistance (AMR) genes were linked to mcr-1 -plasmid-bearing contigs, despite all harbouring multiple AMR genes. The sequence similarity between mcr-1 -plasmid-bearing contigs identified and those found in GB, Chinese and South African human isolates and Danish, French and Estonian livestock-associated isolates was 90%-99%. mcr-1- harbouring plasmids were diverse, implying transposable elements are involved in mcr-1 transmission in GB. The low number of mcr-1 -positive E. coli isolates identified suggested mcr-1 is currently uncommon in E. coli from pigs within GB. The high sequence similarity between mcr-1 plasmid draft genomes identified in pig E. coli and plasmids found in human and livestock-associated isolates globally requires further investigation to understand the full implications. © Crown copyright 2016.

Environmental Risk Assessment of dredging processes - application to Marin harbour (NW Spain)

NASA Astrophysics Data System (ADS)

Gómez, A. G.; García Alba, J.; Puente, A.; Juanes, J. A.

2014-04-01

A methodological procedure to estimate the environmental risk of dredging operations in aquatic systems has been developed. Environmental risk estimations are based on numerical models results, which provide an appropriated spatio-temporal framework analysis to guarantee an effective decision-making process. The methodological procedure has been applied on a real dredging operation in the port of Marin (NW Spain). Results from Marin harbour confirmed the suitability of the developed methodology and the conceptual approaches as a comprehensive and practical management tool.

Clicking in a Killer Whale Habitat: Narrow-Band, High-Frequency Biosonar Clicks of Harbour Porpoise (Phocoena phocoena) and Dall’s Porpoise (Phocoenoides dalli)

PubMed Central

Kyhn, Line A.; Tougaard, Jakob; Beedholm, Kristian; Jensen, Frants H.; Ashe, Erin; Williams, Rob; Madsen, Peter T.

2013-01-01

Odontocetes produce a range of different echolocation clicks but four groups in different families have converged on producing the same stereotyped narrow band high frequency (NBHF) click. In microchiropteran bats, sympatric species have evolved the use of different acoustic niches and subtly different echolocation signals to avoid competition among species. In this study, we examined whether similar adaptations are at play among sympatric porpoise species that use NBHF echolocation clicks. We used a six-element hydrophone array to record harbour and Dall’s porpoises in British Columbia (BC), Canada, and harbour porpoises in Denmark. The click source properties of all porpoise groups were remarkably similar and had an average directivity index of 25 dB. Yet there was a small, but consistent and significant 4 kHz difference in centroid frequency between sympatric Dall’s (137±3 kHz) and Canadian harbour porpoises (141±2 kHz). Danish harbour porpoise clicks (136±3 kHz) were more similar to Dall’s porpoise than to their conspecifics in Canada. We suggest that the spectral differences in echolocation clicks between the sympatric porpoises are consistent with evolution of a prezygotic isolating barrier (i.e., character displacement) to avoid hybridization of sympatric species. In practical terms, these spectral differences have immediate application to passive acoustic monitoring. PMID:23723996

Benthic assemblages, biodiversity and invasiveness in marinas and commercial harbours: an investigation using a bioindicator group.

PubMed

Megina, Cesar; González-Duarte, Manuel M; López-González, Pablo J

2016-01-01

Fouling communities on artificial marine structures are generally different from benthic communities in natural rocky habitats. However, they may also differ among different types of artificial structures. Two artificial structures in direct contact with arriving vessels were compared: floating pontoons within recreational marinas, and sea-walls within commercial harbours. Natural rocky habitats were used as a reference, and the genus Eudendrium (Cnidaria, Hydrozoa) was chosen as a bioindicator. The assemblages were different among the three types of habitat studied, with different species characterising each habitat. The probability of finding an invasive Eudendrium species was significantly higher on pontoons. Diversity was the lowest on pontoons, but it was not significantly different between sea-walls and natural rocks. In general, a barrier to the spread of exotic species exists between harbours and natural rocky habitats. Floating pontoons seem to be a less suitable habitat for native fauna and a key element in marine biological invasions.

The influence of underwater data transmission sounds on the displacement behaviour of captive harbour seals (Phoca vitulina).

PubMed

Kastelein, Ronald A; van der Heul, Sander; Verboom, Willem C; Triesscheijn, Rob J V; Jennings, Nancy V

2006-02-01

To prevent grounding of ships and collisions between ships in shallow coastal waters, an underwater data collection and communication network (ACME) using underwater sounds to encode and transmit data is currently under development. Marine mammals might be affected by ACME sounds since they may use sound of a similar frequency (around 12 kHz) for communication, orientation, and prey location. If marine mammals tend to avoid the vicinity of the acoustic transmitters, they may be kept away from ecologically important areas by ACME sounds. One marine mammal species that may be affected in the North Sea is the harbour seal (Phoca vitulina). No information is available on the effects of ACME-like sounds on harbour seals, so this study was carried out as part of an environmental impact assessment program. Nine captive harbour seals were subjected to four sound types, three of which may be used in the underwater acoustic data communication network. The effect of each sound was judged by comparing the animals' location in a pool during test periods to that during baseline periods, during which no sound was produced. Each of the four sounds could be made into a deterrent by increasing its amplitude. The seals reacted by swimming away from the sound source. The sound pressure level (SPL) at the acoustic discomfort threshold was established for each of the four sounds. The acoustic discomfort threshold is defined as the boundary between the areas that the animals generally occupied during the transmission of the sounds and the areas that they generally did not enter during transmission. The SPLs at the acoustic discomfort thresholds were similar for each of the sounds (107 dB re 1 microPa). Based on this discomfort threshold SPL, discomfort zones at sea for several source levels (130-180 dB re 1 microPa) of the sounds were calculated, using a guideline sound propagation model for shallow water. The discomfort zone is defined as the area around a sound source that harbour

Toxic effects of tributyltin and its metabolites on harbour seal (Phoca vitulina) immune cells in vitro.

PubMed

Frouin, Héloïse; Lebeuf, Michel; Saint-Louis, Richard; Hammill, Mike; Pelletier, Emilien; Fournier, Michel

2008-11-21

The widespread environmental contamination, bioaccumulation and endocrine disruptor effects of butyltins (BTs) to wildlife are well documented. Although suspected, potential effects of BTs exposure on the immune system of marine mammals have been little investigated. In this study, we assessed the effects of tributyltin (TBT) and its dealkylated metabolites dibutyltin (DBT) and monobutyltin (MBT) on the immune responses of harbour seals. Peripheral blood mononuclear cells isolated from pup and adult harbour seals were exposed in vitro to varying concentrations of BTs. DBT resulted in a significant decrease at 100 and 200 nM of phagocytotic activity and reduced significantly phagocytic efficiency at 200 nM in adult seals. There was no effect in phagocytosis with TBT and MBT. In pups, the highest concentration (200 nM) of DBT inhibited phagocytic efficiency. A reduction of tumor-killing capacity of adult natural killer (NK) cells occurred when leukocytes were incubated in vitro with 50 nM DBT and 200 nM TBT for 24h. In adult seals, T-lymphocyte proliferation was significantly suppressed when the cells were exposed to 200 nM TBT and 100 nM DBT. In pups, the proliferative response increased after an exposure to 100 nM TBT and 50 nM DBT, but decreased with 200 nM TBT and 100 nM DBT. The immune functions were more affected by BTs exposure in adults than in pups, suggesting that other unsuspected mechanisms could trigger immune parameters in pups. The toxic potential of BTs followed the order of DBT>TBT>MBT. BT concentrations of harbour seal pups from the St. Lawrence Estuary (Bic National Park) ranged between 0.1-0.4 ng Sn/g wet weight (ww) and 1.2-13.4 ng Sn/g ww in blood and blubber, respectively. For these animals, DBT concentrations were consistently below the quantification limit of 0.04 ng Sn/g ww in blood and 0.2 ng Sn/g ww in blubber. Results suggest that concentrations measured in pups are considered too low to induce toxic effects to their immune system during

Harbour porpoises respond to climate change

PubMed Central

Heide-Jørgensen, Mads Peter; Iversen, Maria; Nielsen, Nynne Hjort; Lockyer, Christina; Stern, Harry; Ribergaard, Mads Hvid

2011-01-01

The effects of climate change on marine ecosystems and in particular on marine top predators are difficult to assess due to, among other things, spatial variability, and lack of clear delineation of marine habitats. The banks of West Greenland are located in a climate sensitive area and are likely to elicit pronounced responses to oceanographic changes in the North Atlantic. The recent increase in sea temperatures on the banks of West Greenland has had cascading effects on sea ice coverage, residency of top predators, and abundance of important prey species like Atlantic cod (Gadus morhua). Here, we report on the response of one of the top predators in West Greenland; the harbour porpoise (Phocoena phocoena). The porpoises depend on locating high densities of prey species with high nutritive value and they have apparently responded to the general warming on the banks of West Greenland by longer residence times, increased consumption of Atlantic cod resulting in improved body condition in the form of larger fat deposits in blubber, compared to the situation during a cold period in the 1990s. This is one of the few examples of a measurable effect of climate change on a marine mammal population. PMID:22393524

Organization and number of orexinergic neurons in the hypothalamus of two species of Cetartiodactyla: A comparison of giraffe (Giraffa camelopardalis) and harbour porpoise (Phocoena phocoena)

PubMed Central

Dell, Leigh-Anne; Patzke, Nina; Bhagwandin, Adhil; Bux, Faiza; Fuxe, Kjell; Barber, Grace; Siegel, Jerome M.; Manger, Paul R.

2012-01-01

The present study describes the organization of the orexinergic (hypocretinergic) neurons in the hypothalamus of the giraffe and harbour porpoise – two members of the mammalian Order Cetartiodactyla which is comprised of the even-toed ungulates and the cetaceans as they share a monophyletic ancestry. Diencephalons from two sub-adult male giraffes and two adult male harbour porpoises were coronally sectioned and immunohistochemically stained for orexin-A. The staining revealed that the orexinergic neurons could be readily divided into two distinct neuronal types based on somal volume, area and length, these being the parvocellular and magnocellular orexin-A immunopositive (OxA+) groups. The magnocellular group could be further subdivided, on topological grounds, into three distinct clusters – a main cluster in the perifornical and lateral hypothalamus, a cluster associated with the zona incerta and a cluster associated with the optic tract. The parvocellular neurons were found in the medial hypothalamus, but could not be subdivided, rather they form a topologically amorphous cluster. The parvocellular cluster appears to be unique to the Cetartiodactyla as these neurons have not been described in other mammals to date, while the magnocellular nuclei appear to be homologous to similar nuclei described in other mammals. The overall size of both the parvocellular and magnocellular neurons (based on somal volume, area and length) were larger in the giraffe than the harbour porpoise, but the harbour porpoise had a higher number of both parvocellular and magnocellular orexinergic neurons than the giraffe despite both having a similar brain mass. The higher number of both parvocellular and magnocellular orexinergic neurons in the harbour porpoise may relate to the unusual sleep mechanisms in the cetaceans. PMID:22683547

Loop-mediated isothermal amplification (LAMP) assay-A rapid detection tool for identifying red fox (Vulpes vulpes) DNA in the carcasses of harbour porpoises (Phocoena phocoena).

PubMed

Heers, Teresa; van Neer, Abbo; Becker, André; Grilo, Miguel Luca; Siebert, Ursula; Abdulmawjood, Amir

2017-01-01

Carcasses of wild animals are often visited by different scavengers. However, determining which scavenger caused certain types of bite marks is particularly difficult and knowledge thereof is lacking. Therefore, a loop-mediated isothermal amplification (LAMP) assay (target sequence cytochrome b) was developed to detect red fox DNA in carcasses of harbour porpoises. The MSwab™ method for direct testing without prior DNA isolation was validated. As a detection device, the portable real-time fluorometer Genie® II was used, which yields rapid results and can be used in field studies without huge laboratory equipment. In addition to in vitro evaluation and validation, a stranded and scavenged harbour porpoise carcass was successfully examined for red fox DNA residues. The developed LAMP method is a valuable diagnostic tool for confirming presumable red fox bite wounds in harbour porpoises without further DNA isolation steps.

Developing a Social, Cultural and Economic Report Card for a Regional Industrial Harbour.

PubMed

Pascoe, Sean; Tobin, Renae; Windle, Jill; Cannard, Toni; Marshall, Nadine; Kabir, Zobaidul; Flint, Nicole

2016-01-01

Report cards are increasingly used to provide ongoing snap-shots of progress towards specific ecosystem health goals, particularly in coastal regions where planners need to balance competing demands for coastal resources from a range of industries. While most previous report cards focus on the biophysical components of the system, there is a growing interest in including the social and economic implications of ecosystem management to provide a greater social-ecological system understanding. Such a report card was requested on the Gladstone Harbour area in central Queensland, Australia. Gladstone Harbour adjoins the southern Great Barrier Reef, and is also a major industrial and shipping port. Balancing social, economic and environmental interests is therefore of great concern to the regional managers. While environmental benchmarking procedures are well established within Australia (and elsewhere), a method for assessing social and economic performance of coastal management is generally lacking. The key aim of this study was to develop and pilot a system for the development of a report card relating to appropriate cultural, social and economic objectives. The approach developed uses a range of multicriteria decision analysis methods to assess and combine different qualitative and quantitative measures, including the use of Bayesian Belief Networks to combine the different measures and provide an overall quantitative score for each of the key management objectives. The approach developed is readily transferable for purposes of similar assessments in other regions.

Bearing the burden of boat harbours: heavy contaminant and fouling loads in a native habitat-forming alga.

PubMed

Johnston, E L; Marzinelli, E M; Wood, C A; Speranza, D; Bishop, J D D

2011-10-01

Boat harbours are an increasingly common form of artificial habitat. This paper presents a comparative study of contaminants and foulers of a habitat-forming native kelp (Saccharina latissima) in four marinas and four reference locations along the south-west coast of the UK. Fouling of algal laminae was light (<2% cover) in reference locations, while epibiota cover ranged from 25% to 80% of laminae in marinas. Metals associated with antifouling paints were up to six times more concentrated in algal tissues from marinas than from the reference locations. Marinas also carried the greatest cover and diversity of non-indigenous epibiota on the kelp laminae. This indicates not only a potential stress to kelps in these environments, but also the possibility that detached laminae will act as vectors for the dispersal of non-indigenous species. The development of boat harbours creates habitats that are high risk source localities for pollution-tolerant fouling organisms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Environmental quality assessment of Grand Harbour (Valletta, Maltese Islands): a case study of a busy harbour in the Central Mediterranean Sea.

PubMed

Romeo, Teresa; D'Alessandro, Michela; Esposito, Valentina; Scotti, Gianfranco; Berto, Daniela; Formalewicz, Malgorzata; Noventa, Seta; Giuliani, Silvia; Macchia, Simona; Sartori, Davide; Mazzola, Angelo; Andaloro, Franco; Giacobbe, Salvatore; Deidun, Alan; Renzi, Monia

2015-12-01

Contamination levels by plastic debris, trace elements and persistent organic pollutants were assessed and related to macrobenthic diversity within soft bottoms of Grand Harbour (Malta, Central Mediterranean). Sediment toxicity was evaluated by ecotoxicological method, deploying Bacteria (Vibrio fischeri), Echinodermata (Paracentrotus lividus) and Crustacea (Corophium orientale). Univariate analysis (Pearson's test) was used to test relationships between biodiversity indices, pollutants and grain size. A multivariate approach (PERMANOVA) was applied to investigate for any significant differences among sampling stations concerning plastic abundances and to test the relationship between infaunal abundances and pollutant concentrations (the BIOENV test). Significant differences in the plastic abundances were found between sampling stations. The lowest value for Shannon-Wiener biodiversity index was associated to the highest sediment pollution level. Multivariate analyses suggest that MBT and TBT were factors that most influenced macrozoobenthic abundance and biodiversity. The bivalve Corbula gibba and the introduced polychaete Monticellina dorsobranchialis were the most abundant found species.

Microbial community dynamics during assays of harbour oil spill bioremediation: a microscale simulation study.

PubMed

Cappello, S; Caruso, G; Zampino, D; Monticelli, L S; Maimone, G; Denaro, R; Tripodo, B; Troussellier, M; Yakimov, M; Giuliano, L

2007-01-01

Microcosm experiments simulating an oil spill event were performed to evaluate the response of the natural microbial community structure of Messina harbour seawater following the accidental load of petroleum. An experimental harbour seawater microcosm, supplemented with nutrients and crude oil, was monitored above 15 days in comparison with unpolluted ones (control microcosms). Bacterial cells were counted with a Live/Dead BacLight viability kit; leucine aminopeptidase, beta-glucosidase, alkaline phosphatase, lipase and esterase enzymes were measured using fluorogenic substrates. The microbial community dynamic was monitored by isolation of total RNA, RT-PCR amplification of 16S rRNA, cloning and sequencing. Oil addition stimulated an increase of the total bacterial abundance, leucine aminopeptidase and phosphatase activity rates, as well as a change in the community structure. This suggested a prompt response of micro-organisms to the load of petroleum hydrocarbons. The present study on the viability, specific composition and metabolic characteristics of the microbial community allows a more precise assessment of oil pollution. Both structural and functional parameters offer interesting perspectives as indicators to monitor changes caused by petroleum hydrocarbons. A better knowledge of microbial structural successions at oil-polluted sites is essential for environmental bioremediation. Data obtained in microcosm studies improve our understanding of natural processes occurring during oil spills.

Effectiveness of deep cleaning followed by hydrogen peroxide decontamination during high Clostridium difficile infection incidence.

PubMed

Best, E L; Parnell, P; Thirkell, G; Verity, P; Copland, M; Else, P; Denton, M; Hobson, R P; Wilcox, M H

2014-05-01

Clostridium difficile infection (CDI) remains an infection control challenge, especially when environmental spore contamination and suboptimal cleaning may increase transmission risk. To substantiate the long-term effectiveness throughout a stroke rehabilitation unit (SRU) of deep cleaning and hydrogen peroxide decontamination (HPD), following a high incidence of CDI. Extensive environmental sampling (342 sites on each occasion) for C. difficile using sponge wipes was performed: before and after deep cleaning with detergent/chlorine agent; immediately following HPD; and on two further occasions, 19 days and 20 weeks following HPD. C. difficile isolates underwent polymerase chain reaction ribotyping and multi-locus variable repeat analysis (MLVA). C. difficile was recovered from 10.8%, 6.1%, 0.9%, 0% and 3.5% of sites at baseline, following deep cleaning, immediately after HPD, and 19 days and 20 weeks after HPD, respectively. C. difficile ribotypes recovered after deep cleaning matched those from CDI cases in the SRU during the previous 10 months. Similarly, 10/12 of the positive sites identified at 20 weeks post-HPD harboured the same C. difficile ribotype (002) and MLVA pattern as the isolate from the first post-HPD CDI case. CDI incidence [number of cases on SRU per 10 months (January-October 2011)] declined from 20 before to seven after the intervention. HPD, after deep cleaning with a detergent/chlorine agent, was highly effective for removing environmental C. difficile contamination. Long-term follow-up demonstrated that a CDI symptomatic patient can rapidly recontaminate the immediate environment. Determining a role for HPD should include long-term cost-effectiveness evaluations. Copyright © 2014 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Respiratory transmission of an avian H3N8 influenza virus isolated from a harbour seal

USGS Publications Warehouse

Karlsson, Erik A.; Ip, Hon S.; Hall, Jeffrey S.; Yoon, Sun W.; Johnson, Jordan; Beck, Melinda A.; Webby, Richard J.; Schultz-Cherry, Stacey

2014-01-01

The ongoing human H7N9 influenza infections highlight the threat of emerging avian influenza viruses. In 2011, an avian H3N8 influenza virus isolated from moribund New England harbour seals was shown to have naturally acquired mutations known to increase the transmissibility of highly pathogenic H5N1 influenza viruses. To elucidate the potential human health threat, here we evaluate a panel of avian H3N8 viruses and find that the harbour seal virus displays increased affinity for mammalian receptors, transmits via respiratory droplets in ferrets and replicates in human lung cells. Analysis of a panel of human sera for H3N8 neutralizing antibodies suggests that there is no population-wide immunity to these viruses. The prevalence of H3N8 viruses in birds and multiple mammalian species including recent isolations from pigs and evidence that it was a past human pandemic virus make the need for surveillance and risk analysis of these viruses of public health importance.

CGPS Implementation and Lidar/Laser Altimeter Experiences at l'Estartit, Ibiza and Barcelona Harbours for Sea Level Monitoring

NASA Astrophysics Data System (ADS)

Martinez-Benjamin, J.; Schutz, B.; Urban, T.; Ortiz Castellon, M.; Martinez-Garcia, M.; Ruiz, A.; Perez, B.; Rodriguez-Velasco, G.

2008-12-01

In the framework of a Spanish Space Project, the instrumentation of sea level measurements has been improved by providing the Barcelona site with a radar tide gauge and with a continuous GPS station nearby. The radar tide gauge is a Datamar 3000C device and a Thales Navigation Internet-Enabled GPS Continuous Geodetic Reference Station (iCGRS) with a choke ring antenna. It is intended that the overall system will constitute a CGPS Station of the ESEAS (European Sea Level) and TIGA (GPS Tide Gauge Benchmark Monitoring) networks. Puertos del Estado (Spanish Harbours) installed the tide gauge station at Ibiza harbour in January 2003. The station belongs to the REDMAR network, composed at this moment by 21 stations distributed along the whole Spanish waters, including also the Canary islands. The tide gauge also belongs to the ESEAS (European Sea Level) network. At the Barcelona harbour they have installed a radar tide gauge near a GPS station belonging to Puerto de Barcelona. L'Estartit floating tide gauge was set up in 1990. Data are taken in graphics registers from each two hours the mean value is recorded in an electronic support. L'Estartit tide gauge series provides good quality information about the changes in the sea heights at centimeter level, that is the magnitude of the common tides in the Mediterranean. Two airborne calibration campaigns carrying an Optech Lidar ALTM-3025 (ICC) were made on June 16, 2007 with a Partenavia P-68 and October 12, 2007, with a Cessna Caravan 208B flying along two ICESat target tracks including crossover near l'Estartit. The validation of this new technology LIDAR may be useful to fill coastal areas where satellite radar altimeters are not measuring due to the large footprint and the resulting gaps of about 15-30 km within the coastline. Measurements with a GPS Buoy at l'Estartit harbour were made during the June experience and a GPS reference station was installed in Aiguablava. On October 12, 2007, another LIDAR campaign was

The Harbour School, A Very Special School. IssueTrak: A CEFPI Brief on Educational Facility Issues

ERIC Educational Resources Information Center

Stenzler, Yale

2005-01-01

The Harbour School in Baltimore County, Maryland and provides a unique and outstanding setting that was designed to enhance and support the programs and services required for 125 special-needs students between the ages of 6 and 21. The director of the school, Dr. Linda Jacobs, had previous experience with establishing a school in a commercial…

Personal exposure to benzene and 1,3-butadiene during petroleum refinery turnarounds and work in the oil harbour.

PubMed

Akerstrom, M; Almerud, P; Andersson, E M; Strandberg, B; Sallsten, G

2016-11-01

Petroleum refinery workers' exposure to the carcinogens benzene and 1,3-butadiene has decreased during normal operations. However, certain occupational groups or events at the refineries still involve a risk of higher exposures. The aim of this study was to examine the personal exposure to benzene and 1,3-butadiene at refinery turnarounds and during work in the oil harbour. Personal exposure measurements of benzene and 1,3-butadiene were taken during work shifts, with a priori assumed higher benzene exposure, using PerkinElmer diffusive samplers filled with Carbopack X. Mean exposure levels were calculated, and repeated exposure measurements, when available, were assessed using mixed effect models. Group and individual compliance with the Swedish occupational exposure limit (OEL) was tested for the different exposure groups. Mean benzene exposure levels for refinery workers during the three measured turnarounds were 150, 610 and 960 µg/m 3 , and mean exposures for oil harbour workers and sewage tanker drivers were 310 and 360 µg/m 3 , respectively. Higher exposures were associated with handling benzene-rich products. Most occupational groups did not comply with the Swedish OEL for benzene nor did the individuals within the groups. The exposure to 1,3-butadiene was very low, between <1 and 3 % of the Swedish OEL. Work within the petroleum refinery industry, with potential exposure to open product streams containing higher fractions of benzene, pose a risk of personal benzene exposures exceeding the OEL. Refinery workers performing these work tasks frequently, such as contractors, sewage tanker drivers and oil harbour workers, need to be identified and protected.

Fostering Ecological Literacy: A Case Study of the Saint John Harbour in Two High School English Language Arts Classrooms

NASA Astrophysics Data System (ADS)

Douglas, Velta

Integrating environmental education into curriculum in a way that tackles the holistic and complicated nature of multi-dimensional issues continues to be a challenge for educators and administrators. There is potential in using ecological literacy to introduce local environmental case studies into English Language Arts high school classrooms. This research examines the experiences of two ELA classrooms in one Saint John, NB, high school with a two-week unit based on stakeholder relationships within the Saint John Harbour. Through presentations by guest speakers and research sourced from local community groups, students learned about the highly complex environmental issues that inform management decisions for the Harbour. Using these materials as background, students participated in a mock stakeholders meeting. Case study methodology was used to explore student learning in both a higher-level and a lower-level grade 10 ELA class. Data for the analysis included: cognitive mapping exercises; oral and written classroom assignments and activities; a videotape of the mock stakeholder meetings; a focus group interview with selected students; and researcher field notes. Data demonstrated significant student learning about environmental issues including increased sophistication in describing links between and among environmental issues affecting the harbour, and much more complex understandings of the positions and roles of the various stakeholder groups. Some important areas of resistance to new learning were also evident. Implications for practice and policy and recommendations for future research are discussed.

Developing a Social, Cultural and Economic Report Card for a Regional Industrial Harbour

PubMed Central

Pascoe, Sean; Tobin, Renae; Windle, Jill; Cannard, Toni; Marshall, Nadine; Kabir, Zobaidul; Flint, Nicole

2016-01-01

Report cards are increasingly used to provide ongoing snap-shots of progress towards specific ecosystem health goals, particularly in coastal regions where planners need to balance competing demands for coastal resources from a range of industries. While most previous report cards focus on the biophysical components of the system, there is a growing interest in including the social and economic implications of ecosystem management to provide a greater social-ecological system understanding. Such a report card was requested on the Gladstone Harbour area in central Queensland, Australia. Gladstone Harbour adjoins the southern Great Barrier Reef, and is also a major industrial and shipping port. Balancing social, economic and environmental interests is therefore of great concern to the regional managers. While environmental benchmarking procedures are well established within Australia (and elsewhere), a method for assessing social and economic performance of coastal management is generally lacking. The key aim of this study was to develop and pilot a system for the development of a report card relating to appropriate cultural, social and economic objectives. The approach developed uses a range of multicriteria decision analysis methods to assess and combine different qualitative and quantitative measures, including the use of Bayesian Belief Networks to combine the different measures and provide an overall quantitative score for each of the key management objectives. The approach developed is readily transferable for purposes of similar assessments in other regions. PMID:26839949

Nutlin‐3a selects for cells harbouring TP 53 mutations

PubMed Central

Hollstein, Monica; Arlt, Volker M.; Phillips, David H.

2016-01-01

TP53 mutations occur in half of all human tumours. Mutagen‐induced or spontaneous TP53 mutagenesis can be studied in vitro using the human TP53 knock‐in (Hupki) mouse embryo fibroblast (HUF) immortalisation assay (HIMA). TP53 mutations arise in up to 30% of mutagen‐treated, immortalised HUFs; however, mutants are not identified until TP53 sequence analysis following immortalisation (2–5 months) and much effort is expended maintaining TP53‐WT cultures. In order to improve the selectivity of the HIMA for HUFs harbouring TP53 mutations, we explored the use of Nutlin‐3a, an MDM2 inhibitor that leads to stabilisation and activation of wild‐type (WT) p53. First, we treated previously established immortal HUF lines carrying WT or mutated TP53 with Nutlin‐3a to examine the effect on cell growth and p53 activation. Nutlin‐3a induced the p53 pathway in TP53‐WT HUFs and inhibited cell growth, whereas most TP53‐mutated HUFs were resistant to Nutlin‐3a. We then assessed whether Nutlin‐3a treatment could discriminate between TP53‐WT and TP53‐mutated cells during the HIMA (n = 72 cultures). As immortal clones emerged from senescent cultures, each was treated with 10 µM Nutlin‐3a for 5 days and observed for sensitivity or resistance. TP53 was subsequently sequenced from all immortalised clones. We found that all Nutlin‐3a‐resistant clones harboured TP53 mutations, which were diverse in position and functional impact, while all but one of the Nutlin‐3a‐sensitive clones were TP53‐WT. These data suggest that including a Nutlin‐3a counter‐screen significantly improves the specificity and efficiency of the HIMA, whereby TP53‐mutated clones are selected prior to sequencing and TP53‐WT clones can be discarded. PMID:27813088

Sources of ambient concentrations and chemical composition of PM 2.5-0.1 in Cork Harbour, Ireland

NASA Astrophysics Data System (ADS)

Hellebust, S.; Allanic, A.; O'Connor, I. P.; Jourdan, C.; Healy, D.; Sodeau, J. R.

2010-02-01

Particulate matter (PM 10-2.5 and PM 2.5-0.1) has been collected over a period of one year in Cork Harbour, Ireland, using a high-volume cascade impactor and polyurethane foam collection substrate. Collected PM 2.5-0.1 was analysed for water-soluble inorganic ions and metal content using ion chromatography and inductively coupled plasma-optical emission spectroscopy. On average approximately 50% by mass of the chemical content of PM was identified. The motivation for the study was to assess the potential impact of shipping emissions on air quality in Cork Harbour and City, with a view to informing public health impacts. The average ambient concentration of PM 10 between May 2007 and April 2008 was 4.6 µgm - 3 and the maximum concentration measured in one sample, representing a 4 day collection period, was 16 µgm - 3 . The major inorganic constituents identified in PM collected in Haulbowline Island in Cork Harbour were sulfate, ammonium, nitrate, chloride and sodium ions, which were mainly attributable to sea salt and secondary inorganic aerosols from regional sources. The results were analysed by principal component analysis for the purpose of source apportionment. Four factors were identified explaining over 80% of the data set variance. The factors were: shipping, sea salt, crustal material and secondary inorganic aerosols (SIA). The smaller size fraction was frequently observed to dominate, as the average concentration was 2.77 µgm - 3 for PM 2.5-0.1 compared to 1.9 µgm - 3 for PM 10-2.5. Fresh ship plumes were not found to make a significant contribution to primary PM 2.5-0.1 concentrations adjacent to the shipping channel. However, this was partially attributed to the ultrafine nature of ship emissions and the majority of the toxic metal content was attributed to emissions associated with heavy oil combustion sources, which include ship engines.

Source apportionment of PAH in Hamilton Harbour suspended sediments: comparison of two factor analysis methods.

PubMed

Sofowote, Uwayemi M; McCarry, Brian E; Marvin, Christopher H

2008-08-15

A total of 26 suspended sediment samples collected over a 5-year period in Hamilton Harbour, Ontario, Canada and surrounding creeks were analyzed for a suite of polycyclic aromatic hydrocarbons and sulfur heterocycles. Hamilton Harbour sediments contain relatively high levels of polycyclic aromatic compounds and heavy metals due to emissions from industrial and mobile sources. Two receptor modeling methods using factor analyses were compared to determine the profiles and relative contributions of pollution sources to the harbor; these methods are principal component analyses (PCA) with multiple linear regression analysis (MLR) and positive matrix factorization (PMF). Both methods identified four factors and gave excellent correlation coefficients between predicted and measured levels of 25 aromatic compounds; both methods predicted similar contributions from coal tar/coal combustion sources to the harbor (19 and 26%, respectively). One PCA factor was identified as contributions from vehicular emissions (61%); PMF was able to differentiate vehicular emissions into two factors, one attributed to gasoline emissions sources (28%) and the other to diesel emissions sources (24%). Overall, PMF afforded better source identification than PCA with MLR. This work constitutes one of the few examples of the application of PMF to the source apportionment of sediments; the addition of sulfur heterocycles to the analyte list greatly aided in the source identification process.

Recent changes in estuarine benthic and suprabenthic communities resulting from the development of harbour infrastructure.

PubMed

Dauvin, J C; Desroy, N; Janson, A L; Vallet, C; Duhamel, S

2006-01-01

Using a Before/During/After sampling protocol, the effects of the Le Havre harbour extension, which was started at the end of 2001, on the macrobenthic and suprabenthic communities in the eastern Bay of Seine (English Channel) were examined. As the construction phase has not yet been completed, the results presented here reflect only the data collected before and during the operations (September 2000 and 2002 for benthos sampling and March 2001, September 2001, October 2002 and March 2003 for suprabenthos sampling). Although bio-sedimentary changes did occur at the mouth of the Seine river, an analysis of benthic assemblages reveals that the dredging and construction operations do not seem to have influenced assemblage structure or the spatial distribution of organisms. Comparisons of the suprabenthic assemblages at each sampling date indicate that seasonal dynamics was mainly responsible for determining species distribution. We conclude that, 1 year into the harbour management plan, the observed changes in benthic and suprabenthic assemblage abundance do not exceed the range of spatial variability that exists naturally in the Seine estuary. Despite this compensatory actions designed to protect the aquatic habitats and to preserve a sustainable and healthy ecosystem have been added to the infrastructure development plan.

Response to erlotinib in a patient with lung adenocarcinoma harbouring the EML4-ALK translocation: A case report.

PubMed

Alì, Greta; Chella, Antonio; Lupi, Cristiana; Proietti, Agnese; Niccoli, Cristina; Boldrini, Laura; Davini, Federico; Mussi, Alfredo; Fontanini, Gabriella

2015-04-01

Lung cancer is the leading cause of cancer-associated mortality worldwide, and the mainstay of treatment remains to be personalised therapy. Tyrosine kinase inhibitors of the epidermal growth factor receptor (EGFR-TKIs) have been reported to exert a significant impact in the treatment of non-small cell lung cancer (NSCLC), particularly in patients harbouring mutations in the EGFR gene. The echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase ( EML4-ALK ) gene translocation has been described in a subset of patients with NSCLC and possesses potent oncogenic activity. This translocation represents one of the most novel molecular targets in the treatment of NSCLC. Patients who harbour the EML4-ALK rearrangement possess lung tumours that lack EGFR or K-ras mutations. The present study reports the case of a patient possessing the EML4-ALK rearrangement that was initially treated with erlotinib and achieved a lasting clinical response. To the best of our knowledge, the current study is the first report of a clinical response to EGFR-TKI in a patient with lung adenocarcinoma harbouring the EML4-ALK fusion gene, but no EGFR mutations. However, as the disease progressed, the ALK gene status of the tumour was investigated, and based upon a positive result, the patient was treated with crizotinib and achieved a complete response. In conclusion, the present study suggests that the EML4-ALK rearrangement is not always associated with resistance to EGFR-TKIs. Further studies are required to clarify the biological features of these tumours and to investigate the mechanisms underlying the primary resistance to EGFR-TKIs when the EML4-ALK rearrangement is present.

Biological variables and health status affecting inorganic element concentrations in harbour porpoises (Phocoena phocoena) from Portugal (western Iberian Peninsula).

PubMed

Ferreira, Marisa; Monteiro, Silvia S; Torres, Jordi; Oliveira, Isabel; Sequeira, Marina; López, Alfredo; Vingada, José; Eira, Catarina

2016-03-01

The coastal preferences of harbour porpoise (Phocoena phocoena) intensify their exposure to human activities. The harbour porpoise Iberian population is presently very small and information about the threats it endures is vital for the conservation efforts that are being implemented to avoid local extinction. The present study explored the possible relation between the accumulation of trace elements by porpoises and their sex, body length, nutritional state, presence of parasites and gross pathologies. The concentrations of arsenic (As), cadmium (Cd), copper (Cu), mercury (Hg), manganese (Mn), nickel (Ni), lead (Pb), zinc (Zn) and selenium (Se) were evaluated in 42 porpoises stranded in Portugal between 2005 and 2013. Considering European waters, porpoises stranded in Portugal present the highest Hg concentrations and the lowest Cd concentrations, which may reflect dietary preferences and the geographic availability of these pollutants. While no effect of sex on trace element concentrations was detected, there was a positive relationship between porpoise body length and the concentration of Cd, Hg and Pb. Animals in worse nutritional condition showed higher levels of Zn. Harbour porpoises with high parasite burdens showed lower levels of Zn and As in all analysed tissues and also lower levels of renal Ni, while those showing gross pathologies presented higher Zn and Hg levels. This is the first data on the relationship between trace elements and health-related variables in porpoises from southern European Atlantic waters, providing valuable baseline information about the contamination status of this vulnerable population. Copyright © 2016 Elsevier Ltd. All rights reserved.

Beta2 toxin is not involved in in vitro cell cytotoxicity caused by human and porcine cpb2-harbouring Clostridium perfringens.

PubMed

Allaart, Janneke G; van Asten, Alphons J A M; Vernooij, Johannes C M; Gröne, Andrea

2014-06-25

Clostridium perfringens is a common cause of intestinal disease in animals and humans. Its pathogenicity is attributed to the toxins it can produce, including the beta2 toxin. The presence of cpb2, the gene encoding the beta2 toxin, has been associated with diarrhoea in neonatal piglets and humans. However, the exact role of the beta2 toxin in the development of diarrhoea is still unknown. In this study we investigated the level of cytotoxicity to porcine IPI-21 and human Caco-2 cell-lines caused by porcine and human cpb2-harbouring C. perfringens and the significance of the beta2 toxin for the induction of cell cytotoxicity. Supernatants of porcine cpb2-harbouring C. perfringens strains were cytotoxic to both cell lines. Cell cytotoxicity caused by supernatant of human cpb2-harbouring C. perfringens strains was variable among strains. However, removal of the beta2 toxin by anti-beta2 toxin antibodies or degradation of the beta2 toxin by trypsin did not reduce the cytotoxic effect of any of the supernatants. These data suggest that beta2 toxin does not play a role in the development of cell cytotoxicity in in vitro experiments. In vivo studies are necessary to definitely define the role of beta2 toxin in the development of cell cytotoxicity and subsequent diarrhoea. Copyright © 2014 Elsevier B.V. All rights reserved.

Listeria monocytogenes isolates from food and food environment harbouring tetM and ermB resistance genes.

PubMed

Haubert, L; Mendonça, M; Lopes, G V; de Itapema Cardoso, M R; da Silva, W P

2016-01-01

Listeria monocytogenes is a foodborne pathogen that has become an important cause of human and animal diseases worldwide. The purpose of this study was to evaluate the serotypes, virulence potential, antimicrobial resistance profile, and genetic relationships of 50 L. monocytogenes isolates from food and food environment in southern Brazil. In this study, the majority of L. monocytogenes isolates belonged to the serotypes 1/2b (42%) and 4b (26%), which are the main serotypes associated with human listeriosis. In addition, all isolates harboured internalin genes (inlA, inlC, inlJ), indicating a virulence potential. The isolates were sensitive to most of the antimicrobial compounds analysed, and five isolates (10%) were multi-resistant. Two isolates harboured antimicrobial resistance genes (tetM and ermB) and in one of them, the gene was present in the plasmid. Moreover, according to the pulsed field gel electrophoresis assay, two multi-resistant isolates were a single clone isolated from food and the processing plant. The isolates were susceptible to the most frequently used antibiotics for listeriosis treatment. However, the presence of multidrug-resistant isolates and antimicrobial resistance genes including in the plasmid could even be transferred between bacterial species, suggesting a potential health risk to consumers and a potential risk of spreading multi-resistance genes to other bacteria. Listeria monocytogenes is an important agent of foodborne diseases. The results of this study suggest a potential capacity of L. monocytogenes isolates from food and food environment to cause human infections. Antimicrobial multi-resistance profiles were detected in 10%, and two isolates harboured tetM and ermB resistance genes. Moreover, the present research can help to build up a better knowledge about antimicrobial resistance of L. monocytogenes. Additionally, we found one isolate carrying tetM resistance gene in a plasmid, that suggests a possible transmission

Haul-Out Behaviour of the World's Northernmost Population of Harbour Seals (Phoca vitulina) throughout the Year

PubMed Central

Hamilton, Charmain D.; Lydersen, Christian; Ims, Rolf A.; Kovacs, Kit M.

2014-01-01

The harbour seal population in Svalbard occurs at the northernmost limit of the species' range. It experiences environmental extremes far beyond the norm for this species, including an extended period of polar night and extensive sea ice cover. In 2009 and 2010, 60 harbour seals (30 pups + 30 immature/mature seals) from this population were equipped with Satellite-Relay Data Loggers (SRDLs) to study their haul-out behaviour, with a special focus on the winter period. Using a combination of Generalized Additive Mixed Models and Cox Proportional Hazard models, the influences of sex, maturity, temporal, spatial and environmental factors on haul-out behaviour were explored. All of the seals continued to haul out even through the coldest periods during the polar night, though clear seasonality in the time spent hauled out daily was displayed by both immature and mature seals. Time spent hauled out daily decreased from ∼5.2 hrs in September to ∼1.2 hrs in February in these age groups, while pups displayed less seasonality (∼2.4 hrs/day throughout most of the year). The average at-sea period also exhibited seasonality, increasing to a maximum of ∼1.6 days in February (monthly maxima for individual animals ranged from 7 to 19 days). The seals showed a strong preference to haul out at low tide when hauling out on land but not when using sea ice as a haul-out platform. A diel rhythm in haul-out behaviour was present during the months with day–night cycling and midnight sun but not during the polar night. Haul-out behaviour was impacted to a greater extent by air pressure, through its effect on wind speed, than by absolute temperature values. The extreme environment in Svalbard likely causes some physiological challenges that might impact survival rates negatively, particularly among pups. Climate warming is likely to have positive effects on Svalbard's harbour seal population. PMID:24465867

Telemetry-Determined Habitat Use Informs Multi-Species Habitat Management in an Urban Harbour.

PubMed

Rous, Andrew M; Midwood, Jonathon D; Gutowsky, Lee F G; Lapointe, Nicolas W R; Portiss, Rick; Sciscione, Thomas; Wells, Mathew G; Doka, Susan E; Cooke, Steven J

2017-01-01

Widespread human development has led to impairment of freshwater coastal wetlands and embayments, which provide critical and unique habitat for many freshwater fish species. This is particularly evident in the Laurentian Great Lakes, where such habitats have been severely altered over the last century as a result of industrial activities, urbanization, dredging and infilling. In Toronto Harbour, extensive restoration efforts have been directed towards improving the amount and quality of aquatic habitat, especially for fishes. To evaluate the effectiveness of this restoration work, use of the restored area by both target species and the fish community as a whole must be assessed. Individuals from four species (Common Carp, Largemouth Bass, Northern Pike and Yellow Perch) were tagged and tracked continuously for 1 year using an acoustic telemetry array in Toronto Harbour area of Lake Ontario. Daily site fidelity was estimated using a mixed-effects logistic regression model. Daily site fidelity was influenced by habitat restoration and its interactions with species and body size, as well as season and its interactions with species and body size. Daily site fidelity was higher in restored sites compared to non-restored sites for Yellow Perch and Northern Pike, but lower for Largemouth Bass and Common Carp. For all species, daily site fidelity estimates were highest during the summer and lowest during autumn. The approach used here has merit for evaluating restoration success and informing future habitat management activities. Creating diverse habitats that serve multiple functions and species are more desirable than single-function-oriented or single-species-oriented designs.

Telemetry-Determined Habitat Use Informs Multi-Species Habitat Management in an Urban Harbour

NASA Astrophysics Data System (ADS)

Rous, Andrew M.; Midwood, Jonathon D.; Gutowsky, Lee F. G.; Lapointe, Nicolas W. R.; Portiss, Rick; Sciscione, Thomas; Wells, Mathew G.; Doka, Susan E.; Cooke, Steven J.

2017-01-01

Widespread human development has led to impairment of freshwater coastal wetlands and embayments, which provide critical and unique habitat for many freshwater fish species. This is particularly evident in the Laurentian Great Lakes, where such habitats have been severely altered over the last century as a result of industrial activities, urbanization, dredging and infilling. In Toronto Harbour, extensive restoration efforts have been directed towards improving the amount and quality of aquatic habitat, especially for fishes. To evaluate the effectiveness of this restoration work, use of the restored area by both target species and the fish community as a whole must be assessed. Individuals from four species (Common Carp, Largemouth Bass, Northern Pike and Yellow Perch) were tagged and tracked continuously for 1 year using an acoustic telemetry array in Toronto Harbour area of Lake Ontario. Daily site fidelity was estimated using a mixed-effects logistic regression model. Daily site fidelity was influenced by habitat restoration and its interactions with species and body size, as well as season and its interactions with species and body size. Daily site fidelity was higher in restored sites compared to non-restored sites for Yellow Perch and Northern Pike, but lower for Largemouth Bass and Common Carp. For all species, daily site fidelity estimates were highest during the summer and lowest during autumn. The approach used here has merit for evaluating restoration success and informing future habitat management activities. Creating diverse habitats that serve multiple functions and species are more desirable than single-function-oriented or single-species-oriented designs.

The influence of acoustic emissions for underwater data transmission on the behaviour of harbour porpoises (Phocoena phocoena) in a floating pen.

PubMed

Kastelein, R A; Verboom, W C; Muijsers, M; Jennings, N V; van der Heul, S

2005-05-01

To prevent grounding of ships and collisions between ships in shallow coastal waters, an underwater data collection and communication network is currently under development: Acoustic Communication network for Monitoring of underwater Environment in coastal areas (ACME). Marine mammals might be affected by ACME sounds since they use sounds of similar frequencies (around 12 kHz) for communication, orientation, and prey location. If marine mammals tend to avoid the vicinity of the transmitters, they may be kept away from ecologically important areas by ACME sounds. One marine mammal species that may be affected in the North Sea is the harbour porpoise. Therefore, as part of an environmental impact assessment program, two captive harbour porpoises were subjected to four sounds, three of which may be used in the underwater acoustic data communication network. The effect of each sound was judged by comparing the animals' positions and respiration rates during a test period with those during a baseline period. Each of the four sounds could be made a deterrent by increasing the amplitude of the sound. The porpoises reacted by swimming away from the sounds and by slightly, but significantly, increasing their respiration rate. From the sound pressure level distribution in the pen, and the distribution of the animals during test sessions, discomfort sound level thresholds were determined for each sound. In combination with information on sound propagation in the areas where the communication system may be deployed, the extent of the 'discomfort zone' can be estimated for several source levels (SLs). The discomfort zone is defined as the area around a sound source that harbour porpoises are expected to avoid. Based on these results, SLs can be selected that have an acceptable effect on harbour porpoises in particular areas. The discomfort zone of a communication sound depends on the selected sound, the selected SL, and the propagation characteristics of the area in which the

Enzymatic activity in the surface microlayer and subsurface water in the harbour channel

NASA Astrophysics Data System (ADS)

Perliński, Piotr; Mudryk, Zbigniew J.; Antonowicz, Józef

2017-09-01

Hydrolytic activity of eight extracellular enzymes was determined spectrofluorimetric method in the surface microlayer and subsurface water in the harbour channel in Ustka. The ranking order of the potential enzyme activity rates in the studied water layers was as follows: lipase > phosphatase > aminopeptidase > β-glucosidase > α-glucosidase > xylanase > cellulase > chitinase. The level of activity of all studied hydrolases was higher in the surface microlayer than subsurface water. No clear gradients in the level of enzymatic activity were determined along the horizontal profile of the studied channel. Activity of extracellular enzymes was strongly influenced by the season.

LIDAR-based coastal landscape reconstruction and harbour location: The Viking-age royal burial site of Borre (Norway)

NASA Astrophysics Data System (ADS)

Draganits, Erich; Doneus, Michael; Gansum, Terje

2013-04-01

Airborne light detection and ranging (LIDAR) has found wide application in archaeological research for the detection and documentation of archaeological and palaeo-environmental features. In this study we demonstrate the analysis of an LIDAR derived 1x1 m digital elevation model (DTM) combined with geoarchaeological research of the coastal Viking-age burial site in Borre, Olso Fjord (Norway). Borre is an exceptional burial site in Scandinavia, containing burial mounds up to 40 m in diameter and 6 m height, mentioned in Nordic Sagas, especially in the skaldic poem Ynglingatal, as the burial place of one or two kings of the Ynglinga dynasty. Archaeological findings and radiocarbon ages indicate that the Borre burial ground had been in use broadly between 600-1000 AD. Despite the reasonable expectation that a coastal site connected with the Viking kings of Vestfold, with hall buildings and ship graves demands a harbour, up to now no harbour has not been found with traditional archaeological surveys. Since the area of Borre is affected by a continuous land uplift related to glacial rebound of Scandinavia, any former harbour site is expected to be exposed to the land surface today. The present day vertical crustal uplift is calculated around 2.5 mm/yr in the area of Borre. Burial mounds and surrounding borrow pits as well as geomorphological features of the uplifted coast of Borre have been analysed by the 1x1 m LIDAR-DTM, using hillshade, slope and local relief model for visualisation. Altogether, 41 burial mounds and further 6 potential mounds are visible in the high-resolution DTM. A succession of more than 14 beach ridges, cross-cut by the burial mounds, is visible from the present shore line up to 18 m asl. They are more or less parallel and similar in size, except between at ca. 4-6 m asl, where the most prominent ridge is located, which probably has been enforced artificially. Using published shoreline displacement curves from nearby areas, the shore-line at

Deep-sea mud in the Pacific Ocean as a potential resource for rare-earth elements

NASA Astrophysics Data System (ADS)

Kato, Yasuhiro; Fujinaga, Koichiro; Nakamura, Kentaro; Takaya, Yutaro; Kitamura, Kenichi; Ohta, Junichiro; Toda, Ryuichi; Nakashima, Takuya; Iwamori, Hikaru

2011-08-01

World demand for rare-earth elements and the metal yttrium--which are crucial for novel electronic equipment and green-energy technologies--is increasing rapidly. Several types of seafloor sediment harbour high concentrations of these elements. However, seafloor sediments have not been regarded as a rare-earth element and yttrium resource, because data on the spatial distribution of these deposits are insufficient. Here, we report measurements of the elemental composition of over 2,000 seafloor sediments, sampled at depth intervals of around one metre, at 78 sites that cover a large part of the Pacific Ocean. We show that deep-sea mud contains high concentrations of rare-earth elements and yttrium at numerous sites throughout the eastern South and central North Pacific. We estimate that an area of just one square kilometre, surrounding one of the sampling sites, could provide one-fifth of the current annual world consumption of these elements. Uptake of rare-earth elements and yttrium by mineral phases such as hydrothermal iron-oxyhydroxides and phillipsite seems to be responsible for their high concentration. We show that rare-earth elements and yttrium are readily recovered from the mud by simple acid leaching, and suggest that deep-sea mud constitutes a highly promising huge resource for these elements.

Diet overlap between harbour porpoise and bottlenose dolphin: An argument in favour of interference competition for food?

NASA Astrophysics Data System (ADS)

Spitz, Jérôme; Rousseau, Yann; Ridoux, Vincent

2006-10-01

In aquatic ecosystems, competitive interactions are occasionally described. Violent attacks on harbour porpoises by bottlenose dolphins were reported and it was proposed that this behavior could result from competitive interactions for food. This hypothesis implies that the two predators should share all or part of they prey range. In this work, we describe the diets of each predator in the Bay of Biscay and adjacent areas from stomach content analysis of stranded animals. The diet of the harbour porpoise was mostly composed of small schooling fish living close to the seafloor (98 percent by mass). The diet of the bottlenose dolphin was characterised by the presence of large specimens of demersal fish (91 percent by mass) and cephalopods. Several prey species are common in the two diets and even the length distributions of some of them, such as sardine or scads, are very similar. However, global indices such as the Mantel test or the Pianka's index indicate no or weak overlap. The dietary results suggest that the two predators show partial dietary overlap over several major dimensions of the foraging niche: prey profile, foraging habitats, prey species and size range. We suggest interference competition is plausible at the scale of a prey school that would be exploited jointly by groups of the two predators.

Assessment of heavy metal and petroleum hydrocarbon contamination in the Sultanate of Oman with emphasis on harbours, marinas, terminals and ports.

PubMed

Jupp, Barry P; Fowler, Scott W; Dobretsov, Sergey; van der Wiele, Henk; Al-Ghafri, Ahmed

2017-08-15

The assessment here includes data on levels of contaminants (petroleum hydrocarbons and heavy metals) in sediments and biomonitor organisms, including the eulittoral rock oyster Saccostrea cucullata and subtidal biomonitors, the barnacle Balanus trigonus and the antipatharian coral Antipathes sp., at harbours, marinas, terminals and large ports along the coastline of Oman. TBT levels in harbour and port sediments up to a maximum of 100ppb TBT dry weight are highlighted. Oysters contained concentrations up to 367ppm mg TPH/kg dry weight. The maximum levels of Cd, Cu, Pb and Zn were found in the subtidal sediments and barnacles at the oil tanker loading Single Buoy Mooring stations in Mina Al Fahal. In general, the levels of most of the contaminants analysed are at low to moderate concentrations compared to those in highly contaminated sites such as shipyards and dry docks, but continued monitoring is recommended especially during any dredging campaigns. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reproductive Failure in UK Harbour Porpoises Phocoena phocoena: Legacy of Pollutant Exposure?

PubMed Central

Murphy, Sinéad; Barber, Jonathan L; Learmonth, Jennifer A.; Read, Fiona L.; Deaville, Robert; Perkins, Matthew W.; Brownlow, Andrew; Davison, Nick; Penrose, Rod; Pierce, Graham J.; Law, Robin J.; Jepson, Paul D.

2015-01-01

Reproductive failure in mammals due to exposure to polychlorinated biphenyls (PCBs) can occur either through endocrine disrupting effects or via immunosuppression and increased disease risk. To investigate further, full necropsies and determination of summed 25 polychlorinated biphenyls congeners (∑PCBs lipid weight) in blubber were undertaken on 329 UK-stranded female harbour porpoises (1990-2012). In sexually mature females, 25/127 (19.7%) showed direct evidence of reproductive failure (foetal death, aborting, dystocia or stillbirth). A further 21/127 (16.5%) had infections of the reproductive tract or tumours of reproductive tract tissues that could contribute to reproductive failure. Resting mature females (non-lactating or non-pregnant) had significantly higher mean ∑PCBs (18.5 mg/kg) than both lactating (7.5 mg/kg) and pregnant females (6 mg/kg), though not significantly different to sexually immature females (14.0 mg/kg). Using multinomial logistic regression models ΣPCBs was found to be a significant predictor of mature female reproductive status, adjusting for the effects of confounding variables. Resting females were more likely to have a higher PCB burden. Health status (proxied by “trauma” or “infectious disease” causes of death) was also a significant predictor, with lactating females (i.e. who successfully reproduced) more likely to be in good health status compared to other individuals. Based on contaminant profiles (>11 mg/kg lipid), at least 29/60 (48%) of resting females had not offloaded their pollutant burden via gestation and primarily lactation. Where data were available, these non-offloading females were previously gravid, which suggests foetal or newborn mortality. Furthermore, a lower pregnancy rate of 50% was estimated for “healthy” females that died of traumatic causes of death, compared to other populations. Whether or not PCBs are part of an underlying mechanism, we used individual PCB burdens to show further evidence

Source apportionment of PM(2.5) in the harbour-industrial area of Brindisi (Italy): identification and estimation of the contribution of in-port ship emissions.

PubMed

Cesari, D; Genga, A; Ielpo, P; Siciliano, M; Mascolo, G; Grasso, F M; Contini, D

2014-11-01

Harbours are important for economic and social development of coastal areas but they also represent an anthropogenic source of emissions often located near urban centres and industrial areas. This increases the difficulties in distinguishing the harbour contribution with respect to other sources. The aim of this work is the characterisation of main sources of PM2.5 acting on the Brindisi harbour-industrial area, trying to pinpoint the contribution of in-port ship emissions to primary and secondary PM2.5. Brindisi is an important port-city of the Adriatic Sea considered a hot-spot for anthropogenic environmental pressures at National level. Measurements were performed collecting PM2.5 samples and characterising the concentrations of 23 chemical species (water soluble organic and inorganic carbon; major ions: SO4(2-), NO3(-), NH4(+), Cl(-), C2O4(2-), Na(+), K(+), Mg(2+), Ca(2+); and elements: Ni, Cu, V, Mn, As, Pb, Cr, Sb, Fe, Al, Zn, and Ti). These species represent, on average, 51.4% of PM2.5 and were used for source apportionment via PMF. The contributions of eight sources were estimated: crustal (16.4±0.9% of PM2.5), aged marine (2.6±0.5%), crustal carbonates (7.7±0.3%), ammonium sulphate (27.3±0.8%), biomass burning-fires (11.7±0.7%), traffic (16.4±1.7 %), industrial (0.4±0.3%) and a mixed source oil combustion-industrial including ship emissions in harbour (15.3±1.3%). The PMF did not separate the in-port ship emission contribution from industrial releases. The correlation of estimated contribution with meteorology showed directionality with an increase of oil combustion and sulphate contribution in the harbour direction with respect to the direction of the urban area and an increase of the V/Ni ratio. This allowed for the use of V as marker of primary ship contribution to PM2.5 (2.8%+/-1.1%). The secondary contribution of oil combustion to non-sea-salt-sulphate, nssSO4(2-), was estimated to be 1.3 μg/m(3) (about 40% of total nssSO4(2-) or 11% of PM2

Study of resonant modes of the harbour of Siracusa, Italy, and of the effects of breakwaters in case of a tsunami event.

NASA Astrophysics Data System (ADS)

Pagnoni, Gianluca; Tinti, Stefano

2016-04-01

The eastern coast of Sicily has been hit by many historical tsunamis of local and remote origin. This zone and in particular Siracusa, as test site, was selected in the FP7 European project ASTARTE (Assessment, Strategy And Risk Reduction for Tsunamis in Europe - FP7-ENV2013 6.4-3, Grant 603839). According to the project goals, in this work oscillations modes of the Siracusa harbour were analysed with focus on the typical tsunami periods range, and on the protecting effects of breakwaters by using linear and non-linear simulation models. The city of Siracusa is located north of the homonymous gulf and has two harbours, called "Piccolo" (small) and "Grande" (grand) that are connected through a narrow channel. The harbour "Piccolo" is the object of this work. It is located at the end of a bay facing east and bordered on the south by the peninsula of Ortigia and on the north by the mainland. The basin has an area of approximately 100,000 m2 and is very shallow with an average depth of 2.5 m. It is protected by two breakwaters reducing its mouth to only 40 m width. This study was carried out using the numerical code UBO-TSUFD that solves linear and non-linear shallow-water equations on a high-resolution 2m x 2m regular grid. Resonant modes were searched by sinusoidal forcing on the open boundary with periods in a range from about 60 s to 1600 s covering the typical tsunami spectrum. The work was divided into three phases. First we studied the natural resonance frequencies, and in particular the Helmholtz resonance mode by using a linear fixed-geometry model and assuming that the connecting channel between the two Siracusa ports is closed. Second, we repeated the analysis by using a non-linear simulation model accounting for flooding and for an open connection channel. Eventually, we forced the harbour by means of synthetic signals with amplitude, period and duration of the main historical tsunamis attacking Siracusa, namely the AD 365, the 1693 and the 1908 tsunami

Determination of low-level mercury in coralline aragonite by calcination-isotope dilution-inductively coupled plasma-mass spectrometry and its application to Diploria specimens from Castle Harbour, Bermuda

NASA Astrophysics Data System (ADS)

Lamborg, Carl H.; Swarr, Gretchen; Hughen, Konrad; Jones, Ross J.; Birdwhistell, Scot; Furby, Kathryn; Murty, Sujata A.; Prouty, Nancy; Tseng, Chun-Mao

2013-05-01

We have developed a technique that combines a high temperature quartz furnace with inductively coupled plasma-mass spectrometry for the determination of Hg stored in the annual CaCO3 bands found in coral skeletons. Substantial matrix effects, presumably due to the discontinuous introduction of CO2 to the gas stream, were corrected for by simultaneously supplying a stream of argon containing highly enriched elemental 202Hgo and observing peaks in the 200Hg/202Hg signal as the sample was decomposed. Primary signal calibration for Hg was achieved using gas injections from a saturated vapor standard. The absolute instrument detection limit was low (about 0.2 fmol), with a practical limit of detection (3σ of blanks) of 2 fmol. Reproducibility of samples was (RSD) 15-27%. We applied this method to the determination of Hg concentrations in two colonies of Diploria labyrinthiformis collected from Castle Harbour, Bermuda, at a site about to be buried under the municipal waste landfill. The temporal reconstructions of Castle Harbour seawater Hg concentrations implied by the coral record show a decline throughout the period of record (1949-2008). The coral archived no apparent signal associated with waste disposal practices in the Harbour (bulk waste land-filling or, since 1994, disposal of waste incinerator ash), and mercury concentrations in the coral did not correlate to growth rate as assessed by linear extension. There was, however, a large and nearly exponential decrease in apparent Hg concentration in the Harbour which circumstantially implicates the dredging and/or landfilling operations associated with the construction of the airport on St. David's Island.

[Landscape pattern change of Dongzhai Harbour mangrove, South China analyzed with a patch-based method and its driving forces].

PubMed

Huang, Xing; Xin, Kun; Li, Xiu-zhen; Wang, Xue-ping; Ren, Lin-jing; Li, Xi-zhi; Yan, Zhong-zheng

2015-05-01

According to the interpreted results of three satellite images of Dongzhai Harbour obtained in 1988, 1998 and 2009, the changes of landscape pattern and the differences of its driving forces of mangrove forest in Dongzhai Harbour were analyzed with a patch-based method on spatial distribution dynamics. The results showed that the areas of mangrove forest in 1988, 1998 and 2009 were 1809.4, 1738.7 and 1608.2 hm2 respectively, which presented a trend of decrease with enhanced degree of landscape fragmentation. The transformations among different landscape types indicated that the mangrove, agricultural land and forest land were mainly changed into built-up land and aquaculture pond. The statistical results obtained from three different methods, i.e., accumulative counting, percentage counting and main transformation route counting, showed that natural factors were the main reason for the changes of patch number, responsible for 58.6%, 72.2% and 72.1% of patch number change, respectively, while the percentages of patch area change induced by human activities were 70.4%, 70.3% and 76.4%, respectively, indicating that human activities were the primary factors of the change of patch areas.

The impact of glide phases on the trackability of hydrodynamic trails in harbour seals (Phoca vitulina).

PubMed

Wieskotten, S; Dehnhardt, G; Mauck, B; Miersch, L; Hanke, W

2010-11-01

The mystacial vibrissae of harbour seals (Phoca vitulina) constitute a highly sensitive hydrodynamic receptor system enabling the seals to detect and follow hydrodynamic trails. In the wild, hydrodynamic trails, as generated by swimming fish, consist of cyclic burst-and-glide phases, associated with various differences in the physical parameters of the trail. Here, we investigated the impact of glide phases on the trackability of differently aged hydrodynamic trails in a harbour seal. As fish are not easily trained to swim certain paths with predetermined burst-and-glide phases, the respective hydrodynamic trails were generated using a remote-controlled miniature submarine. Gliding phases in hydrodynamic trails had a negative impact on the trackability when trails were 15 s old. The seal lost the generated trails more often within the transition zones, when the submarine switched from a burst to a glide moving pattern. Hydrodynamic parameter analysis (particle image velocimetry) revealed that the smaller dimensions and faster decay of hydrodynamic trails generated by the gliding submarine are responsible for the impaired success of the seal tracking the gliding phase. Furthermore, the change of gross water flow generated by the submarine from a rearwards-directed stream in the burst phase to a water flow passively dragged behind the submarine during gliding might influence the ability of the seal to follow the trail as this might cause a weaker deflection of the vibrissae. The possible ecological implications of intermittent swimming behaviour in fish for piscivorous predators are discussed.

Identification and typing of Brucella spp. in stranded harbour porpoises (Phocoena phocoena) on the Dutch coast.

PubMed

Maio, Elisa; Begeman, Lineke; Bisselink, Yvette; van Tulden, Peter; Wiersma, Lidewij; Hiemstra, Sjoukje; Ruuls, Robin; Gröne, Andrea; Roest, Hendrik-Ido-Jan; Willemsen, Peter; van der Giessen, Joke

2014-09-17

The presence of Brucella (B.) spp. in harbour porpoises stranded between 2008 and 2011 along the Dutch coast was studied. A selection of 265 tissue samples from 112 animals was analysed using conventional and molecular methods. In total, 4.5% (5/112) of the animals corresponding with 2.3% (6/265) Brucella positive tissue samples were Brucella positive by culture and these were all confirmed by real-time polymerase chain reaction (real-time PCR) based on the insertion element 711 (IS711). In addition, two more Brucella-positive tissue samples from two animals collected in 2011 were identified using real-time PCR resulting in an overall Brucella prevalence of 6.3% (7/112 animals). Brucella spp. were obtained from lungs (n=3), pulmonary lymph node (n=3) and lungworms (n=2). Multi Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) typing based on the MLVA-16 showed that the Brucella isolates were B. ceti. Additional in silico Multi Locus Sequence typing (MLST) after whole genome sequencing of the 6 Brucella isolates confirmed B. ceti ST 23. According to the Brucella 2010 MLVA database, the isolated Brucella strains encountered were of five genotypes, in two distinct subclusters divided in two different time periods of harbour porpoises collection. This study is the first population based analyses for Brucella spp. infections in cetaceans stranded along the Dutch coast. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Variation in harbour porpoise activity in response to seismic survey noise

PubMed Central

Pirotta, Enrico; Brookes, Kate L.; Graham, Isla M.; Thompson, Paul M.

2014-01-01

Animals exposed to anthropogenic disturbance make trade-offs between perceived risk and the cost of leaving disturbed areas. Impact assessments tend to focus on overt behavioural responses leading to displacement, but trade-offs may also impact individual energy budgets through reduced foraging performance. Previous studies found no evidence for broad-scale displacement of harbour porpoises exposed to impulse noise from a 10 day two-dimensional seismic survey. Here, we used an array of passive acoustic loggers coupled with calibrated noise measurements to test whether the seismic survey influenced the activity patterns of porpoises remaining in the area. We showed that the probability of recording a buzz declined by 15% in the ensonified area and was positively related to distance from the source vessel. We also estimated received levels at the hydrophones and characterized the noise response curve. Our results demonstrate how environmental impact assessments can be developed to assess more subtle effects of noise disturbance on activity patterns and foraging efficiency. PMID:24850891

Histopathological lesions of molluscs in the harbour of Norderney, Lower Saxony, North Sea (Germany)

NASA Astrophysics Data System (ADS)

Watermann, Burkard; Thomsen, Anja; Kolodzey, Heike; Daehne, Bernd; Meemken, Maike; Pijanowska, Ute; Liebezeit, Gert

2008-06-01

During a combined research project at several stations along the Lower Saxony coast (German North Sea) antifouling biocides were analysed in water, sediment and biota. Pathological alterations in blue mussel, Pacific oyster and periwinkle found in the harbour of Norderney and a reference station are presented here and discussed on the background of chemical analyses. The molluscan species from the reference station Borkum East flat did not show any pathological effects in central organs, except those provoked by an infestation in the gastro-intestinal tract by the copepod Mytilicola intestinalis and trematode larvae. In most animals, the metacercaria were found in the interstitial tissue without any inflammatory reaction. In a minor number of specimens, an inflammatory reaction in the mucosa and sub-mucosa of the intestine occurred in association with Mytilicola infestation. These reactions may be evoked through mechanical irritation of the gut epithelium, metabolic products of the parasites or invading bacteria. In contrast to the observed pathological changes of mussels, oysters and periwinkles in Norderney harbour were not found to be associated with parasitic infestation. The most prominent pathological alterations were observed in the digestive system and in the gonad. In the gastro-intestinal tract inflammatory reactions, atrophy and necrosis of tubules in the mid gut gland were most pronounced in spring at the beginning of the pleasure boat season in the Pacific oyster and to a minor degree in the blue mussel and the periwinkle. The latter displayed additional inflammatory and necrotic processes in the gills. Especially in the gonad, an elevated resorption rate of gametes was present in the Pacific oyster and in the periwinkle. In addition, impact of organotin compounds was reflected in an intersex index of up to 1.4 in Littorina littorea in coincidence with masculinization of the reproductive organs.

Harbour seals (Phoca vitulina) can steer by the stars.

PubMed

Mauck, Björn; Gläser, Nele; Schlosser, Wolfhard; Dehnhardt, Guido

2008-10-01

Offshore orientation in marine mammals is still a mystery. For visual orientation during night-time foraging and travelling in the open seas, seals cannot rely on distant terrestrial landmarks, and thus might use celestial cues as repeatedly shown for nocturnally migrating birds. Although seals detect enough stars to probably allow for astronavigation, it was unclear whether they can orient by the night sky. The widely accepted cognitive mechanism for bird night-time orientation by celestial cues is a time-independent star compass with learned geometrical star configurations used to pinpoint north as the rotational centre of the starry sky while there is no conclusive evidence for a time-compensated star compass or true star navigation. Here, we present results for two harbour seals orienting in a custom made swimming planetarium. Both seals learned to highly accurately identify a lodestar out of a pseudo-randomly oriented, realistic projection of the northern hemisphere night sky. Providing the first evidence for star orientation capability in a marine mammal, our seals' outstanding directional precision would allow them to steer by following lodestars of learned star courses, a celestial orientation mechanism that has been known to be used by Polynesian navigators but has not been considered for animals yet.

Preimplantation death of xenomitochondrial mouse embryo harbouring bovine mitochondria

PubMed Central

Kawahara, Manabu; Koyama, Shiori; Iimura, Satomi; Yamazaki, Wataru; Tanaka, Aiko; Kohri, Nanami; Sasaki, Keisuke; Takahashi, Masashi

2015-01-01

Mitochondria, cellular organelles playing essential roles in eukaryotic cell metabolism, are thought to have evolved from bacteria. The organization of mtDNA is remarkably uniform across species, reflecting its vital and conserved role in oxidative phosphorylation (OXPHOS). Our objectives were to evaluate the compatibility of xenogeneic mitochondria in the development of preimplantation embryos in mammals. Mouse embryos harbouring bovine mitochondria (mtB-M embryos) were prepared by the cell-fusion technique employing the haemagglutinating virus of Japan (HVJ). The mtB-M embryos showed developmental delay at embryonic days (E) 3.5 after insemination. Furthermore, none of the mtB-M embryos could implant into the maternal uterus after embryo transfer, whereas control mouse embryos into which mitochondria from another mouse had been transferred developed as well as did non-manipulated embryos. When we performed quantitative PCR (qPCR) of mouse and bovine ND5, we found that the mtB-M embryos contained 8.3% of bovine mitochondria at the blastocyst stage. Thus, contamination with mitochondria from another species induces embryonic lethality prior to implantation into the maternal uterus. The heteroplasmic state of these xenogeneic mitochondria could have detrimental effects on preimplantation development, leading to preservation of species-specific mitochondrial integrity in mammals. PMID:26416548

Insect symbiotic bacteria harbour viral pathogens for transovarial transmission.

PubMed

Jia, Dongsheng; Mao, Qianzhuo; Chen, Yong; Liu, Yuyan; Chen, Qian; Wu, Wei; Zhang, Xiaofeng; Chen, Hongyan; Li, Yi; Wei, Taiyun

2017-03-06

Many insects, including mosquitoes, planthoppers, aphids and leafhoppers, are the hosts of bacterial symbionts and the vectors for transmitting viral pathogens 1-3 . In general, symbiotic bacteria can indirectly affect viral transmission by enhancing immunity and resistance to viruses in insects 3-5 . Whether symbiotic bacteria can directly interact with the virus and mediate its transmission has been unknown. Here, we show that an insect symbiotic bacterium directly harbours a viral pathogen and mediates its transovarial transmission to offspring. We observe rice dwarf virus (a plant reovirus) binding to the envelopes of the bacterium Sulcia, a common obligate symbiont of leafhoppers 6-8 , allowing the virus to exploit the ancient oocyte entry path of Sulcia in rice leafhopper vectors. Such virus-bacterium binding is mediated by the specific interaction of the viral capsid protein and the Sulcia outer membrane protein. Treatment with antibiotics or antibodies against Sulcia outer membrane protein interferes with this interaction and strongly prevents viral transmission to insect offspring. This newly discovered virus-bacterium interaction represents the first evidence that a viral pathogen can directly exploit a symbiotic bacterium for its transmission. We believe that such a model of virus-bacterium communication is a common phenomenon in nature.

Likely effects of construction of Scroby Sands offshore wind farm on a mixed population of harbour Phoca vitulina and grey Halichoerus grypus seals.

PubMed

Skeate, Eleanor R; Perrow, Martin R; Gilroy, James J

2012-04-01

Scroby Sands offshore wind farm was built close to a haul-out and breeding site for harbour seal, a species of conservation concern. An aerial survey programme conducted during a five-year period spanning wind farm construction, revealed a significant post-construction decline in haul-out counts. Multivariate model selection suggested that the decline was not related to the environmental factors considered, nor did it mirror wider population trends. Although cause and effect could not be unequivocally established, the theoretical basis of hearing in pinnipeds and previous studies suggested that extreme noise (to 257 dB re 1 μ Pa(pp) @ 1m) generated by pile-driving of turbine bases led to displacement of seals. A lack of full recovery of harbour seal during the study was also linked to their sensitivity to vessel activity and/or rapid colonisation of competing grey seal. Any impact of offshore wind farm development upon pinnipeds would be much reduced without pile-driving. Copyright © 2012 Elsevier Ltd. All rights reserved.

Harbour surveillance with cameras calibrated with AIS data

NASA Astrophysics Data System (ADS)

Palmieri, F. A. N.; Castaldo, F.; Marino, G.

The inexpensive availability of surveillance cameras, easily connected in network configurations, suggests the deployment of this additional sensor modality in port surveillance. Vessels appearing within cameras fields of view can be recognized and localized providing to fusion centers information that can be added to data coming from Radar, Lidar, AIS, etc. Camera systems, that are used as localizers however, must be properly calibrated in changing scenarios where often there is limited choice on the position on which they are deployed. Automatic Identification System (AIS) data, that includes position, course and vessel's identity, freely available through inexpensive receivers, for some of the vessels appearing within the field of view, provide the opportunity to achieve proper camera calibration to be used for the localization of vessels not equipped with AIS transponders. In this paper we assume a pinhole model for camera geometry and propose perspective matrices computation using AIS positional data. Images obtained from calibrated cameras are then matched and pixel association is utilized for other vessel's localization. We report preliminary experimental results of calibration and localization using two cameras deployed on the Gulf of Naples coastline. The two cameras overlook a section of the harbour and record short video sequences that are synchronized offline with AIS positional information of easily-identified passenger ships. Other small vessels, not equipped with AIS transponders, are localized using camera matrices and pixel matching. Localization accuracy is experimentally evaluated as a function of target distance from the sensors.

Ecotoxicological effects of a semi-submerged municipal dump (Castle harbour, Bermuda) on the Calico scallop Argopecten gibbus.

PubMed

Quinn, Brian; Gagné, Francois; Weber, Jean-Philippe; Blaise, Christian

2005-01-01

A biomarker study was undertaken using the Calico scallop Argopecten gibbus to assess the ecotoxicological effects of a semi-submerged municipal dump on the adjacent patch reef lagoon ecosystem (Castle harbour, Bermuda). Caged scallops were deployed in situ for 2 months at various distances from the dump (50 m, 900 m and 2.7 km) and at a reference site (14 km). A suite of biomarkers comprising metallothionein (MT), lipid peroxidation (LPO), vitellin-like proteins (Vn), glutathione S-transferase (GST), DNA strand breaks and condition factor (CF) were investigated in various tissues of the scallop (gill, digestive gland and gonad). Levels of heavy metals were also measured in the whole scallop soft tissue. While there was some variation in response between tissues, in general the results indicated that the dump was negatively impacting scallops deployed in the adjacent marine environment: elevated levels of MT, DNA strand breaks, Vn and GST and reduced condition factor were found for scallops deployed nearest to the dump and at the site 1.5 km from this point source of contamination (Tuckers town) in Castle harbour, with respect to the reference site, North Rock (although this exhibited some degree of metal contamination). The gills from scallops deployed at the dump site were the most responsive tissue, with the highest expression of MT, LPO and DNA damage. This study indicates the potential of the Calico scallop as a convenient bioindicator species in the marine tropical benthos.

Framework for assessing impacts of pile-driving noise from offshore wind farm construction on a harbour seal population

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Paul M., E-mail: lighthouse@abdn.ac.uk; Hastie, Gordon D., E-mail: gdh10@st-andrews.ac.uk; Nedwell, Jeremy, E-mail: Jeremy.Nedwell@subacoustech.com

2013-11-15

Offshore wind farm developments may impact protected marine mammal populations, requiring appropriate assessment under the EU Habitats Directive. We describe a framework developed to assess population level impacts of disturbance from piling noise on a protected harbour seal population in the vicinity of proposed wind farm developments in NE Scotland. Spatial patterns of seal distribution and received noise levels are integrated with available data on the potential impacts of noise to predict how many individuals are displaced or experience auditory injury. Expert judgement is used to link these impacts to changes in vital rates and applied to population models thatmore » compare population changes under baseline and construction scenarios over a 25 year period. We use published data and hypothetical piling scenarios to illustrate how the assessment framework has been used to support environmental assessments, explore the sensitivity of the framework to key assumptions, and discuss its potential application to other populations of marine mammals. -- Highlights: • We develop a framework to support Appropriate Assessment for harbour seal populations. • We assessed potential impacts of wind farm construction noise. • Data on distribution of seals and noise were used to predict effects on individuals. • Expert judgement linked these impacts to vital rates to model population change. • We explore the sensitivity of the framework to key assumptions and uncertainties.« less

Whole-genome sequencing enabling the detection of a colistin-resistant hypermutating Citrobacter werkmanii strain harbouring a novel metallo-β-lactamase VIM-48.

PubMed

Peter, S; Bezdan, D; Oberhettinger, P; Vogel, W; Dörfel, D; Dick, J; Marschal, M; Liese, J; Weidenmaier, C; Autenrieth, I; Ossowski, S; Willmann, M

2018-06-01

Citrobacter spp. harbouring metallo-β-lactamases (MBLs) have been reported from various countries and different sources, but their isolation from clinical specimens remains a rare event in Europe. MBL-harbouring Enterobacteriaceae are considered a major threat in infection control as therapeutic options are often limited to colistin. In this study, whole-genome sequencing was applied to characterise five clinical isolates of multidrug-resistant Citrobacter werkmanii obtained from rectal swabs. Four strains possessed a class 1 integron with a novel bla VIM-48 MBL resistance gene and the aminoglycoside acetyltransferase gene aacA4, whilst one isolate harboured a bla IMP-8 MBL. Resistance to colistin evolved in one strain isolated from a patient who had received colistin orally for 8 days. Genomic comparison of this strain with a colistin-susceptible pre-treatment isolate from the same patient revealed 66 single nucleotide polymorphisms (SNPs) and 26 indels, indicating the presence of a mutator phenotype. This was confirmed by the finding of a SNP in the mutL gene that led to a significantly truncated protein. Additionally, an amino acid change from glycine to serine at position 53 was observed in PmrA. Mutations in the pmrA gene have been previously described as mediating colistin resistance in different bacterial species and are the most likely reason for the susceptibility change observed. To the best of our knowledge, this is the first description of a colistin-resistant Citrobacter spp. isolated from a human sample. This study demonstrates the power of applying next-generation sequencing in a hospital setting to trace and understand evolving resistance at the level of individual patients. Copyright © 2018 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

The role of houseflies (Musca domestica) in harbouring Corynebacterium pseudotuberculosis in dairy herds in Israel.

PubMed

Braverman, Y; Chizov-Ginzburg, A; Saran, A; Winkler, M

1999-12-01

A study was conducted to assess the role of houseflies, Musca domestica L. in harbouring Corynebacterium pseudotuberculosis in dairy farms in Israel. The bacterium was isolated in June 1993 from 40 wild houseflies which had fed on a lesion on a cow, and from 28 laboratory flies fed on contaminated milk from a cow infected with mastitis. The bacterium was recovered from the body surface of 10 flies (of a total of 160) 10 min after being dipped entirely in a bacterial broth. The bacterium was recovered from the body surface of 10 flies (of a total of 40) 5 min after being fed on contaminated milk. When 110 flies were fed on contaminated sugar cubes, the bacterium was recovered externally from 70 flies 5 min later, and from an additional 20 flies 10 min after feeding. Of 110 flies, 80 excreted bacteria in saliva from 5 min to 3 h after feeding on contaminated milk. Bacteria were isolated from the intestine of 40 of 60 flies between 1 h and 4 h after feeding on contaminated milk. Bacteria were found in the faeces of 30 of 60 flies, between 1 h and 4 h after feeding on contaminated milk. In the light of these findings, and given the fact that this species of fly has a predilection to feed on milk residues of cow teats, the authors concluded that the housefly plays an important role in harbouring and disseminating C. pseudotuberculosis in dairy herds in Israel. In contrast, stable flies (Stomoxys calcitrans L.) are not important in the habouring and dissemination of the bacteria, since bacteria were not recovered 5, 10, 15, 30 min, 2 h or 24 h after membrane feeding on a mixture of bacterial broth and blood.

Spatial avoidance to experimental increase of intermittent and continuous sound in two captive harbour porpoises.

PubMed

Kok, Annebelle C M; Engelberts, J Pamela; Kastelein, Ronald A; Helder-Hoek, Lean; Van de Voorde, Shirley; Visser, Fleur; Slabbekoorn, Hans

2018-02-01

The continuing rise in underwater sound levels in the oceans leads to disturbance of marine life. It is thought that one of the main impacts of sound exposure is the alteration of foraging behaviour of marine species, for example by deterring animals from a prey location, or by distracting them while they are trying to catch prey. So far, only limited knowledge is available on both mechanisms in the same species. The harbour porpoise (Phocoena phocoena) is a relatively small marine mammal that could quickly suffer fitness consequences from a reduction of foraging success. To investigate effects of anthropogenic sound on their foraging efficiency, we tested whether experimentally elevated sound levels would deter two captive harbour porpoises from a noisy pool into a quiet pool (Experiment 1) and reduce their prey-search performance, measured as prey-search time in the noisy pool (Experiment 2). Furthermore, we tested the influence of the temporal structure and amplitude of the sound on the avoidance response of both animals. Both individuals avoided the pool with elevated sound levels, but they did not show a change in search time for prey when trying to find a fish hidden in one of three cages. The combination of temporal structure and SPL caused variable patterns. When the sound was intermittent, increased SPL caused increased avoidance times. When the sound was continuous, avoidance was equal for all SPLs above a threshold of 100 dB re 1 μPa. Hence, we found no evidence for an effect of sound exposure on search efficiency, but sounds of different temporal patterns did cause spatial avoidance with distinct dose-response patterns. Copyright © 2017 Elsevier Ltd. All rights reserved.

Abundance and recruitment data for Undaria pinnatifida in Brest harbour, France: Model versus field results.

PubMed

Murphy, James T; Voisin, Marie; Johnson, Mark; Viard, Frédérique

2016-06-01

The data presented in this article are related to the research article entitled "A modelling approach to explore the critical environmental parameters influencing the growth and establishment of the invasive seaweed Undaria pinnatifida in Europe" [1]. This article describes raw simulation data output from a novel individual-based model of the invasive kelp species Undaria pinnatifida. It also includes field data of monthly abundance and recruitment values for a population of invasive U. pinnatifida (in Brest harbour, France) that were used to validate the model. The raw model output and field data are made publicly available in order to enable critical analysis of the model predictions and to inform future modelling efforts of the study species.

Measuring biological responses at different levels of organisation to assess the effects of diffuse contamination derived from harbour and industrial activities in estuarine areas.

PubMed

de Los Ríos, A; Pérez, L; Echavarri-Erasun, B; Serrano, T; Barbero, M C; Ortiz-Zarragoitia, M; Orbea, A; Juanes, J A; Cajaraville, M P

2016-02-15

To evaluate the effects of diffuse contamination, biological measurements were applied in a scrap cargo harbour, a marina and an industrial area. Metal accumulation and biomarkers (survival in air, digestive gland and gonad histopathology, lysosomal membrane stability, intralysosomal metal accumulation, transcription of vitellogenin and MT20, peroxisome proliferation and micronuclei formation) were measured in transplanted mussels, together with metrics of benthic invertebrates. Benthic species were classified into ecological groups and univariate indexes were calculated. The marina showed high richness (16) and percentage of opportunistic species (55.1%) and low metal accumulation. Mussels in the scrap cargo harbour showed high metal accumulation, up-regulation of MT20 transcription, reduced health status (LP<6 min) and increased micronuclei frequencies (up to 11.3‰). At the industrial area, low species richness (4) and badly organised assemblages were detected and chemical analyses indicated significant amounts of bioavailable metals. Overall, selected biological measurements showed potential for the assessment of diffuse contamination. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biodiversity of the Deep-Sea Continental Margin Bordering the Gulf of Maine (NW Atlantic): Relationships among Sub-Regions and to Shelf Systems

PubMed Central

Kelly, Noreen E.; Shea, Elizabeth K.; Metaxas, Anna; Haedrich, Richard L.; Auster, Peter J.

2010-01-01

Background In contrast to the well-studied continental shelf region of the Gulf of Maine, fundamental questions regarding the diversity, distribution, and abundance of species living in deep-sea habitats along the adjacent continental margin remain unanswered. Lack of such knowledge precludes a greater understanding of the Gulf of Maine ecosystem and limits development of alternatives for conservation and management. Methodology/Principal Findings We use data from the published literature, unpublished studies, museum records and online sources, to: (1) assess the current state of knowledge of species diversity in the deep-sea habitats adjacent to the Gulf of Maine (39–43°N, 63–71°W, 150–3000 m depth); (2) compare patterns of taxonomic diversity and distribution of megafaunal and macrofaunal species among six distinct sub-regions and to the continental shelf; and (3) estimate the amount of unknown diversity in the region. Known diversity for the deep-sea region is 1,671 species; most are narrowly distributed and known to occur within only one sub-region. The number of species varies by sub-region and is directly related to sampling effort occurring within each. Fishes, corals, decapod crustaceans, molluscs, and echinoderms are relatively well known, while most other taxonomic groups are poorly known. Taxonomic diversity decreases with increasing distance from the continental shelf and with changes in benthic topography. Low similarity in faunal composition suggests the deep-sea region harbours faunal communities distinct from those of the continental shelf. Non-parametric estimators of species richness suggest a minimum of 50% of the deep-sea species inventory remains to be discovered. Conclusions/Significance The current state of knowledge of biodiversity in this deep-sea region is rudimentary. Our ability to answer questions is hampered by a lack of sufficient data for many taxonomic groups, which is constrained by sampling biases, life

Are conventional statistical techniques exhaustive for defining metal background concentrations in harbour sediments? A case study: The Coastal Area of Bari (Southeast Italy).

PubMed

Mali, Matilda; Dell'Anna, Maria Michela; Mastrorilli, Piero; Damiani, Leonardo; Ungaro, Nicola; Belviso, Claudia; Fiore, Saverio

2015-11-01

Sediment contamination by metals poses significant risks to coastal ecosystems and is considered to be problematic for dredging operations. The determination of the background values of metal and metalloid distribution based on site-specific variability is fundamental in assessing pollution levels in harbour sediments. The novelty of the present work consists of addressing the scope and limitation of analysing port sediments through the use of conventional statistical techniques (such as: linear regression analysis, construction of cumulative frequency curves and the iterative 2σ technique), that are commonly employed for assessing Regional Geochemical Background (RGB) values in coastal sediments. This study ascertained that although the tout court use of such techniques in determining the RGB values in harbour sediments seems appropriate (the chemical-physical parameters of port sediments fit well with statistical equations), it should nevertheless be avoided because it may be misleading and can mask key aspects of the study area that can only be revealed by further investigations, such as mineralogical and multivariate statistical analyses. Copyright © 2015 Elsevier Ltd. All rights reserved.

In situ growth rates of deep-water octocorals determined from 3D photogrammetric reconstructions

NASA Astrophysics Data System (ADS)

Bennecke, Swaantje; Kwasnitschka, Tom; Metaxas, Anna; Dullo, Wolf-Christian

2016-12-01

Growth rates of deep-water corals provide important information on the recovery potential of these ecosystems, for example from fisheries-induced impacts. Here, we present in situ growth dynamics that are currently largely unknown for deep-water octocorals, calculated by applying a non-destructive method. Videos of a boulder harbouring multiple colonies of Paragorgia arborea and Primnoa resedaeformis in the Northeast Channel Coral Conservation Area at the entrance to the Gulf of Maine at 863 m depth were collected in 2006, 2010 and 2014. Photogrammetric reconstructions of the boulder and the fauna yielded georeferenced 3D models for all sampling years. Repeated measurements of total length and cross-sectional area of the same colonies allowed the observation of growth dynamics. Growth rates of total length of Paragorgia arborea decreased over time with higher rates between 2006 and 2010 than between 2010 and 2014, while growth rates of cross-sectional area remained comparatively constant. A general trend of decreasing growth rates of total length with size of the coral colony was documented. While no growth was observed for the largest colony (165 cm in length) between 2010 and 2014, a colony 50-65 cm in length grew 3.7 cm yr-1 between 2006 and 2010. Minimum growth rates of 1.6-2.7 cm yr-1 were estimated for two recruits (<23 cm in 2014) of Primnoa resedaeformis. We successfully extracted biologically meaningful data from photogrammetric models and present the first in situ growth rates for these coral species in the Northwest Atlantic.

Under the sea: microbial life in volcanic oceanic crust.

PubMed

Edwards, Katrina J; Wheat, C Geoffrey; Sylvan, Jason B

2011-09-06

Exploration of the microbiology in igneous, 'hard rock' oceanic crust represents a major scientific frontier. The igneous crust harbours the largest aquifer system on Earth, most of which is hydrologically active, resulting in a substantial exchange of fluids, chemicals and microorganisms between oceanic basins and crustal reservoirs. Study of the deep-subsurface biosphere in the igneous crust is technically challenging. However, technologies have improved over the past decade, providing exciting new opportunities for the study of deep-seated marine life, including in situ and cross-disciplinary experimentation in microbiology, geochemistry and hydrogeology. In this Progress article, we describe the recent advances, available technology and remaining challenges in the study of the marine intraterrestrial microbial life that is harboured in igneous oceanic crust.

Amerindian-specific regions under positive selection harbour new lipid variants in Latinos

PubMed Central

Ko, Arthur; Cantor, Rita M.; Weissglas-Volkov, Daphna; Nikkola, Elina; Reddy, Prasad M. V. Linga; Sinsheimer, Janet S.; Pasaniuc, Bogdan; Brown, Robert; Alvarez, Marcus; Rodriguez, Alejandra; Rodriguez-Guillen, Rosario; Bautista, Ivette C.; Arellano-Campos, Olimpia; Muñoz-Hernández, Linda L.; Salomaa, Veikko; Kaprio, Jaakko; Jula, Antti; Jauhiainen, Matti; Heliövaara, Markku; Raitakari, Olli; Lehtimäki, Terho; Eriksson, Johan G.; Perola, Markus; Lohmueller, Kirk E.; Matikainen, Niina; Taskinen, Marja-Riitta; Rodriguez-Torres, Maribel; Riba, Laura; Tusie-Luna, Teresa; Aguilar-Salinas, Carlos A.; Pajukanta, Päivi

2014-01-01

Dyslipidemia and obesity are especially prevalent in populations with Amerindian backgrounds, such as Mexican–Americans, which predispose these populations to cardiovascular disease. Here we design an approach, known as the cross-population allele screen (CPAS), which we conduct prior to a genome-wide association study (GWAS) in 19,273 Europeans and Mexicans, in order to identify Amerindian risk genes in Mexicans. Utilizing CPAS to restrict the GWAS input variants to only those differing in frequency between the two populations, we identify novel Amerindian lipid genes, receptor-related orphan receptor alpha (RORA) and salt-inducible kinase 3 (SIK3), and three loci previously unassociated with dyslipidemia or obesity. We also detect lipoprotein lipase (LPL) and apolipoprotein A5 (APOA5) harbouring specific Amerindian signatures of risk variants and haplotypes. Notably, we observe that SIK3 and one novel lipid locus underwent positive selection in Mexicans. Furthermore, after a high-fat meal, the SIK3 risk variant carriers display high triglyceride levels. These findings suggest that Amerindian-specific genetic architecture leads to a higher incidence of dyslipidemia and obesity in modern Mexicans. PMID:24886709

Impact on demersal fish of a large-scale and deep sand extraction site with ecosystem-based landscaped sandbars

NASA Astrophysics Data System (ADS)

de Jong, Maarten F.; Baptist, Martin J.; van Hal, Ralf; de Boois, Ingeborg J.; Lindeboom, Han J.; Hoekstra, Piet

2014-06-01

For the seaward harbour extension of the Port of Rotterdam in the Netherlands, approximately 220 million m3 sand was extracted between 2009 and 2013. In order to decrease the surface area of direct impact, the authorities permitted deep sand extraction, down to 20 m below the seabed. Biological and physical impacts of large-scale and deep sand extraction are still being investigated and largely unknown. For this reason, we investigated the colonization of demersal fish in a deep sand extraction site. Two sandbars were artificially created by selective dredging, copying naturally occurring meso-scale bedforms to increase habitat heterogeneity and increasing post-dredging benthic and demersal fish species richness and biomass. Significant differences in demersal fish species assemblages in the sand extraction site were associated with variables such as water depth, median grain size, fraction of very fine sand, biomass of white furrow shell (Abra alba) and time after the cessation of sand extraction. Large quantities of undigested crushed white furrow shell fragments were found in all stomachs and intestines of plaice (Pleuronectes platessa), indicating that it is an important prey item. One and two years after cessation, a significant 20-fold increase in demersal fish biomass was observed in deep parts of the extraction site. In the troughs of a landscaped sandbar however, a significant drop in biomass down to reference levels and a significant change in species assemblage was observed two years after cessation. The fish assemblage at the crests of the sandbars differed significantly from the troughs with tub gurnard (Chelidonichthys lucerna) being a Dufrêne-Legendre indicator species of the crests. This is a first indication of the applicability of landscaping techniques to induce heterogeneity of the seabed although it remains difficult to draw a strong conclusion due the lack of replication in the experiment. A new ecological equilibrium is not reached after 2

Growth of plants on TBT-contaminated harbour sludge and effect on TBT removal.

PubMed

Novak, Jana; Trapp, Stefan

2005-11-01

Worldwide, large amounts of sediments have to be dredged annually from waterways and harbours. These sediments are sometimes polluted with a variety of toxic compounds. In some countries, including Belgium, the load with the biocide tributyltin (TBT) from ship coatings prohibits the dumping of harbour sludge into the sea. Land-based dumping is a commonly used alternative. This research investigated the feasibility to use land-deposited harbour sludge for plant production. In a field trial, the growth of 38 more or less salt-tolerant plant species on low and high TBT-contaminated sediments was studied. The elimination of TBT from sludge with and without vegetation was compared. The uptake of TBT and its degradation products di- and monobutyltin (DBT and MBT) into harvest products under field conditions was determined. EXPERIMENTAL SET-UP: Sediments dredged in May 2003 from the brackish waters of the port of Antwerp were analysed in the laboratory for soil texture, pH, electroconductivity, sodium, magnesium, potassium, calcium, ammonium, nitrate, total nitrogen, chloride, sulphur and the organotins TBT, DBT and MBT. The sediments were lagooned for one year to dewater, desalinate and improve their structure. Salt-tolerant domestic and wild plants were selected and sown in May 2004. In August 2004, plants were harvested and the produced biomass was determined. Samples were taken from vegetated and non-vegetated top and bottom sediments and from plants growing above soil and analysed for TBT, DBT and MBT. The fresh sediments showed a good supply with nutrients and a neutral pH, but were rather saline (EC 14 mS cm(-1) of the saturated paste extract). The salinity decreased to 3.7 mS cm(-1) during lagoonation. The high and the low contaminated sediment had initially 43 and 1.6 mg TBT kg(-1) dry weight, respectively. Besides TBT, several other contaminants were present in the sediments at critical levels. The biomass production of the plant species from the field trial

Effects of pile-driving on harbour porpoises (Phocoena phocoena) at the first offshore wind farm in Germany

NASA Astrophysics Data System (ADS)

Dähne, Michael; Gilles, Anita; Lucke, Klaus; Peschko, Verena; Adler, Sven; Krügel, Kathrin; Sundermeyer, Janne; Siebert, Ursula

2013-06-01

The first offshore wind farm ‘alpha ventus’ in the German North Sea was constructed north east of Borkum Reef Ground approximately 45 km north off the German coast in 2008 and 2009 using percussive piling for the foundations of 12 wind turbines. Visual monitoring of harbour porpoises was conducted prior to as well as during construction and operation by means of 15 aerial line transect distance sampling surveys, from 2008 to 2010. Static acoustic monitoring (SAM) with echolocation click loggers at 12 positions was performed additionally from 2008 to 2011. SAM devices were deployed between 1 and 50 km from the centre of the wind farm. During aerial surveys, 18 600 km of transect lines were covered in two survey areas (10 934 and 11 824 km2) and 1392 harbour porpoise sightings were recorded. Lowest densities were documented during the construction period in 2009. The spatial distribution pattern recorded on two aerial surveys three weeks before and exactly during pile-driving points towards a strong avoidance response within 20 km distance of the noise source. Generalized additive modelling of SAM data showed a negative impact of pile-driving on relative porpoise detection rates at eight positions at distances less than 10.8 km. Increased detection rates were found at two positions at 25 and 50 km distance suggesting that porpoises were displaced towards these positions. A pile-driving related behavioural reaction could thus be detected using SAM at a much larger distance than a pure avoidance radius would suggest. The first waiting time (interval between porpoise detections of at least 10 min), after piling started, increased with longer piling durations. A gradient in avoidance, a gradual fading of the avoidance reaction with increasing distance from the piling site, is hence most probably a product of an incomplete displacement during shorter piling events.

Plants of the fynbos biome harbour host species-specific bacterial communities.

PubMed

Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

2016-08-01

The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

MOCCA-SURVEY Database I: Galactic Globular Clusters Harbouring a Black Hole Subsystem

NASA Astrophysics Data System (ADS)

Askar, Abbas; Sedda, Manuel Arca; Giersz, Mirek

2018-05-01

There have been increasing theoretical speculations and observational indications that certain globular clusters (GCs) could contain a sizeable population of stellar mass black holes (BHs). In this paper, we shortlist at least 29 Galactic GCs that could be hosting a subsystem of BHs (BHS). In a companion paper, we analysed results from a wide array of GC models (simulated with the MOCCA code for cluster simulations) that retained few tens to several hundreds of BHs at 12 Gyr and showed that the properties of the BHS in those GCs correlate with the GC's observable properties. Building on those results, we use available observational properties of 140 Galactic GCs to identify 29 GCs that could potentially be harbouring up to a few hundreds of BHs. Utilizing observational properties and theoretical scaling relations, we estimate the density, size and mass of the BHS in these GCs. We also calculate the total number of BHs and the fraction of BHs contained in a binary system for our shortlisted Galactic GCs. Additionally, we mention other Galactic GCs that could also contain significant number of single BHs or BHs in binary systems.

Does the Deep Layer of the Deep Temporalis Fascia Really Exist?

PubMed

Li, Hui; Li, Kaide; Jia, Wenhao; Han, Chaoying; Chen, Jinlong; Liu, Lei

2018-04-14

It has been widely accepted that a split of the deep temporal fascia occurs approximately 2 to 3 cm above the zygomatic arch and extends into the superficial and deep layers. The deep layer of the deep temporal fascia is between the superficial temporal fat pad and the temporal muscle. However, during procedures, the authors noted the absence of the deep layer of the deep temporal fascia between the superficial temporal fat pad and the temporal muscle. This prospective study was conducted to clarify the presence or absence of a deep layer of the deep temporal fascia. Anatomic layers of the soft tissues of the temporal region, with reference to the deep temporal fascia, were investigated in 130 cases operated on for zygomaticofacial fractures using the supratemporal approach from June 2013 to June 2017. Of 130 surgeries, the authors found the absence of a thick, obviously identifiable, fascial layer between the superficial temporal fat pad and the temporal muscle. In fact, the authors found nothing above the temporal muscle in most cases. In a few cases, the authors observed only a small amount of scattered loose connective tissue between the superficial temporal fat pad and the temporal muscle. This clinical study showed the absence of a thick, obviously identifiable, fascial layer between the superficial temporal fat pad and the temporal muscle, which suggests that a "deep layer of the deep temporal fascia" might not exist. Copyright © 2018. Published by Elsevier Inc.

Underwater recordings of the whistles of bottlenose dolphins in Fremantle Inner Harbour, Western Australia

NASA Astrophysics Data System (ADS)

Marley, Sarah A.; Erbe, Christine; Kent, Chandra P. Salgado

2017-09-01

Dolphins use frequency-modulated whistles for a variety of social functions. Whistles vary in their characteristics according to context, such as activity state, group size, group composition, geographic location, and ambient noise levels. Therefore, comparison of whistle characteristics can be used to address numerous research questions regarding dolphin populations and behaviour. However, logistical and economic constraints on dolphin research have resulted in data collection biases, inconsistent analytical approaches, and knowledge gaps. This Data Descriptor presents an acoustic dataset of bottlenose dolphin (Tursiops aduncus) whistles recorded in the Fremantle Inner Harbour, Western Australia. Data were collected using an autonomous recorder and analysed using a range of acoustic measurements. Acoustic data review identified 336 whistles, which were subsequently measured for six key characteristics using Raven Pro software. Of these, 164 'high-quality' whistles were manually measured to provide an additional five acoustic characteristics. Digital files of individual whistles and corresponding measurements make this dataset available to researchers to address future questions regarding variations within and between dolphin communities.

Spatial and temporal impacts of the Skjervøy harbour diesel spill on native population of blue mussels: A sub-Arctic case study.

PubMed

Breitwieser, Marine; Thomas-Guyon, Hélène; Huet, Valérie; Sagerup, Kjetil; Geraudie, Perrine

2018-05-30

This work was designed to investigate biological impacts on blue mussels (Mytilus edulis spp) after being exposed to diesel spill. On December 2013, an 180,000-litre accidental acute diesel spill was reported in a small harbour of northern Norway (Skjervøy). In order to assess the biological effects on the wild population of blue mussels, bivalves were collected at three different locations: at the oil-spill spot, at the other side of the harbour (opposite the oil-spill area), and in an uncontaminated site. Body burden and seawater samples were collected from a few days up to five months after the diesel spill. Biomarkers of oxidative stress and immunological effects were assessed in the blue mussels digestive glands. Our findings reported significant modulation of GST (detoxification), SOD (antioxidant response) and MDA (lipid peroxidation) in bivalves exposed to diesel with a similar response at two and five months after the spill. Laccase-type enzyme also highlighted an important aspect in terms of biomarker response of the immune function. Overall, our study demonstrated that some biomarkers returned to basal levels a few months after the diesel spill. Consequently, it highlighted the usefulness of normalised tools and guidelines for biomonitoring strategies after a diesel spill. Copyright © 2018 Elsevier Inc. All rights reserved.

A deep reef in deep trouble

USGS Publications Warehouse

Menza, Charles; Kendall, M.; Rogers, C.; Miller, J.

2007-01-01

The well-documented degradation of shallower reefs which are often closer to land and more vulnerable to pollution, sewage and other human-related stressors has led to the suggestion that deeper, more remote offshore reefs could possibly serve as sources of coral and fish larvae to replenish the shallower reefs. Yet, the distribution, status, and ecological roles of deep (>30 m) Caribbean reefs are not well known. In this report, an observation of a deep reef which has undergone a recent extensive loss of coral cover is presented. In stark contrast to the typical pattern of coral loss in shallow reefs, the deeper corals were most affected. This report is the first description of such a pattern of coral loss on a deep reef.

DeepSynergy: predicting anti-cancer drug synergy with Deep Learning

PubMed Central

Preuer, Kristina; Lewis, Richard P I; Hochreiter, Sepp; Bender, Andreas; Bulusu, Krishna C; Klambauer, Günter

2018-01-01

Abstract Motivation While drug combination therapies are a well-established concept in cancer treatment, identifying novel synergistic combinations is challenging due to the size of combinatorial space. However, computational approaches have emerged as a time- and cost-efficient way to prioritize combinations to test, based on recently available large-scale combination screening data. Recently, Deep Learning has had an impact in many research areas by achieving new state-of-the-art model performance. However, Deep Learning has not yet been applied to drug synergy prediction, which is the approach we present here, termed DeepSynergy. DeepSynergy uses chemical and genomic information as input information, a normalization strategy to account for input data heterogeneity, and conical layers to model drug synergies. Results DeepSynergy was compared to other machine learning methods such as Gradient Boosting Machines, Random Forests, Support Vector Machines and Elastic Nets on the largest publicly available synergy dataset with respect to mean squared error. DeepSynergy significantly outperformed the other methods with an improvement of 7.2% over the second best method at the prediction of novel drug combinations within the space of explored drugs and cell lines. At this task, the mean Pearson correlation coefficient between the measured and the predicted values of DeepSynergy was 0.73. Applying DeepSynergy for classification of these novel drug combinations resulted in a high predictive performance of an AUC of 0.90. Furthermore, we found that all compared methods exhibit low predictive performance when extrapolating to unexplored drugs or cell lines, which we suggest is due to limitations in the size and diversity of the dataset. We envision that DeepSynergy could be a valuable tool for selecting novel synergistic drug combinations. Availability and implementation DeepSynergy is available via www.bioinf.jku.at/software/DeepSynergy. Contact klambauer

Deep Logic Networks: Inserting and Extracting Knowledge From Deep Belief Networks.

PubMed

Tran, Son N; d'Avila Garcez, Artur S

2018-02-01

Developments in deep learning have seen the use of layerwise unsupervised learning combined with supervised learning for fine-tuning. With this layerwise approach, a deep network can be seen as a more modular system that lends itself well to learning representations. In this paper, we investigate whether such modularity can be useful to the insertion of background knowledge into deep networks, whether it can improve learning performance when it is available, and to the extraction of knowledge from trained deep networks, and whether it can offer a better understanding of the representations learned by such networks. To this end, we use a simple symbolic language-a set of logical rules that we call confidence rules-and show that it is suitable for the representation of quantitative reasoning in deep networks. We show by knowledge extraction that confidence rules can offer a low-cost representation for layerwise networks (or restricted Boltzmann machines). We also show that layerwise extraction can produce an improvement in the accuracy of deep belief networks. Furthermore, the proposed symbolic characterization of deep networks provides a novel method for the insertion of prior knowledge and training of deep networks. With the use of this method, a deep neural-symbolic system is proposed and evaluated, with the experimental results indicating that modularity through the use of confidence rules and knowledge insertion can be beneficial to network performance.

Deep Vein Thrombosis

MedlinePlus

Deep vein thrombosis, or DVT, is a blood clot that forms in a vein deep in the body. Most ... vein swells, the condition is called thrombophlebitis. A deep vein thrombosis can break loose and cause a serious problem ...

Marine litter on deep Arctic seafloor continues to increase and spreads to the North at the HAUSGARTEN observatory

NASA Astrophysics Data System (ADS)

Tekman, Mine B.; Krumpen, Thomas; Bergmann, Melanie

2017-02-01

The increased global production of plastics has been mirrored by greater accumulations of plastic litter in marine environments worldwide. Global plastic litter estimates based on field observations account only for 1% of the total volumes of plastic assumed to enter the marine ecosystem from land, raising again the question 'Where is all the plastic? '. Scant information exists on temporal trends on litter transport and litter accumulation on the deep seafloor. Here, we present the results of photographic time-series surveys indicating a strong increase in marine litter over the period of 2002-2014 at two stations of the HAUSGARTEN observatory in the Arctic (2500 m depth). Plastic accounted for the highest proportion (47%) of litter recorded at HAUSGARTEN for the whole study period. When the most southern station was considered separately, the proportion of plastic items was even higher (65%). Increasing quantities of small plastics raise concerns about fragmentation and future microplastic contamination. Analysis of litter types and sizes indicate temporal and spatial differences in the transport pathways to the deep sea for different categories of litter. Litter densities were positively correlated with the counts of ship entering harbour at Longyearbyen, the number of active fishing vessels and extent of summer sea ice. Sea ice may act as a transport vehicle for entrained litter, being released during periods of melting. The receding sea ice coverage associated with global change has opened hitherto largely inaccessible environments to humans and the impacts of tourism, industrial activities including shipping and fisheries, all of which are potential sources of marine litter.

Investigations of Cu, Pb and Zn partitioning by sequential extraction in harbour sediments after electrodialytic remediation.

PubMed

Kirkelund, Gunvor M; Ottosen, Lisbeth M; Villumsen, Arne

2010-05-01

Electrodialytic remediation was used to remove Cu, Zn and Pb from three different contaminated harbour sediments. Electrodialytic experiments lasting 2 and 4 weeks were performed and 48-86% Cu, 74-90% Zn and 62-88% Pb were removed from the different sediments and the removal increased with longer remediation time. A three step sequential extraction scheme (BCR), with an extra residual step, was used to evaluate the heavy metal distribution in the sediments before and after electrodialytic remediation. Cu was mainly associated with the oxidisable phase of the sediment, both before and after remediation. Zn and Pb were found in the exchangeable and reducible phases before remediation. Zn was still found in the exchangeable and reducible phases after remediation, whereas most Pb was removed from these phases during electrodialytic remediation. Copyright 2010 Elsevier Ltd. All rights reserved.

Kidnapping small icy asteroids in Earth near encounter to harbour life and to deflect trajectory

NASA Astrophysics Data System (ADS)

Fargion, Daniele

2016-07-01

The inter-planetary flight for human being is under danger because of unscreened and lethal solar flare radioactive showers. The screening of the astronauts by huge superconducting magnetic fields is unrealistic by many reasons. On the contrary the ability to reach nearby icy asteroids, to harbour there a complete undergound room where ecological life systems are first set, this goal may offer a later natural and safe currier for future human stations and enterprise. The need to deflect such a small size (a few thousands tons objects) maybe achieved by micro nuclear engines able to dig the asteroid icy skin, to heat and propel the soil by a synchronous jet engine array, bending and driving it to any desired trajectories. The need for such a wide collection of icy asteroid stations, often in a robotic ibernated state, it will offer the safe help station, raft in the wide space sea, where to collect material or energy in long human planetary travels.

Homogenous stands of a wetland grass harbour diverse consortia of arbuscular mycorrhizal fungi.

PubMed

Wirsel, Stefan G R

2004-05-01

A molecular approach was applied to investigate the colonisation of arbuscular mycorrhizal fungi (AMF) on the wetland grass Phragmites australis. A PCR assay targeting the traditional families of the Glomeromycota yielded products that were used to construct libraries of 18S rDNA. Five hundred and forty six clones were typed by restriction analysis and 76 representatives were sequenced. The majority corresponded to a wide range of taxa within Glomus group A, a few belonged to the "Diversisporaceae" and none to the genera Scutellospora or Acaulospora. Among these sequences, some were very similar to those reported earlier, e.g. Glomus mosseae and G. fasciculatum, other pointed to various new taxa. Although this wetland habitat harboured just one single plant species, phylogenetic analysis exhibited 21 AMF phylotypes, which is in the same range as reported for other natural ecosystems composed of more diverse host communities. Diversity indices supported the perception that the AMF mycoflora associated with this natural grass "monoculture" is not depauperate as it had been described for grasses of crop monocultures. Soil conditions determined the mycorrhizal state of the host, since AMF were not detected at the lakeward front of the reed belt, which is permanently waterlogged.

MOCCA-SURVEY Database I: Is NGC 6535 a dark star cluster harbouring an IMBH?

NASA Astrophysics Data System (ADS)

Askar, Abbas; Bianchini, Paolo; de Vita, Ruggero; Giersz, Mirek; Hypki, Arkadiusz; Kamann, Sebastian

2017-01-01

We describe the dynamical evolution of a unique type of dark star cluster model in which the majority of the cluster mass at Hubble time is dominated by an intermediate-mass black hole (IMBH). We analysed results from about 2000 star cluster models (Survey Database I) simulated using the Monte Carlo code MOnte Carlo Cluster simulAtor and identified these dark star cluster models. Taking one of these models, we apply the method of simulating realistic `mock observations' by utilizing the Cluster simulatiOn Comparison with ObservAtions (COCOA) and Simulating Stellar Cluster Observation (SISCO) codes to obtain the photometric and kinematic observational properties of the dark star cluster model at 12 Gyr. We find that the perplexing Galactic globular cluster NGC 6535 closely matches the observational photometric and kinematic properties of the dark star cluster model presented in this paper. Based on our analysis and currently observed properties of NGC 6535, we suggest that this globular cluster could potentially harbour an IMBH. If it exists, the presence of this IMBH can be detected robustly with proposed kinematic observations of NGC 6535.

Deep Space Telecommunications

NASA Technical Reports Server (NTRS)

Kuiper, T. B. H.; Resch, G. M.

2000-01-01

The increasing load on NASA's deep Space Network, the new capabilities for deep space missions inherent in a next-generation radio telescope, and the potential of new telescope technology for reducing construction and operation costs suggest a natural marriage between radio astronomy and deep space telecommunications in developing advanced radio telescope concepts.

Co-occurrence correlations of heavy metals in sediments revealed using network analysis.

PubMed

Liu, Lili; Wang, Zhiping; Ju, Feng; Zhang, Tong

2015-01-01

In this study, the correlation-based study was used to identify the co-occurrence correlations among metals in marine sediment of Hong Kong, based on the long-term (from 1991 to 2011) temporal and spatial monitoring data. 14 stations out of the total 45 marine sediment monitoring stations were selected from three representative areas, including Deep Bay, Victoria Harbour and Mirs Bay. Firstly, Spearman's rank correlation-based network analysis was conducted as the first step to identify the co-occurrence correlations of metals from raw metadata, and then for further analysis using the normalized metadata. The correlations patterns obtained by network were consistent with those obtained by the other statistic normalization methods, including annual ratios, R-squared coefficient and Pearson correlation coefficient. Both Deep Bay and Victoria Harbour have been polluted by heavy metals, especially for Pb and Cu, which showed strong co-occurrence with other heavy metals (e.g. Cr, Ni, Zn and etc.) and little correlations with the reference parameters (Fe or Al). For Mirs Bay, which has better marine sediment quality compared with Deep Bay and Victoria Harbour, the co-occurrence patterns revealed by network analysis indicated that the metals in sediment dominantly followed the natural geography process. Besides the wide applications in biology, sociology and informatics, it is the first time to apply network analysis in the researches of environment pollutions. This study demonstrated its powerful application for revealing the co-occurrence correlations among heavy metals in marine sediments, which could be further applied for other pollutants in various environment systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Surfing the vegetal pole in a small population: extracellular vertical transmission of an 'intracellular' deep-sea clam symbiont.

PubMed

Ikuta, Tetsuro; Igawa, Kanae; Tame, Akihiro; Kuroiwa, Tsuneyoshi; Kuroiwa, Haruko; Aoki, Yui; Takaki, Yoshihiro; Nagai, Yukiko; Ozawa, Genki; Yamamoto, Masahiro; Deguchi, Ryusaku; Fujikura, Katsunori; Maruyama, Tadashi; Yoshida, Takao

2016-05-01

Symbiont transmission is a key event for understanding the processes underlying symbiotic associations and their evolution. However, our understanding of the mechanisms of symbiont transmission remains still fragmentary. The deep-sea clam Calyptogena okutanii harbours obligate sulfur-oxidizing intracellular symbiotic bacteria in the gill epithelial cells. In this study, we determined the localization of their symbiont associating with the spawned eggs, and the population size of the symbiont transmitted via the eggs. We show that the symbionts are located on the outer surface of the egg plasma membrane at the vegetal pole, and that each egg carries approximately 400 symbiont cells, each of which contains close to 10 genomic copies. The very small population size of the symbiont transmitted via the eggs might narrow the bottleneck and increase genetic drift, while polyploidy and its transient extracellular lifestyle might slow the rate of genome reduction. Additionally, the extracellular localization of the symbiont on the egg surface may increase the chance of symbiont exchange. This new type of extracellular transovarial transmission provides insights into complex interactions between the host and symbiont, development of both host and symbiont, as well as the population dynamics underlying genetic drift and genome evolution in microorganisms.

Pathogenicity of pan-drug-resistant Serratia marcescens harbouring blaNDM-1.

PubMed

Gruber, Teresa M; Göttig, Stephan; Mark, Laura; Christ, Sara; Kempf, Volkhard A J; Wichelhaus, Thomas A; Hamprecht, Axel

2015-04-01

To characterize a pan-drug-resistant Serratia marcescens clinical isolate carrying the New Delhi metallo-β-lactamase (NDM)-1. The presence of β-lactamase genes was examined by PCR and sequencing. Antibiotic susceptibility was determined by antibiotic gradient test. Transformation assays, transconjugation assays, PFGE and PCR-based replicon typing were used for plasmid analysis. Horizontal gene transfer was evaluated by liquid mating using Escherichia coli J53 as a recipient. Pathogenicity of NDM-1 expressing S. marcescens was analysed using the Galleria mellonella infection model. S. marcescens isolate SM1890 was non-susceptible to all tested antibiotics, with minocycline retaining intermediate activity. blaNDM-1 was located on a 140 kb IncA/C-type plasmid which was transferable to E. coli and Klebsiella pneumoniae by conjugation. The LD50 of the NDM-positive, SM1890 isolate was higher than that of other, NDM-1 negative, S. marcescens strains. The presence of a blaNDM-1-harbouring IncA/C plasmid resulted in marked resistance to β-lactam antibiotics, but had no significant effect on virulence of isogenic strains. Because of the intrinsic resistance of S. marcescens to colistin and reduced susceptibility to tigecycline, treatment options for infections by NDM-1-positive isolates are extremely limited in this species. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Deep Web video

ScienceCinema

None Available

2018-02-06

To make the web work better for science, OSTI has developed state-of-the-art technologies and services including a deep web search capability. The deep web includes content in searchable databases available to web users but not accessible by popular search engines, such as Google. This video provides an introduction to the deep web search engine.

Bt rice harbouring cry genes controlled by a constitutive or wound-inducible promoter: protection and transgene expression under Mediterranean field conditions.

PubMed

Breitler, Jean Christophe; Vassal, Jean Michel; del Mar Catala, Maria; Meynard, Donaldo; Marfà, Victoria; Melé, Enric; Royer, Monique; Murillo, Isabel; San Segundo, Blanca; Guiderdoni, Emmanuel; Messeguer, Joaquima

2004-09-01

Seven homozygous transgenic lines of two European commercial cultivars of rice (Ariete (A) and Senia (S)), harbouring the cry1B or cry1Aa Bacillus thuringiensis (Bt) delta-endotoxin genes, were field evaluated for protection from striped stem borer (SSB) (Chilo suppressalis) damage during the 2001 and 2002 summer crop seasons in the Delta de l'Ebre region, Spain. The plant codon-optimized toxin gene was placed under the control of the promoter of either the constitutive ubi1 gene or the wound-inducible mpi gene from maize. Stable, high-level, insecticidal protein accumulation was observed throughout root, leaf and seed tissues of field-grown plants harbouring the cry1B (lines A64.1, A33.1, A3.4 and S98.9) or cry1Aa (lines S05.1 and A19.14) genes under the control of the ubi1 promoter. Conversely, no toxin was detected in unwounded vegetative tissues of the A9.1 line harbouring the cry1B gene controlled by the mpi promoter, indicating that natural environmental stresses did not trigger the activity of the wound-inducible promoter. However, the toxin accumulated at 0.2% total soluble proteins in A9.1 sheath tissue exhibiting brown lesions resulting from SSB damage. The agronomical traits and performance of the transgenic lines were generally comparable with parental controls, except in the two lines accumulating Cry1Aa, which exhibited a high frequency of plants non-true to type. Natural infestation was assisted with manual infestations of L2/L3 SSB larvae in border control plants surrounding the experimental plots, which served as a reservoir for the second-cycle SSB population. The observation of damage (brown lesions and dead hearts) during the crop season and dissection of plants at harvest stage revealed a range of protection amongst the transgenic lines, which was highly consistent with the level of toxin accumulation and with previous experience in greenhouse assays. Lines A3.4 and S05.1 were found to exhibit stable and full protection against SSB attacks

Avoidance of wind farms by harbour seals is limited to pile driving activities.

PubMed

Russell, Debbie J F; Hastie, Gordon D; Thompson, David; Janik, Vincent M; Hammond, Philip S; Scott-Hayward, Lindesay A S; Matthiopoulos, Jason; Jones, Esther L; McConnell, Bernie J

2016-12-01

As part of global efforts to reduce dependence on carbon-based energy sources there has been a rapid increase in the installation of renewable energy devices. The installation and operation of these devices can result in conflicts with wildlife. In the marine environment, mammals may avoid wind farms that are under construction or operating. Such avoidance may lead to more time spent travelling or displacement from key habitats. A paucity of data on at-sea movements of marine mammals around wind farms limits our understanding of the nature of their potential impacts.Here, we present the results of a telemetry study on harbour seals Phoca vitulina in The Wash, south-east England, an area where wind farms are being constructed using impact pile driving. We investigated whether seals avoid wind farms during operation, construction in its entirety, or during piling activity. The study was carried out using historical telemetry data collected prior to any wind farm development and telemetry data collected in 2012 during the construction of one wind farm and the operation of another.Within an operational wind farm, there was a close-to-significant increase in seal usage compared to prior to wind farm development. However, the wind farm was at the edge of a large area of increased usage, so the presence of the wind farm was unlikely to be the cause.There was no significant displacement during construction as a whole. However, during piling, seal usage (abundance) was significantly reduced up to 25 km from the piling activity; within 25 km of the centre of the wind farm, there was a 19 to 83% (95% confidence intervals) decrease in usage compared to during breaks in piling, equating to a mean estimated displacement of 440 individuals. This amounts to significant displacement starting from predicted received levels of between 166 and 178 dB re 1 μPa (p-p) . Displacement was limited to piling activity; within 2 h of cessation of pile driving, seals were distributed as

DeepInfer: open-source deep learning deployment toolkit for image-guided therapy

NASA Astrophysics Data System (ADS)

Mehrtash, Alireza; Pesteie, Mehran; Hetherington, Jorden; Behringer, Peter A.; Kapur, Tina; Wells, William M.; Rohling, Robert; Fedorov, Andriy; Abolmaesumi, Purang

2017-03-01

Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. Instead of using hand-engineered features, deep models attempt to automatically extract hierarchical representations at multiple levels of abstraction from the data. Therefore, deep models are usually considered to be more flexible and robust solutions for image analysis problems compared to conventional computer vision models. They have demonstrated significant improvements in computer-aided diagnosis and automatic medical image analysis applied to such tasks as image segmentation, classification and registration. However, deploying deep learning models often has a steep learning curve and requires detailed knowledge of various software packages. Thus, many deep models have not been integrated into the clinical research work ows causing a gap between the state-of-the-art machine learning in medical applications and evaluation in clinical research procedures. In this paper, we propose "DeepInfer" - an open-source toolkit for developing and deploying deep learning models within the 3D Slicer medical image analysis platform. Utilizing a repository of task-specific models, DeepInfer allows clinical researchers and biomedical engineers to deploy a trained model selected from the public registry, and apply it to new data without the need for software development or configuration. As two practical use cases, we demonstrate the application of DeepInfer in prostate segmentation for targeted MRI-guided biopsy and identification of the target plane in 3D ultrasound for spinal injections.

DeepInfer: Open-Source Deep Learning Deployment Toolkit for Image-Guided Therapy.

PubMed

Mehrtash, Alireza; Pesteie, Mehran; Hetherington, Jorden; Behringer, Peter A; Kapur, Tina; Wells, William M; Rohling, Robert; Fedorov, Andriy; Abolmaesumi, Purang

2017-02-11

Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. Instead of using hand-engineered features, deep models attempt to automatically extract hierarchical representations at multiple levels of abstraction from the data. Therefore, deep models are usually considered to be more flexible and robust solutions for image analysis problems compared to conventional computer vision models. They have demonstrated significant improvements in computer-aided diagnosis and automatic medical image analysis applied to such tasks as image segmentation, classification and registration. However, deploying deep learning models often has a steep learning curve and requires detailed knowledge of various software packages. Thus, many deep models have not been integrated into the clinical research workflows causing a gap between the state-of-the-art machine learning in medical applications and evaluation in clinical research procedures. In this paper, we propose "DeepInfer" - an open-source toolkit for developing and deploying deep learning models within the 3D Slicer medical image analysis platform. Utilizing a repository of task-specific models, DeepInfer allows clinical researchers and biomedical engineers to deploy a trained model selected from the public registry, and apply it to new data without the need for software development or configuration. As two practical use cases, we demonstrate the application of DeepInfer in prostate segmentation for targeted MRI-guided biopsy and identification of the target plane in 3D ultrasound for spinal injections.

DeepInfer: Open-Source Deep Learning Deployment Toolkit for Image-Guided Therapy

PubMed Central

Mehrtash, Alireza; Pesteie, Mehran; Hetherington, Jorden; Behringer, Peter A.; Kapur, Tina; Wells, William M.; Rohling, Robert; Fedorov, Andriy; Abolmaesumi, Purang

2017-01-01

Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. Instead of using hand-engineered features, deep models attempt to automatically extract hierarchical representations at multiple levels of abstraction from the data. Therefore, deep models are usually considered to be more flexible and robust solutions for image analysis problems compared to conventional computer vision models. They have demonstrated significant improvements in computer-aided diagnosis and automatic medical image analysis applied to such tasks as image segmentation, classification and registration. However, deploying deep learning models often has a steep learning curve and requires detailed knowledge of various software packages. Thus, many deep models have not been integrated into the clinical research workflows causing a gap between the state-of-the-art machine learning in medical applications and evaluation in clinical research procedures. In this paper, we propose “DeepInfer” – an open-source toolkit for developing and deploying deep learning models within the 3D Slicer medical image analysis platform. Utilizing a repository of task-specific models, DeepInfer allows clinical researchers and biomedical engineers to deploy a trained model selected from the public registry, and apply it to new data without the need for software development or configuration. As two practical use cases, we demonstrate the application of DeepInfer in prostate segmentation for targeted MRI-guided biopsy and identification of the target plane in 3D ultrasound for spinal injections. PMID:28615794

DeepNeuron: an open deep learning toolbox for neuron tracing.

PubMed

Zhou, Zhi; Kuo, Hsien-Chi; Peng, Hanchuan; Long, Fuhui

2018-06-06

Reconstructing three-dimensional (3D) morphology of neurons is essential for understanding brain structures and functions. Over the past decades, a number of neuron tracing tools including manual, semiautomatic, and fully automatic approaches have been developed to extract and analyze 3D neuronal structures. Nevertheless, most of them were developed based on coding certain rules to extract and connect structural components of a neuron, showing limited performance on complicated neuron morphology. Recently, deep learning outperforms many other machine learning methods in a wide range of image analysis and computer vision tasks. Here we developed a new Open Source toolbox, DeepNeuron, which uses deep learning networks to learn features and rules from data and trace neuron morphology in light microscopy images. DeepNeuron provides a family of modules to solve basic yet challenging problems in neuron tracing. These problems include but not limited to: (1) detecting neuron signal under different image conditions, (2) connecting neuronal signals into tree(s), (3) pruning and refining tree morphology, (4) quantifying the quality of morphology, and (5) classifying dendrites and axons in real time. We have tested DeepNeuron using light microscopy images including bright-field and confocal images of human and mouse brain, on which DeepNeuron demonstrates robustness and accuracy in neuron tracing.

DeepSig: deep learning improves signal peptide detection in proteins.

PubMed

Savojardo, Castrense; Martelli, Pier Luigi; Fariselli, Piero; Casadio, Rita

2018-05-15

The identification of signal peptides in protein sequences is an important step toward protein localization and function characterization. Here, we present DeepSig, an improved approach for signal peptide detection and cleavage-site prediction based on deep learning methods. Comparative benchmarks performed on an updated independent dataset of proteins show that DeepSig is the current best performing method, scoring better than other available state-of-the-art approaches on both signal peptide detection and precise cleavage-site identification. DeepSig is available as both standalone program and web server at https://deepsig.biocomp.unibo.it. All datasets used in this study can be obtained from the same website. pierluigi.martelli@unibo.it. Supplementary data are available at Bioinformatics online.

Recurrent and functional regulatory mutations in breast cancer.

PubMed

Rheinbay, Esther; Parasuraman, Prasanna; Grimsby, Jonna; Tiao, Grace; Engreitz, Jesse M; Kim, Jaegil; Lawrence, Michael S; Taylor-Weiner, Amaro; Rodriguez-Cuevas, Sergio; Rosenberg, Mara; Hess, Julian; Stewart, Chip; Maruvka, Yosef E; Stojanov, Petar; Cortes, Maria L; Seepo, Sara; Cibulskis, Carrie; Tracy, Adam; Pugh, Trevor J; Lee, Jesse; Zheng, Zongli; Ellisen, Leif W; Iafrate, A John; Boehm, Jesse S; Gabriel, Stacey B; Meyerson, Matthew; Golub, Todd R; Baselga, Jose; Hidalgo-Miranda, Alfredo; Shioda, Toshi; Bernards, Andre; Lander, Eric S; Getz, Gad

2017-07-06

Genomic analysis of tumours has led to the identification of hundreds of cancer genes on the basis of the presence of mutations in protein-coding regions. By contrast, much less is known about cancer-causing mutations in non-coding regions. Here we perform deep sequencing in 360 primary breast cancers and develop computational methods to identify significantly mutated promoters. Clear signals are found in the promoters of three genes. FOXA1, a known driver of hormone-receptor positive breast cancer, harbours a mutational hotspot in its promoter leading to overexpression through increased E2F binding. RMRP and NEAT1, two non-coding RNA genes, carry mutations that affect protein binding to their promoters and alter expression levels. Our study shows that promoter regions harbour recurrent mutations in cancer with functional consequences and that the mutations occur at similar frequencies as in coding regions. Power analyses indicate that more such regions remain to be discovered through deep sequencing of adequately sized cohorts of patients.

DeepMitosis: Mitosis detection via deep detection, verification and segmentation networks.

PubMed

Li, Chao; Wang, Xinggang; Liu, Wenyu; Latecki, Longin Jan

2018-04-01

Mitotic count is a critical predictor of tumor aggressiveness in the breast cancer diagnosis. Nowadays mitosis counting is mainly performed by pathologists manually, which is extremely arduous and time-consuming. In this paper, we propose an accurate method for detecting the mitotic cells from histopathological slides using a novel multi-stage deep learning framework. Our method consists of a deep segmentation network for generating mitosis region when only a weak label is given (i.e., only the centroid pixel of mitosis is annotated), an elaborately designed deep detection network for localizing mitosis by using contextual region information, and a deep verification network for improving detection accuracy by removing false positives. We validate the proposed deep learning method on two widely used Mitosis Detection in Breast Cancer Histological Images (MITOSIS) datasets. Experimental results show that we can achieve the highest F-score on the MITOSIS dataset from ICPR 2012 grand challenge merely using the deep detection network. For the ICPR 2014 MITOSIS dataset that only provides the centroid location of mitosis, we employ the segmentation model to estimate the bounding box annotation for training the deep detection network. We also apply the verification model to eliminate some false positives produced from the detection model. By fusing scores of the detection and verification models, we achieve the state-of-the-art results. Moreover, our method is very fast with GPU computing, which makes it feasible for clinical practice. Copyright © 2018 Elsevier B.V. All rights reserved.

Surveillance of borders, coastlines, and harbours (SOBCAH): a European commission preparatory action on security research

NASA Astrophysics Data System (ADS)

Clarke, David J.; Davis, Eric; Varco, Alan G.

2008-10-01

Surveillance Of Borders Coastlines And Harbours (SOBCAH ) is becoming increasingly challenging in Europe due to the expansion of new European borders coupled with the increased risks from the potential quantity and variety of terrorist activities. SOBCAH was an 18-month programme undertaken as a European Commission funded Preparatory Action in the field of Security Research (PASR) initiative to identify and demonstrate improvements in security; initially focusing on techniques to maximise the surveillance and detection effectiveness of existing sensor systems and technologies. This paper discusses the rationale in identifying the requirements, establishing a system architecture and the findings of building a security system demonstrator that underwent trials in the Port of Genoa, Italy in July 2007. It will provide an overview of the main drivers for a European-wide concept to standardise the development of enhanced border security systems. The paper will focus on techniques employed in the demonstrator to maximise the intelligence gathered from many disparate sensor sources without burdening the work load of the operators; providing enhanced situational awareness of the threat environment.

Hot, deep origin of petroleum: deep basin evidence and application

USGS Publications Warehouse

Price, Leigh C.

1978-01-01

Use of the model of a hot deep origin of oil places rigid constraints on the migration and entrapment of crude oil. Specifically, oil originating from depth migrates vertically up faults and is emplaced in traps at shallower depths. Review of petroleum-producing basins worldwide shows oil occurrence in these basins conforms to the restraints of and therefore supports the hypothesis. Most of the world's oil is found in the very deepest sedimentary basins, and production over or adjacent to the deep basin is cut by or directly updip from faults dipping into the basin deep. Generally the greater the fault throw the greater the reserves. Fault-block highs next to deep sedimentary troughs are the best target areas by the present concept. Traps along major basin-forming faults are quite prospective. The structural style of a basin governs the distribution, types, and amounts of hydrocarbons expected and hence the exploration strategy. Production in delta depocenters (Niger) is in structures cut by or updip from major growth faults, and structures not associated with such faults are barren. Production in block fault basins is on horsts next to deep sedimentary troughs (Sirte, North Sea). In basins whose sediment thickness, structure and geologic history are known to a moderate degree, the main oil occurrences can be specifically predicted by analysis of fault systems and possible hydrocarbon migration routes. Use of the concept permits the identification of significant targets which have either been downgraded or ignored in the past, such as production in or just updip from thrust belts, stratigraphic traps over the deep basin associated with major faulting, production over the basin deep, and regional stratigraphic trapping updip from established production along major fault zones.

deepTools: a flexible platform for exploring deep-sequencing data.

PubMed

Ramírez, Fidel; Dündar, Friederike; Diehl, Sarah; Grüning, Björn A; Manke, Thomas

2014-07-01

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Deep learning

NASA Astrophysics Data System (ADS)

Lecun, Yann; Bengio, Yoshua; Hinton, Geoffrey

2015-05-01

Deep learning allows computational models that are composed of multiple processing layers to learn representations of data with multiple levels of abstraction. These methods have dramatically improved the state-of-the-art in speech recognition, visual object recognition, object detection and many other domains such as drug discovery and genomics. Deep learning discovers intricate structure in large data sets by using the backpropagation algorithm to indicate how a machine should change its internal parameters that are used to compute the representation in each layer from the representation in the previous layer. Deep convolutional nets have brought about breakthroughs in processing images, video, speech and audio, whereas recurrent nets have shone light on sequential data such as text and speech.

Deep learning.

PubMed

LeCun, Yann; Bengio, Yoshua; Hinton, Geoffrey

2015-05-28

Deep learning allows computational models that are composed of multiple processing layers to learn representations of data with multiple levels of abstraction. These methods have dramatically improved the state-of-the-art in speech recognition, visual object recognition, object detection and many other domains such as drug discovery and genomics. Deep learning discovers intricate structure in large data sets by using the backpropagation algorithm to indicate how a machine should change its internal parameters that are used to compute the representation in each layer from the representation in the previous layer. Deep convolutional nets have brought about breakthroughs in processing images, video, speech and audio, whereas recurrent nets have shone light on sequential data such as text and speech.

Deep learning in bioinformatics.

PubMed

Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

2017-09-01

In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e. omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e. deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Distribution of polychlorinated biphenyl residues in sediments and blue mussels (Mytilus galloprovincialis) from Port Elizabeth Harbour, South Africa.

PubMed

Kampire, E; Rubidge, G; Adams, J B

2015-02-15

Sediment and Mytilus galloprovincialis samples collected from the Port Elizabeth Harbour were analysed for six indicator PCB congeners to assess their contamination status. The concentrations of total PCBs in sediments and M. galloprovincialis ranged from 0.56 to 2.35 ng/g dry weight and 14.48 to 21.37 ng/g wet weight, respectively. Congeners 138 and 153 were dominant and accounted for an average of 29% and 24% of total PCBs in M. galloprovincialis; 32% and 30% in sediments, respectively. Sediments are home to a wide variety of aquatic life. None of the sediments analysed exceeded the PCB limits recommended the Canadian interim sediment quality guideline and the South African recommended sediment guidelines (21.6 ng/g). Both humans and aquatic life are sensitive to the toxic effects of PCBs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Metazoan fish parasites of Macrourus berglax Lacepède, 1801 and other macrourids of the North Atlantic: Invasion of the deep sea from the continental shelf

NASA Astrophysics Data System (ADS)

Palm, H. W.; Klimpel, S.

2008-01-01

Between 2001 and 2003, a total of 105 Macrourus berglax Lacepède, 1801 were collected from Irminger Sea, at depths between 250 and 450 m, and were studied for parasites. Twenty-four different parasite species were identified. Nematodes (eight spp.) and digeneans (six spp.) were the most species rich, followed by crustaceans (four spp.), cestodes (three spp.), acanthocephalans (two spp.) and monogeneans (one sp.). Core species included the digenean Gonocerca phycidis (maximum 62.9% prevalence), the nematodes Anisakis sp. (62.9%), Capillaria gracilis (65.8%), Hysterothylacium aduncum (60.0%), Neoascarophis macrouri (88.6%), Spinitectus oviflagellis (82.9%), and the acanthocephalan Echinorhynchus gadi (97.1%). M. berglax was the final host for most of the parasites, and was infested with only a few larval forms. The species composition, diversity as well as the prevalence and intensity of infestation for most parasite species collected, were similar in the different years, indicating no distinct interannual variation at this deep-sea locality. Comparisons of the parasite fauna of M. berglax with macrourids belonging to the genera Macrourus, Coryphaenoides, Coelorhynchus and Nezumia revealed a similar infestation pattern amongst these deep-sea fish, consisting of the same or closely related species. This observation suggests that the parasite life-cycles in these benthopelagic deep-sea fishes follow similar pathways independent of geographical location. A similar habitat and food preference of macrourids results in a similar parasite fauna. The host specificity of some of the parasites is low, with most species (nine) infesting Teleostei, Gadiformes (six), Macrouridae (two), Macrourus spp. (one) and specifically M. berglax (five). Overlapping infestation patterns of M. berglax parasites with phylogenetically related gadiform fish from the continental shelf region suggest that the deep-sea parasite fauna in macrourids has evolved along with their hosts from parasite

Autonomously hyperfunctioning cystic nodule harbouring thyroid carcinoma - Case report and literature review.

PubMed

Lima, Maria João; Soares, Virgínia; Koch, Pedro; Silva, Artur; Taveira-Gomes, António

2018-01-01

Hyperthyroidism is rarely associated with malignancy, but it cannot rule out thyroid cancer. Although there is published data describing this coexistence, thyroid carcinomas inside autonomously functioning nodules are uncommon. A 49-year-old woman presented with a cervical mass, unexplained weight loss and anxiousness, sweating and insomnia. On physical examination, she had a palpable left thyroid nodule. Thyroid function tests showed suppressed TSH (<0,1 uUI/mL), thyroxine 1,44 ng/dL (normal range 0,70-1,48) and triiodothyronine 4,33 pg/mL (normal range 1,71-3,71). Ultrasound imaging revealed a left lobe, 4 cm partial cystic nodule. 99mTC thyroid scintigraphy showed a hyperfunctioning nodule with suppression of the remainder parenchyma. Fine-needle aspiration cytology was nondiagnostic (cystic fluid). The patient was started on thiamazole 5 mg daily with subsequent normalization of thyroid function, but she developed cervical foreign body sensation and a left hemithyroidectomy was performed. Histology showed a 4 cm cystic nodule with a follicular variant papillary carcinoma and the patient underwent completion thyroidectomy, followed by radio-iodine ablation. Published literature showed an increased prevalence of autonomously functioning nodules, harbouring thyroid carcinomas in adults. Papillary carcinoma is the most frequently described but the follicular variant is rare. Although rare, thyroid cancer is not definitively excluded in hyperthyroid patients and it should always be considered as differential diagnosis. Copyright © 2018. Published by Elsevier Ltd.

The formation of Greenland Sea Deep Water: double diffusion or deep convection?

NASA Astrophysics Data System (ADS)

Clarke, R. Allyn; Swift, James H.; Reid, Joseph L.; Koltermann, K. Peter

1990-09-01

An examination of the extensive hydrographic data sets collected by C.S.S. Hudson and F.S. Meteor in the Norwegian and Greenland Seas during February-June 1982 reveals property distributions and circulation patterns broadly similar to those seen in earlier data sets. These data sets, however, reveal the even stronger role played by topography, with evidence of separate circulation patterns and separate water masses in each of the deep basins. The high precision temperature, salinity and oxygen data obtained reveals significant differences in the deep and bottom waters found in the various basins of the Norwegian and Greenland Seas. A comparison of the 1982 data set with earlier sets shows that the renewal of Greenland Sea Deep Water must have taken place sometime over the last decade; however there is no evidence that deep convective renewal of any of the deep and bottom waters in this region was taking place at the time of the observations. The large-scale density fields, however, do suggest that deep convection to the bottom is most likely to occure in the Greenland Basin due to its deep cyclonic circulation. The hypothesis that Greenland Sea Deep Water (GSDW) is formed through dipycnal mixing processes acting on the warm salty core of Atlantic Water entering the Greenland Sea is examined. θ-S correlations and oxygen concentrations suggest that the salinity maxima in the Greenland Sea are the product of at least two separate mixing processes, not the hypothesized single mixing process leading to GSDW. A simple one-dimensional mixed layer model with ice growth and decay demonstrates that convective renewal of GSDW would have occurred within the Greenland Sea had the winter been a little more severe. The new GSDW produced would have only 0.003 less salt and less than 0.04 ml 1 -1 greater oxygen concentration than that already in the basin. Consequently, detection of whether new deep water has been produced following a winter cooling season could be difficult even

Deep subsurface microbial processes

USGS Publications Warehouse

Lovley, D.R.; Chapelle, F.H.

1995-01-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

Stomach Temperature Records Reveal Nursing Behaviour and Transition to Solid Food Consumption in an Unweaned Mammal, the Harbour Seal Pup (Phoca vitulina)

PubMed Central

Sauvé, Caroline C.; Van de Walle, Joanie; Hammill, Mike O.; Arnould, John P. Y.; Beauplet, Gwénaël

2014-01-01

Knowledge of milk transfer from mother to offspring and early solid food ingestions in mammals allows for a greater understanding of the factors affecting transition to nutritional independence and pre-weaning growth and survival. Yet studies monitoring suckling behaviour have often relied on visual observations, which might not accurately represent milk intake. We assessed the use of stomach temperature telemetry to monitor suckling and foraging behaviour in free-ranging harbour seal (Phoca vitulina) pups during lactation. Stomach temperature declines were analysed using principal component and cluster analyses, as well as trials using simulated stomachs resulting in a precise classification of stomach temperature drops into milk, seawater and solid food ingestions. Seawater and solid food ingestions represented on average 15.3±1.6% [0–40.0%] and 0.7±0.2% [0–13.0%], respectively, of individual ingestions. Overall, 63.7% of milk ingestions occurred while the pups were in the water, of which 13.9% were preceded by seawater ingestion. The average time between subsequent ingestions was significantly less for seawater than for milk ingestions. These results suggest that seawater ingestion might represent collateral ingestion during aquatic suckling attempts. Alternatively, as solid food ingestions (n = 19) were observed among 7 pups, seawater ingestion could result from missed prey capture attempts. This study shows that some harbour seals start ingesting prey while still being nursed, indicating that weaning occurs more gradually than previously thought in this species. Stomach temperature telemetry represents a promising method to study suckling behaviour in wild mammals and transition to nutritional independence in various endotherm species. PMID:24587327

Do deep convolutional neural networks really need to be deep when applied for remote scene classification?

NASA Astrophysics Data System (ADS)

Luo, Chang; Wang, Jie; Feng, Gang; Xu, Suhui; Wang, Shiqiang

2017-10-01

Deep convolutional neural networks (CNNs) have been widely used to obtain high-level representation in various computer vision tasks. However, for remote scene classification, there are not sufficient images to train a very deep CNN from scratch. From two viewpoints of generalization power, we propose two promising kinds of deep CNNs for remote scenes and try to find whether deep CNNs need to be deep for remote scene classification. First, we transfer successful pretrained deep CNNs to remote scenes based on the theory that depth of CNNs brings the generalization power by learning available hypothesis for finite data samples. Second, according to the opposite viewpoint that generalization power of deep CNNs comes from massive memorization and shallow CNNs with enough neural nodes have perfect finite sample expressivity, we design a lightweight deep CNN (LDCNN) for remote scene classification. With five well-known pretrained deep CNNs, experimental results on two independent remote-sensing datasets demonstrate that transferred deep CNNs can achieve state-of-the-art results in an unsupervised setting. However, because of its shallow architecture, LDCNN cannot obtain satisfactory performance, regardless of whether in an unsupervised, semisupervised, or supervised setting. CNNs really need depth to obtain general features for remote scenes. This paper also provides baseline for applying deep CNNs to other remote sensing tasks.

Towards The Operational Oceanographic Model System In Estonian Coastal Sea, Baltic Sea

NASA Astrophysics Data System (ADS)

Kõuts, T.; Elken, J.; Raudsepp, U.

evaluate environmental impacts of three different deep-port construction options in Saaremaa, NW the Baltic Sea. Intensive campaign of field measurements, consisting the high-resolution surveys of thermohaline properties of water masses (CTD) and timeseries as well horisontal structure of currents were in good agreement with model calculations. Model system well simulated the transport of pollution by surface currents originating from potential port locations at NW coast of the Saaremaa. It allowed to choose the optimum location for port and give also some hindcasts for port construction and exploitation.

DeepSurv: personalized treatment recommender system using a Cox proportional hazards deep neural network.

PubMed

Katzman, Jared L; Shaham, Uri; Cloninger, Alexander; Bates, Jonathan; Jiang, Tingting; Kluger, Yuval

2018-02-26

Medical practitioners use survival models to explore and understand the relationships between patients' covariates (e.g. clinical and genetic features) and the effectiveness of various treatment options. Standard survival models like the linear Cox proportional hazards model require extensive feature engineering or prior medical knowledge to model treatment interaction at an individual level. While nonlinear survival methods, such as neural networks and survival forests, can inherently model these high-level interaction terms, they have yet to be shown as effective treatment recommender systems. We introduce DeepSurv, a Cox proportional hazards deep neural network and state-of-the-art survival method for modeling interactions between a patient's covariates and treatment effectiveness in order to provide personalized treatment recommendations. We perform a number of experiments training DeepSurv on simulated and real survival data. We demonstrate that DeepSurv performs as well as or better than other state-of-the-art survival models and validate that DeepSurv successfully models increasingly complex relationships between a patient's covariates and their risk of failure. We then show how DeepSurv models the relationship between a patient's features and effectiveness of different treatment options to show how DeepSurv can be used to provide individual treatment recommendations. Finally, we train DeepSurv on real clinical studies to demonstrate how it's personalized treatment recommendations would increase the survival time of a set of patients. The predictive and modeling capabilities of DeepSurv will enable medical researchers to use deep neural networks as a tool in their exploration, understanding, and prediction of the effects of a patient's characteristics on their risk of failure.

Pathogenesis of deep endometriosis.

PubMed

Gordts, Stephan; Koninckx, Philippe; Brosens, Ivo

2017-12-01

The pathophysiology of (deep) endometriosis is still unclear. As originally suggested by Cullen, change the definition "deeper than 5 mm" to "adenomyosis externa." With the discovery of the old European literature on uterine bleeding in 5%-10% of the neonates and histologic evidence that the bleeding represents decidual shedding, it is postulated/hypothesized that endometrial stem/progenitor cells, implanted in the pelvic cavity after birth, may be at the origin of adolescent and even the occasionally premenarcheal pelvic endometriosis. Endometriosis in the adolescent is characterized by angiogenic and hemorrhagic peritoneal and ovarian lesions. The development of deep endometriosis at a later age suggests that deep infiltrating endometriosis is a delayed stage of endometriosis. Another hypothesis is that the endometriotic cell has undergone genetic or epigenetic changes and those specific changes determine the development into deep endometriosis. This is compatible with the hereditary aspects, and with the clonality of deep and cystic ovarian endometriosis. It explains the predisposition and an eventual causal effect by dioxin or radiation. Specific genetic/epigenetic changes could explain the various expressions and thus typical, cystic, and deep endometriosis become three different diseases. Subtle lesions are not a disease until epi(genetic) changes occur. A classification should reflect that deep endometriosis is a specific disease. In conclusion the pathophysiology of deep endometriosis remains debated and the mechanisms of disease progression, as well as the role of genetics and epigenetics in the process, still needs to be unraveled. Copyright © 2017 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Human-ecosystem interactions in relation to Holocene environmental change in Port Joli Harbour, southwestern Nova Scotia, Canada

NASA Astrophysics Data System (ADS)

Neil, Karen; Gajewski, Konrad; Betts, Matthew

2014-03-01

A high-resolution pollen record from Path Lake in Port Joli Harbour, Nova Scotia, Canada, provides a paleo-ecological perspective on Holocene climate and vegetation variability within the context of local archaeological research. Pollen assemblages in the early Holocene reflect a post-glacial forest dominated by Pinus, Tsuga, Betula and Quercus. During this time, a lower frequency of radiocarbon dated cultural material suggests lower human settlement intensity. Shallow water aquatic (Isoetes) and wetland (Alnus, Sphagnum) taxa increased after 3400 cal yr BP in response to a transition towards wetter climatic conditions. Culturally significant periods, where settlement intensity increased in the Maritimes and Maine, coincide with maximum values of reconstructed total annual precipitation, suggesting that environmental conditions may have influenced prehistoric human activity. European settlement, after 350 cal yr BP, was marked by a rise in Ambrosia. The impact of anthropogenic fire disturbances on the landscape was evidenced by peak charcoal accumulations after European settlement.

Dining in the Deep: The Feeding Ecology of Deep-Sea Fishes

NASA Astrophysics Data System (ADS)

Drazen, Jeffrey C.; Sutton, Tracey T.

2017-01-01

Deep-sea fishes inhabit ˜75% of the biosphere and are a critical part of deep-sea food webs. Diet analysis and more recent trophic biomarker approaches, such as stable isotopes and fatty-acid profiles, have enabled the description of feeding guilds and an increased recognition of the vertical connectivity in food webs in a whole-water-column sense, including benthic-pelagic coupling. Ecosystem modeling requires data on feeding rates; the available estimates indicate that deep-sea fishes have lower per-individual feeding rates than coastal and epipelagic fishes, but the overall predation impact may be high. A limited number of studies have measured the vertical flux of carbon by mesopelagic fishes, which appears to be substantial. Anthropogenic activities are altering deep-sea ecosystems and their services, which are mediated by trophic interactions. We also summarize outstanding data gaps.

Characterisation of physical environmental factors on an intertidal sandflat, Manukau Harbour, New Zealand

USGS Publications Warehouse

Bell, R.G.; Hume, T.M.; Dolphin, T.J.; Green, M.O.; Walters, R.A.

1997-01-01

Physical environmental factors, including sediment characteristics, inundation time, tidal currents and wind waves, likely to influence the structure of the benthic community at meso-scales (1-100 m) were characterised for a sandflat off Wiroa Island (Manukau Harbour, New Zealand). In a 500 x 250 m study site, sediment characteristics and bed topography were mostly homogenous apart from patches of low-relief ridges and runnels. Field measurements and hydrodynamic modelling portray a complex picture of sediment or particulate transport on the intertidal flat, involving interactions between the larger scale tidal processes and the smaller scale wave dynamics (1-4 s; 1-15 m). Peak tidal currents in isolation are incapable of eroding bottom sediments, but in combination with near-bed orbital currents generated by only very small wind waves, sediment transport can be initiated. Work done on the bed integrated over an entire tidal cycle by prevailing wind waves is greatest on the elevated and flatter slopes of the study site, where waves shoal over a wider surf zone and water depths remain shallow e enough for wave-orbital currents to disturb the bed. The study also provided physical descriptors quantifying static and hydrodynamic (tidal and wave) factors which were used in companion studies on ecological spatial modelling of bivalve distributions and micro-scale sediment reworking and transport.

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data.

PubMed

Arango-Argoty, Gustavo; Garner, Emily; Pruden, Amy; Heath, Lenwood S; Vikesland, Peter; Zhang, Liqing

2018-02-01

Growing concerns about increasing rates of antibiotic resistance call for expanded and comprehensive global monitoring. Advancing methods for monitoring of environmental media (e.g., wastewater, agricultural waste, food, and water) is especially needed for identifying potential resources of novel antibiotic resistance genes (ARGs), hot spots for gene exchange, and as pathways for the spread of ARGs and human exposure. Next-generation sequencing now enables direct access and profiling of the total metagenomic DNA pool, where ARGs are typically identified or predicted based on the "best hits" of sequence searches against existing databases. Unfortunately, this approach produces a high rate of false negatives. To address such limitations, we propose here a deep learning approach, taking into account a dissimilarity matrix created using all known categories of ARGs. Two deep learning models, DeepARG-SS and DeepARG-LS, were constructed for short read sequences and full gene length sequences, respectively. Evaluation of the deep learning models over 30 antibiotic resistance categories demonstrates that the DeepARG models can predict ARGs with both high precision (> 0.97) and recall (> 0.90). The models displayed an advantage over the typical best hit approach, yielding consistently lower false negative rates and thus higher overall recall (> 0.9). As more data become available for under-represented ARG categories, the DeepARG models' performance can be expected to be further enhanced due to the nature of the underlying neural networks. Our newly developed ARG database, DeepARG-DB, encompasses ARGs predicted with a high degree of confidence and extensive manual inspection, greatly expanding current ARG repositories. The deep learning models developed here offer more accurate antimicrobial resistance annotation relative to current bioinformatics practice. DeepARG does not require strict cutoffs, which enables identification of a much broader diversity of ARGs. The

Deep South Atlantic carbonate chemistry and increased interocean deep water exchange during last deglaciation

NASA Astrophysics Data System (ADS)

Yu, Jimin; Anderson, Robert F.; Jin, Zhangdong; Menviel, Laurie; Zhang, Fei; Ryerson, Fredrick J.; Rohling, Eelco J.

2014-04-01

Carbon release from the deep ocean at glacial terminations is a critical component of past climate change, but the underlying mechanisms remain poorly understood. We present a 28,000-year high-resolution record of carbonate ion concentration, a key parameter of the global carbon cycle, at 5-km water depth in the South Atlantic. We observe similar carbonate ion concentrations between the Last Glacial Maximum and the late Holocene, despite elevated concentrations in the glacial surface ocean. This strongly supports the importance of respiratory carbon accumulation in a stratified deep ocean for atmospheric CO2 reduction during the last ice age. After ˜9 μmol/kg decline during Heinrich Stadial 1, deep South Atlantic carbonate ion concentration rose by ˜24 μmol/kg from the onset of Bølling to Pre-boreal, likely caused by strengthening North Atlantic Deep Water formation (Bølling) or increased ventilation in the Southern Ocean (Younger Drays) or both (Pre-boreal). The ˜15 μmol/kg decline in deep water carbonate ion since ˜10 ka is consistent with extraction of alkalinity from seawater by deep-sea CaCO3 compensation and coral reef growth on continental shelves during the Holocene. Between 16,600 and 15,000 years ago, deep South Atlantic carbonate ion values converged with those at 3.4-km water depth in the western equatorial Pacific, as did carbon isotope and radiocarbon values. These observations suggest a period of enhanced lateral exchange of carbon between the deep South Atlantic and Pacific Oceans, probably due to an increased transfer of momentum from southern westerlies to the Southern Ocean. By spreading carbon-rich deep Pacific waters around Antarctica for upwelling, invigorated interocean deep water exchange would lead to more efficient CO2 degassing from the Southern Ocean, and thus to an atmospheric CO2 rise, during the early deglaciation.

DeepQA: improving the estimation of single protein model quality with deep belief networks.

PubMed

Cao, Renzhi; Bhattacharya, Debswapna; Hou, Jie; Cheng, Jianlin

2016-12-05

Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model pool consisting of mostly low-quality models, is still a largely unsolved problem. We introduce a novel single-model quality assessment method DeepQA based on deep belief network that utilizes a number of selected features describing the quality of a model from different perspectives, such as energy, physio-chemical characteristics, and structural information. The deep belief network is trained on several large datasets consisting of models from the Critical Assessment of Protein Structure Prediction (CASP) experiments, several publicly available datasets, and models generated by our in-house ab initio method. Our experiments demonstrate that deep belief network has better performance compared to Support Vector Machines and Neural Networks on the protein model quality assessment problem, and our method DeepQA achieves the state-of-the-art performance on CASP11 dataset. It also outperformed two well-established methods in selecting good outlier models from a large set of models of mostly low quality generated by ab initio modeling methods. DeepQA is a useful deep learning tool for protein single model quality assessment and protein structure prediction. The source code, executable, document and training/test datasets of DeepQA for Linux is freely available to non-commercial users at http://cactus.rnet.missouri.edu/DeepQA/ .

DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.

PubMed

Wang, Feng; Gong, Huichao; Liu, Gaochao; Li, Meijing; Yan, Chuangye; Xia, Tian; Li, Xueming; Zeng, Jianyang

2016-09-01

Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python. Copyright © 2016 Elsevier Inc. All rights reserved.

DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data.

PubMed

Yang, Jian-Hua; Qu, Liang-Hu

2012-01-01

Recent advances in high-throughput deep-sequencing technology have produced large numbers of short and long RNA sequences and enabled the detection and profiling of known and novel microRNAs (miRNAs) and other noncoding RNAs (ncRNAs) at unprecedented sensitivity and depth. In this chapter, we describe the use of deepBase, a database that we have developed to integrate all public deep-sequencing data and to facilitate the comprehensive annotation and discovery of miRNAs and other ncRNAs from these data. deepBase provides an integrative, interactive, and versatile web graphical interface to evaluate miRBase-annotated miRNA genes and other known ncRNAs, explores the expression patterns of miRNAs and other ncRNAs, and discovers novel miRNAs and other ncRNAs from deep-sequencing data. deepBase also provides a deepView genome browser to comparatively analyze these data at multiple levels. deepBase is available at http://deepbase.sysu.edu.cn/.

Exploration of cultivable fungal communities in deep coal-bearing sediments from ∼1.3 to 2.5 km below the ocean floor.

PubMed

Liu, Chang-Hong; Huang, Xin; Xie, Tian-Ning; Duan, Ning; Xue, Ya-Rong; Zhao, Tan-Xi; Lever, Mark A; Hinrichs, Kai-Uwe; Inagaki, Fumio

2017-02-01

Although subseafloor sediments are known to harbour a vast number of microbial cells, the distribution, diversity, and origins of fungal populations remain largely unexplored. In this study, we cultivated fungi from 34 of 47 deep coal-associated sediment samples collected at depths ranging from 1289 to 2457 m below the seafloor (mbsf) off the Shimokita Peninsula, Japan (1118 m water depth). We obtained a total of 69 fungal isolates under strict contamination controls, representing 61 Ascomycota (14 genera, 23 species) and 8 Basidiomycota (4 genera, 4 species). Penicillium and Aspergillus relatives were the most dominant genera within the Ascomycetes, followed by the members of genera Cladosporium, Hamigera, Chaetomium, Eutypella, Acremonium, Aureobasidium, Candida, Eurotium, Exophiala, Nigrospora, Bionectria and Pseudocercosporella. Four Basidiomycota species were identified as genera Schizophyllum, Irpex, Bjerkandera and Termitomyces. Among these isolates, Cladosporium sphaerospermum and Aspergillus sydowii relatives were isolated from a thin lignite coal-sandstone formation at 2457 mbsf. Our results indicate that these cultivable fungal populations are indigenous, originating from past terrigenous environments, which have persisted, possibly as spores, through ∼20 million years of depositional history. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

De novo identification of replication-timing domains in the human genome by deep learning.

PubMed

Liu, Feng; Ren, Chao; Li, Hao; Zhou, Pingkun; Bo, Xiaochen; Shu, Wenjie

2016-03-01

The de novo identification of the initiation and termination zones-regions that replicate earlier or later than their upstream and downstream neighbours, respectively-remains a key challenge in DNA replication. Building on advances in deep learning, we developed a novel hybrid architecture combining a pre-trained, deep neural network and a hidden Markov model (DNN-HMM) for the de novo identification of replication domains using replication timing profiles. Our results demonstrate that DNN-HMM can significantly outperform strong, discriminatively trained Gaussian mixture model-HMM (GMM-HMM) systems and other six reported methods that can be applied to this challenge. We applied our trained DNN-HMM to identify distinct replication domain types, namely the early replication domain (ERD), the down transition zone (DTZ), the late replication domain (LRD) and the up transition zone (UTZ), using newly replicated DNA sequencing (Repli-Seq) data across 15 human cells. A subsequent integrative analysis revealed that these replication domains harbour unique genomic and epigenetic patterns, transcriptional activity and higher-order chromosomal structure. Our findings support the 'replication-domain' model, which states (1) that ERDs and LRDs, connected by UTZs and DTZs, are spatially compartmentalized structural and functional units of higher-order chromosomal structure, (2) that the adjacent DTZ-UTZ pairs form chromatin loops and (3) that intra-interactions within ERDs and LRDs tend to be short-range and long-range, respectively. Our model reveals an important chromatin organizational principle of the human genome and represents a critical step towards understanding the mechanisms regulating replication timing. Our DNN-HMM method and three additional algorithms can be freely accessed at https://github.com/wenjiegroup/DNN-HMM The replication domain regions identified in this study are available in GEO under the accession ID GSE53984. shuwj@bmi.ac.cn or boxc

pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning.

PubMed

Zhou, Xie-Xuan; Zeng, Wen-Feng; Chi, Hao; Luo, Chunjie; Liu, Chao; Zhan, Jianfeng; He, Si-Min; Zhang, Zhifei

2017-12-05

In tandem mass spectrometry (MS/MS)-based proteomics, search engines rely on comparison between an experimental MS/MS spectrum and the theoretical spectra of the candidate peptides. Hence, accurate prediction of the theoretical spectra of peptides appears to be particularly important. Here, we present pDeep, a deep neural network-based model for the spectrum prediction of peptides. Using the bidirectional long short-term memory (BiLSTM), pDeep can predict higher-energy collisional dissociation, electron-transfer dissociation, and electron-transfer and higher-energy collision dissociation MS/MS spectra of peptides with >0.9 median Pearson correlation coefficients. Further, we showed that intermediate layer of the neural network could reveal physicochemical properties of amino acids, for example the similarities of fragmentation behaviors between amino acids. We also showed the potential of pDeep to distinguish extremely similar peptides (peptides that contain isobaric amino acids, for example, GG = N, AG = Q, or even I = L), which were very difficult to distinguish using traditional search engines.

Bite injuries of grey seals (Halichoerus grypus) on harbour porpoises (Phocoena phocoena).

PubMed

Jauniaux, Thierry; Garigliany, Mutien-Marie; Loos, Pauline; Bourgain, Jean-Luc; Bouveroux, Thibaut; Coignoul, Freddy; Haelters, Jan; Karpouzopoulos, Jacky; Pezeril, Sylvain; Desmecht, Daniel

2014-01-01

Bite-like skin lesions on harbour porpoises (Phocoena phocoena) have been suspected to be caused by grey seals (Halichoerus grypus), and a few field observations have been reported. Bite-like skin lesions observed on stranded animals were characterized by two main components: large flaps of loose or missing skin and blubber with frayed edges and puncture lesions. Definitive demonstration of predation by a grey seal was not reported so far in those stranded animals. In this study, five stranded porpoises with bite-like skin lesions were swabbed for genetic investigations. In addition, the head of a recently dead grey seal was used to mimic bite-like skin injuries on a porpoise carcass. Subsequently, the artificial skin injuries were swabbed, along with the gum of the seal used for inflicting them (positive controls). Total DNA was extracted from the swabs and was used to retrieve a fragment of mitochondrial DNA by PCR. Primers were designed to amplify a specific stretch of mitochondrial DNA known to differ between grey seals and porpoises. The amplicon targeted was successfully amplified from the positive control and from two of the stranded porpoises, and grey seal-specific mitochondrial DNA was retrieved from all those samples. We conclude that (1) it is possible to detect grey seal DNA from dead porpoises even after several days in seawater and (2) bite-like skin lesions found on dead porpoises definitively result from grey seals attacks. The attacks are most likely linked with predation although, in a number of cases, scavenging and aggressive behaviour cannot be excluded.

Deep learning for computational chemistry.

PubMed

Goh, Garrett B; Hodas, Nathan O; Vishnu, Abhinav

2017-06-15

The rise and fall of artificial neural networks is well documented in the scientific literature of both computer science and computational chemistry. Yet almost two decades later, we are now seeing a resurgence of interest in deep learning, a machine learning algorithm based on multilayer neural networks. Within the last few years, we have seen the transformative impact of deep learning in many domains, particularly in speech recognition and computer vision, to the extent that the majority of expert practitioners in those field are now regularly eschewing prior established models in favor of deep learning models. In this review, we provide an introductory overview into the theory of deep neural networks and their unique properties that distinguish them from traditional machine learning algorithms used in cheminformatics. By providing an overview of the variety of emerging applications of deep neural networks, we highlight its ubiquity and broad applicability to a wide range of challenges in the field, including quantitative structure activity relationship, virtual screening, protein structure prediction, quantum chemistry, materials design, and property prediction. In reviewing the performance of deep neural networks, we observed a consistent outperformance against non-neural networks state-of-the-art models across disparate research topics, and deep neural network-based models often exceeded the "glass ceiling" expectations of their respective tasks. Coupled with the maturity of GPU-accelerated computing for training deep neural networks and the exponential growth of chemical data on which to train these networks on, we anticipate that deep learning algorithms will be a valuable tool for computational chemistry. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Deep learning for computational chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goh, Garrett B.; Hodas, Nathan O.; Vishnu, Abhinav

The rise and fall of artificial neural networks is well documented in the scientific literature of both the fields of computer science and computational chemistry. Yet almost two decades later, we are now seeing a resurgence of interest in deep learning, a machine learning algorithm based on “deep” neural networks. Within the last few years, we have seen the transformative impact of deep learning the computer science domain, notably in speech recognition and computer vision, to the extent that the majority of practitioners in those field are now regularly eschewing prior established models in favor of deep learning models. Inmore » this review, we provide an introductory overview into the theory of deep neural networks and their unique properties as compared to traditional machine learning algorithms used in cheminformatics. By providing an overview of the variety of emerging applications of deep neural networks, we highlight its ubiquity and broad applicability to a wide range of challenges in the field, including QSAR, virtual screening, protein structure modeling, QM calculations, materials synthesis and property prediction. In reviewing the performance of deep neural networks, we observed a consistent outperformance against non neural networks state-of-the-art models across disparate research topics, and deep neural network based models often exceeded the “glass ceiling” expectations of their respective tasks. Coupled with the maturity of GPU-accelerated computing for training deep neural networks and the exponential growth of chemical data on which to train these networks on, we anticipate that deep learning algorithms will be a useful tool and may grow into a pivotal role for various challenges in the computational chemistry field.« less

Biochemical analysis of respiratory function in cybrid cell lines harbouring mitochondrial DNA mutations

PubMed Central

2004-01-01

We analysed key biochemical features that reflect the balance between glycolysis and glucose oxidation in cybrids (cytoplasmic hybrids) harbouring a representative sample of mitochondrial DNA point mutations and deletions. The cybrids analysed had the same 143B cell nuclear background and were isogenic for the mitochondrial background. The 143B cell line and its ρ0 counterpart were used as controls. All cells analysed were in a dynamic state, and cell number, time of plating, culture medium, extracellular volume and time of harvest and assay were strictly controlled. Intra- and extra-cellular lactate and pyruvate levels were measured in homoplasmic wild-type and mutant cells, and correlated with rates of ATP synthesis and O2 consumption. In all mutant cell lines, except those with the T8993C mutation in the ATPase 6 gene, glycolysis was increased even under conditions of low glucose, as demonstrated by increased levels of extracellular lactate and pyruvate. Extracellular lactate levels were strictly and inversely correlated with rates of ATP synthesis and O2 consumption. These results show increased glycolysis and defective oxidative phosphorylation, irrespective of the type or site of the point mutation or deletion in the mitochondrial genome. The different biochemical consequences of the T8993C mutation suggest a uniquely different pathogenic mechanism for this mutation. However, the distinct clinical features associated with some of these mutations still remain to be elucidated. PMID:15324306

Taoism and Deep Ecology.

ERIC Educational Resources Information Center

Sylvan, Richard; Bennett, David

1988-01-01

Contrasted are the philosophies of Deep Ecology and ancient Chinese. Discusses the cosmology, morality, lifestyle, views of power, politics, and environmental philosophies of each. Concludes that Deep Ecology could gain much from Taoism. (CW)

DeepID-Net: Deformable Deep Convolutional Neural Networks for Object Detection.

PubMed

Ouyang, Wanli; Zeng, Xingyu; Wang, Xiaogang; Qiu, Shi; Luo, Ping; Tian, Yonglong; Li, Hongsheng; Yang, Shuo; Wang, Zhe; Li, Hongyang; Loy, Chen Change; Wang, Kun; Yan, Junjie; Tang, Xiaoou

2016-07-07

In this paper, we propose deformable deep convolutional neural networks for generic object detection. This new deep learning object detection framework has innovations in multiple aspects. In the proposed new deep architecture, a new deformation constrained pooling (def-pooling) layer models the deformation of object parts with geometric constraint and penalty. A new pre-training strategy is proposed to learn feature representations more suitable for the object detection task and with good generalization capability. By changing the net structures, training strategies, adding and removing some key components in the detection pipeline, a set of models with large diversity are obtained, which significantly improves the effectiveness of model averaging. The proposed approach improves the mean averaged precision obtained by RCNN [16], which was the state-of-the-art, from 31% to 50.3% on the ILSVRC2014 detection test set. It also outperforms the winner of ILSVRC2014, GoogLeNet, by 6.1%. Detailed component-wise analysis is also provided through extensive experimental evaluation, which provides a global view for people to understand the deep learning object detection pipeline.

deepTools2: a next generation web server for deep-sequencing data analysis.

PubMed

Ramírez, Fidel; Ryan, Devon P; Grüning, Björn; Bhardwaj, Vivek; Kilpert, Fabian; Richter, Andreas S; Heyne, Steffen; Dündar, Friederike; Manke, Thomas

2016-07-08

We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Rapid differentiation of Staphylococcus aureus isolates harbouring egc loci with pseudogenes psient1 and psient2 and the selu or seluv gene using PCR-RFLP.

PubMed

Collery, Mark M; Smyth, Cyril J

2007-02-01

The egc locus of Staphylococus aureus harbours two enterotoxin genes (seg and sei) and three enterotoxin-like genes (selm, seln and selo). Between the sei and seln genes are located two pseudogenes, psient1 and psient2, or the selu or seluv gene. While these two alternative sei-seln intergenic regions can be distinguished by PCR, to date, DNA sequencing has been the only confirmatory option because of the very high degree of sequence similarity between egc loci bearing the pseudogenes and the selu or seluv gene. In silico restriction enzyme digestion of genomic regions encompassing the egc locus from the 3' end of the sei gene through the 5' first quarter of the seln gene allowed pseudogene- and selu- or seluv-bearing egc loci to be distinguished by PCR-RFLP. Experimental application of these findings demonstrated that endonuclease HindIII cleaved PCR amplimers bearing pseudogenes but not those with a selu or seluv gene, while selu- or seluv-bearing amplimers were susceptible to cleavage by endonuclease HphI, but not by endonuclease HindIII. The restriction enzyme BccI cleaved selu- or seluv-harbouring amplimers at a unique restriction site created by their signature 15 bp insertion compared with pseudogene-bearing amplimers, thereby allowing distinction of these egc loci. PCR-RFLP analysis using these restriction enzymes provides a rapid, easy to interpret alternative to DNA sequencing for verification of PCR findings on the nature of an egc locus type, and can also be used for the primary identification of the intergenic sei-seln egc locus type.

MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction.

PubMed

Wang, Duolin; Zeng, Shuai; Xu, Chunhui; Qiu, Wangren; Liang, Yanchun; Joshi, Trupti; Xu, Dong

2017-12-15

Computational methods for phosphorylation site prediction play important roles in protein function studies and experimental design. Most existing methods are based on feature extraction, which may result in incomplete or biased features. Deep learning as the cutting-edge machine learning method has the ability to automatically discover complex representations of phosphorylation patterns from the raw sequences, and hence it provides a powerful tool for improvement of phosphorylation site prediction. We present MusiteDeep, the first deep-learning framework for predicting general and kinase-specific phosphorylation sites. MusiteDeep takes raw sequence data as input and uses convolutional neural networks with a novel two-dimensional attention mechanism. It achieves over a 50% relative improvement in the area under the precision-recall curve in general phosphorylation site prediction and obtains competitive results in kinase-specific prediction compared to other well-known tools on the benchmark data. MusiteDeep is provided as an open-source tool available at https://github.com/duolinwang/MusiteDeep. xudong@missouri.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Searching for prostate cancer by fully automated magnetic resonance imaging classification: deep learning versus non-deep learning.

PubMed

Wang, Xinggang; Yang, Wei; Weinreb, Jeffrey; Han, Juan; Li, Qiubai; Kong, Xiangchuang; Yan, Yongluan; Ke, Zan; Luo, Bo; Liu, Tao; Wang, Liang

2017-11-13

Prostate cancer (PCa) is a major cause of death since ancient time documented in Egyptian Ptolemaic mummy imaging. PCa detection is critical to personalized medicine and varies considerably under an MRI scan. 172 patients with 2,602 morphologic images (axial 2D T2-weighted imaging) of the prostate were obtained. A deep learning with deep convolutional neural network (DCNN) and a non-deep learning with SIFT image feature and bag-of-word (BoW), a representative method for image recognition and analysis, were used to distinguish pathologically confirmed PCa patients from prostate benign conditions (BCs) patients with prostatitis or prostate benign hyperplasia (BPH). In fully automated detection of PCa patients, deep learning had a statistically higher area under the receiver operating characteristics curve (AUC) than non-deep learning (P = 0.0007 < 0.001). The AUCs were 0.84 (95% CI 0.78-0.89) for deep learning method and 0.70 (95% CI 0.63-0.77) for non-deep learning method, respectively. Our results suggest that deep learning with DCNN is superior to non-deep learning with SIFT image feature and BoW model for fully automated PCa patients differentiation from prostate BCs patients. Our deep learning method is extensible to image modalities such as MR imaging, CT and PET of other organs.

Deep breathing after surgery

MedlinePlus

... and taking big breaths can be uncomfortable. A device called an incentive spirometer can help you take deep breaths correctly. If you do not have this device, you can still practice deep breathing on your ...

Is Multitask Deep Learning Practical for Pharma?

PubMed

Ramsundar, Bharath; Liu, Bowen; Wu, Zhenqin; Verras, Andreas; Tudor, Matthew; Sheridan, Robert P; Pande, Vijay

2017-08-28

Multitask deep learning has emerged as a powerful tool for computational drug discovery. However, despite a number of preliminary studies, multitask deep networks have yet to be widely deployed in the pharmaceutical and biotech industries. This lack of acceptance stems from both software difficulties and lack of understanding of the robustness of multitask deep networks. Our work aims to resolve both of these barriers to adoption. We introduce a high-quality open-source implementation of multitask deep networks as part of the DeepChem open-source platform. Our implementation enables simple python scripts to construct, fit, and evaluate sophisticated deep models. We use our implementation to analyze the performance of multitask deep networks and related deep models on four collections of pharmaceutical data (three of which have not previously been analyzed in the literature). We split these data sets into train/valid/test using time and neighbor splits to test multitask deep learning performance under challenging conditions. Our results demonstrate that multitask deep networks are surprisingly robust and can offer strong improvement over random forests. Our analysis and open-source implementation in DeepChem provide an argument that multitask deep networks are ready for widespread use in commercial drug discovery.

Deep Space Quantum Link

NASA Astrophysics Data System (ADS)

Mohageg, M.; Strekalov, D.; Dolinar, S.; Shaw, M.; Yu, N.

2018-02-01

The Deep Space Quantum Link will test the effects of gravity on quantum systems, test the non-locality of quantum states at deep space distances, and perform long distance quantum teleportation to an Earth-based receiver.

The effects of marine traffic on the behaviour of Black Sea harbour porpoises (Phocoena phocoena relicta) within the Istanbul Strait, Turkey.

PubMed

Akkaya Bas, Aylin; Christiansen, Fredrik; Amaha Öztürk, Ayaka; Öztürk, Bayram; McIntosh, Caley

2017-01-01

Marine traffic is threatening cetaceans on a local and global scale. The Istanbul Strait is one of the busiest waterways, with up to 2,500 vessels present daily. This is the first study to assess the magnitude of short- and long-term behavioural changes of the endangered Black Sea harbour porpoises (Phocoena phocoena relicta) in the presence of marine vessels within the Istanbul Strait. Markov chains were used to investigate the effect of vessel presence on the transition probability between behavioural states (diving, surface-feeding and travelling), and to quantify the effect on the behavioural budget and bout length (duration of time spent in a given state) of porpoises. Further, the changes on swimming directions of porpoises in relation to vessel speed and distance was investigated using generalized linear models. In vessel presence, porpoises were less likely to remain in a given behavioural state and instead more likely to switch to another state. Because of this, the bout length of all three behavioural states decreased significantly in the presence of vessels. The vessel effect was sufficiently large to alter the behavioural budget, with surface-feeding decreasing significantly in the presence of vessels. However, when taking into account the proportion of time that porpoises were exposed to vessels (i.e. 50%), the measured effect size was not large enough to significantly alter the animals' cumulative (diurnal) behavioural budget. Additionally, vessel speed and distance had a significant effect on the probability of porpoises showing a response in their swimming directions. The southern and middle sections of the Istanbul Strait, which have the heaviest marine traffic pressure, had the lowest porpoise sightings throughout the year. Conversely, northern sections that were exposed to a lesser degree of marine traffic hold the highest porpoise sightings. The effect shown in this study in combination with increasing human impacts within the northern sections

The effects of marine traffic on the behaviour of Black Sea harbour porpoises (Phocoena phocoena relicta) within the Istanbul Strait, Turkey

PubMed Central

Christiansen, Fredrik; Amaha Öztürk, Ayaka; Öztürk, Bayram; McIntosh, Caley

2017-01-01

Marine traffic is threatening cetaceans on a local and global scale. The Istanbul Strait is one of the busiest waterways, with up to 2,500 vessels present daily. This is the first study to assess the magnitude of short- and long-term behavioural changes of the endangered Black Sea harbour porpoises (Phocoena phocoena relicta) in the presence of marine vessels within the Istanbul Strait. Markov chains were used to investigate the effect of vessel presence on the transition probability between behavioural states (diving, surface-feeding and travelling), and to quantify the effect on the behavioural budget and bout length (duration of time spent in a given state) of porpoises. Further, the changes on swimming directions of porpoises in relation to vessel speed and distance was investigated using generalized linear models. In vessel presence, porpoises were less likely to remain in a given behavioural state and instead more likely to switch to another state. Because of this, the bout length of all three behavioural states decreased significantly in the presence of vessels. The vessel effect was sufficiently large to alter the behavioural budget, with surface-feeding decreasing significantly in the presence of vessels. However, when taking into account the proportion of time that porpoises were exposed to vessels (i.e. 50%), the measured effect size was not large enough to significantly alter the animals’ cumulative (diurnal) behavioural budget. Additionally, vessel speed and distance had a significant effect on the probability of porpoises showing a response in their swimming directions. The southern and middle sections of the Istanbul Strait, which have the heaviest marine traffic pressure, had the lowest porpoise sightings throughout the year. Conversely, northern sections that were exposed to a lesser degree of marine traffic hold the highest porpoise sightings. The effect shown in this study in combination with increasing human impacts within the northern

Keeping returns optimal: gain control exerted through sensitivity adjustments in the harbour porpoise auditory system

PubMed Central

Linnenschmidt, Meike; Beedholm, Kristian; Wahlberg, Magnus; Højer-Kristensen, Jakob; Nachtigall, Paul E.

2012-01-01

Animals that use echolocation (biosonar) listen to acoustic signals with a large range of intensities, because echo levels vary with the fourth power of the animal's distance to the target. In man-made sonar, engineers apply automatic gain control to stabilize the echo energy levels, thereby rendering them independent of distance to the target. Both toothed whales and bats vary the level of their echolocation clicks to compensate for the distance-related energy loss. By monitoring the auditory brainstem response (ABR) during a psychophysical task, we found that a harbour porpoise (Phocoena phocoena), in addition to adjusting the sound level of the outgoing signals up to 5.4 dB, also reduces its ABR threshold by 6 dB when the target distance doubles. This self-induced threshold shift increases the dynamic range of the biosonar system and compensates for half of the variation of energy that is caused by changes in the distance to the target. In combination with an increased source level as a function of target range, this helps the porpoise to maintain a stable echo-evoked ABR amplitude irrespective of target range, and is therefore probably an important tool enabling porpoises to efficiently analyse and classify received echoes. PMID:22279169

Complex dissemination of the diversified mcr-1-harbouring plasmids in Escherichia coli of different sequence types

PubMed Central

Lin, Jingxia; Wang, Xiuna; Deng, Xianbo; Feng, Youjun

2016-01-01

The emergence of the mobilized colistin resistance gene, representing a novel mechanism for bacterial drug resistance, challenges the last resort against the severe infections by Gram-negative bacteria with multi-drug resistances. Very recently, we showed the diversity in the mcr-1-carrying plasmid reservoirs from the gut microbiota. Here, we reported that a similar but more complex scenario is present in the healthy swine populations, Southern China, 2016. Amongst the 1026 pieces of Escherichia coli isolates from 3 different pig farms, 302 E. coli isolates were determined to be positive for the mcr-1 gene (30%, 302/1026). Multi-locus sequence typing assigned no less than 11 kinds of sequence types including one novel Sequence Type to these mcr-1-positive strains. PCR analyses combined with the direct DNA sequencing revealed unexpected complexity of the mcr-1-harbouring plasmids whose backbones are at least grouped into 6 types four of which are new. Transcriptional analyses showed that the mcr-1 promoter of different origins exhibits similar activity. It seems likely that complex dissemination of the diversified mcr-1-bearing plasmids occurs amongst the various ST E. coli inhabiting the healthy swine populations, in Southern China. PMID:27741523

Multivariate methods for evaluating the efficiency of electrodialytic removal of heavy metals from polluted harbour sediments.

PubMed

Pedersen, Kristine Bondo; Kirkelund, Gunvor M; Ottosen, Lisbeth M; Jensen, Pernille E; Lejon, Tore

2015-01-01

Chemometrics was used to develop a multivariate model based on 46 previously reported electrodialytic remediation experiments (EDR) of five different harbour sediments. The model predicted final concentrations of Cd, Cu, Pb and Zn as a function of current density, remediation time, stirring rate, dry/wet sediment, cell set-up as well as sediment properties. Evaluation of the model showed that remediation time and current density had the highest comparative influence on the clean-up levels. Individual models for each heavy metal showed variance in the variable importance, indicating that the targeted heavy metals were bound to different sediment fractions. Based on the results, a PLS model was used to design five new EDR experiments of a sixth sediment to achieve specified clean-up levels of Cu and Pb. The removal efficiencies were up to 82% for Cu and 87% for Pb and the targeted clean-up levels were met in four out of five experiments. The clean-up levels were better than predicted by the model, which could hence be used for predicting an approximate remediation strategy; the modelling power will however improve with more data included. Copyright © 2014 Elsevier B.V. All rights reserved.

DeepGene: an advanced cancer type classifier based on deep learning and somatic point mutations.

PubMed

Yuan, Yuchen; Shi, Yi; Li, Changyang; Kim, Jinman; Cai, Weidong; Han, Zeguang; Feng, David Dagan

2016-12-23

With the developments of DNA sequencing technology, large amounts of sequencing data have become available in recent years and provide unprecedented opportunities for advanced association studies between somatic point mutations and cancer types/subtypes, which may contribute to more accurate somatic point mutation based cancer classification (SMCC). However in existing SMCC methods, issues like high data sparsity, small volume of sample size, and the application of simple linear classifiers, are major obstacles in improving the classification performance. To address the obstacles in existing SMCC studies, we propose DeepGene, an advanced deep neural network (DNN) based classifier, that consists of three steps: firstly, the clustered gene filtering (CGF) concentrates the gene data by mutation occurrence frequency, filtering out the majority of irrelevant genes; secondly, the indexed sparsity reduction (ISR) converts the gene data into indexes of its non-zero elements, thereby significantly suppressing the impact of data sparsity; finally, the data after CGF and ISR is fed into a DNN classifier, which extracts high-level features for accurate classification. Experimental results on our curated TCGA-DeepGene dataset, which is a reformulated subset of the TCGA dataset containing 12 selected types of cancer, show that CGF, ISR and DNN all contribute in improving the overall classification performance. We further compare DeepGene with three widely adopted classifiers and demonstrate that DeepGene has at least 24% performance improvement in terms of testing accuracy. Based on deep learning and somatic point mutation data, we devise DeepGene, an advanced cancer type classifier, which addresses the obstacles in existing SMCC studies. Experiments indicate that DeepGene outperforms three widely adopted existing classifiers, which is mainly attributed to its deep learning module that is able to extract the high level features between combinatorial somatic point mutations and

Deep Water Ocean Acoustics

DTIC Science & Technology

2015-04-15

0 A S S PROGRESS REPORT NO. QSR-14C0172-0CEAN ACOUSTICS-033115 Contract No. N00014-14-C-0172 Office of Naval Research Task Reporting: Deep ...AND SUBTITLE Deep Water Ocean Acoustics 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e...298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 Cost Summary OASIS, INC. JOB STATUS RB’ORT 1172 DEEP WATER ACOUSTICS FOP. 9/27f13-316/16

Stable architectures for deep neural networks

NASA Astrophysics Data System (ADS)

Haber, Eldad; Ruthotto, Lars

2018-01-01

Deep neural networks have become invaluable tools for supervised machine learning, e.g. classification of text or images. While often offering superior results over traditional techniques and successfully expressing complicated patterns in data, deep architectures are known to be challenging to design and train such that they generalize well to new data. Critical issues with deep architectures are numerical instabilities in derivative-based learning algorithms commonly called exploding or vanishing gradients. In this paper, we propose new forward propagation techniques inspired by systems of ordinary differential equations (ODE) that overcome this challenge and lead to well-posed learning problems for arbitrarily deep networks. The backbone of our approach is our interpretation of deep learning as a parameter estimation problem of nonlinear dynamical systems. Given this formulation, we analyze stability and well-posedness of deep learning and use this new understanding to develop new network architectures. We relate the exploding and vanishing gradient phenomenon to the stability of the discrete ODE and present several strategies for stabilizing deep learning for very deep networks. While our new architectures restrict the solution space, several numerical experiments show their competitiveness with state-of-the-art networks.

The deep-sea under global change.

PubMed

Danovaro, Roberto; Corinaldesi, Cinzia; Dell'Anno, Antonio; Snelgrove, Paul V R

2017-06-05

The deep ocean encompasses 95% of the oceans' volume and is the largest and least explored biome of Earth's Biosphere. New life forms are continuously being discovered. The physiological mechanisms allowing organisms to adapt to extreme conditions of the deep ocean (high pressures, from very low to very high temperatures, food shortage, lack of solar light) are still largely unknown. Some deep-sea species have very long life-spans, whereas others can tolerate toxic compounds at high concentrations; these characteristics offer an opportunity to explore the specialized biochemical and physiological mechanisms associated with these responses. Widespread symbiotic relationships play fundamental roles in driving host functions, nutrition, health, and evolution. Deep-sea organisms communicate and interact through sound emissions, chemical signals and bioluminescence. Several giants of the oceans hunt exclusively at depth, and new studies reveal a tight connection between processes in the shallow water and some deep-sea species. Limited biological knowledge of the deep-sea limits our capacity to predict future response of deep-sea organisms subject to increasing human pressure and changing global environmental conditions. Molecular tools, sensor-tagged animals, in situ and laboratory experiments, and new technologies can enable unprecedented advancement of deep-sea biology, and facilitate the sustainable management of deep ocean use under global change. Copyright © 2017. Published by Elsevier Ltd.

Conservation of deep pelagic biodiversity.

PubMed

Robison, Bruce H

2009-08-01

The deep ocean is home to the largest ecosystems on our planet. This vast realm contains what may be the greatest number of animal species, the greatest biomass, and the greatest number of individual organisms in the living world. Humans have explored the deep ocean for about 150 years, and most of what is known is based on studies of the deep seafloor. In contrast, the water column above the deep seabed comprises more than 90% of the living space, yet less than 1% of this biome has been explored. The deep pelagic biota is the largest and least-known major faunal group on Earth despite its obvious importance at the global scale. Pelagic species represent an incomparable reservoir of biodiversity. Although we have yet to discover and describe the majority of these species, the threats to their continued existence are numerous and growing. Conserving deep pelagic biodiversity is a problem of global proportions that has never been addressed comprehensively. The potential effects of these threats include the extensive restructuring of entire ecosystems, changes in the geographical ranges of many species, large-scale elimination of taxa, and a decline in biodiversity at all scales. This review provides an initial framework of threat assessment for confronting the challenge of conserving deep pelagic biodiversity; and it outlines the need for baseline surveys and protected areas as preliminary policy goals.

The 3'-UTR of the adiponectin Q gene harbours susceptibility loci for atherosclerosis and its metabolic risk traits.

PubMed

Muiya, Nzioka; Al-Najai, Mohammed; Tahir, Asma I; Elhawari, Samar; Gueco, Daisy; Andres, Editha; Mazhar, Nejat; Altassan, Nada; Meyer, Brian F; Alshahid, Maie; Dzimiri, Nduna

2013-12-13

Adiponectin Q is a hormone that modulates several metabolic processes and contributes to the suppression of biochemical pathways leading to metabolic syndrome. Hence, polymorphic changes in the adiponectin Q (ADIPOQ) gene are likely to contribute to metabolic disorders, and consequently lead to atherosclerosis. In the present study, we performed a population-based association study for 8 SNPs in 4646 Saudi individuals (2339 CAD cases versus angiographed 2307 controls) by real-time PCR. Linkage analysis was done by the Affymetrix Gene Chip array, sequencing by the MegaBACE DNA analysis system and genotyping accomplished by TaqMan chemistry with the Applied Biosystem real-time Prism 7900HT Sequence Detection System. The rs2241766 (TG + GG) [Odds ratio(95% Confidence Interval = 1.35(1.01-1.72); p = 0.015] and rs9842733A > T [1.48(1.01-2.07); p = 0.042] were associated with hypertension [HTN; 3541 cases vs 1101 controls), following adjustment for the presence of other cardiovascular risk traits. The rs2241766 (TG + GG) was further implicated in harbouring of low high density lipoprotein levels (LHDL; 1353 versus 2156 controls) [1.35(1.10-1.67); p = 0.005], but lost its association with obesity after the adjustment for confounders. Besides, low high density lipoprotein was also linked with rs6444174 (TC + CC) [1.28(1.05-1.59)]. On the other hand, while initial univariate logistic regression analysis pointed to rs1063537 C > T (p = 0.010), rs2082940 C > T (p = 0.035) and rs1063539 G > C (p = 0.035) as being associated with myocardial infarction, significance levels of these relationships were diminished following adjustment for the influence of confounding covariates. Interestingly, haplotyping showed that an 8-mer haplotype GTGCCTCA and several of its derivatives constructed from the studied SNPs were commonly implicated in MI (χ² = 4.12; p = 0.042), HTN (χ² = 6.40; p = 0.011) and OBS (�

Deep Seawater Intrusion Enhanced by Geothermal Through Deep Faults in Xinzhou Geothermal Field in Guangdong, China

NASA Astrophysics Data System (ADS)

Lu, G.; Ou, H.; Hu, B. X.; Wang, X.

2017-12-01

This study investigates abnormal sea water intrusion from deep depth, riding an inland-ward deep groundwater flow, which is enhanced by deep faults and geothermal processes. The study site Xinzhou geothermal field is 20 km from the coast line. It is in southern China's Guangdong coast, a part of China's long coastal geothermal belt. The geothermal water is salty, having fueled an speculation that it was ancient sea water retained. However, the perpetual "pumping" of the self-flowing outflow of geothermal waters might alter the deep underground flow to favor large-scale or long distant sea water intrusion. We studied geochemical characteristics of the geothermal water and found it as a mixture of the sea water with rain water or pore water, with no indication of dilution involved. And we conducted numerical studies of the buoyancy-driven geothermal flow in the deep ground and find that deep down in thousand meters there is favorable hydraulic gradient favoring inland-ward groundwater flow, allowing seawater intrude inland for an unusually long tens of kilometers in a granitic groundwater flow system. This work formed the first in understanding geo-environment for deep ground water flow.

76 FR 66078 - Notice of Industry Workshop on Technical and Regulatory Challenges in Deep and Ultra-Deep Outer...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-25

...-0087] Notice of Industry Workshop on Technical and Regulatory Challenges in Deep and Ultra-Deep Outer... and gas exploration and production in deep and ultra-deep OCS waters. Through this workshop, BSEE will... structured venue for consultation among offshore deepwater oil and gas industry and regulatory experts in...

Deep Chandra study of the truncated cool core of the Ophiuchus cluster

NASA Astrophysics Data System (ADS)

Werner, N.; Zhuravleva, I.; Canning, R. E. A.; Allen, S. W.; King, A. L.; Sanders, J. S.; Simionescu, A.; Taylor, G. B.; Morris, R. G.; Fabian, A. C.

2016-08-01

We present the results of a deep Chandra observation of the Ophiuchus cluster, the second brightest galaxy cluster in the X-ray sky. The cluster hosts a truncated cool core, with a temperature increasing from kT ˜ 1 keV in the core to kT ˜ 9 keV at r ˜ 30 kpc. Beyond r ˜ 30 kpc, the intracluster medium (ICM) appears remarkably isothermal. The core is dynamically disturbed with multiple sloshing-induced cold fronts, with indications for both Rayleigh-Taylor and Kelvin-Helmholtz instabilities. The residual image reveals a likely subcluster south of the core at the projected distance of r ˜ 280 kpc. The cluster also harbours a likely radio phoenix, a source revived by adiabatic compression by gas motions in the ICM. Even though the Ophiuchus cluster is strongly dynamically active, the amplitude of density fluctuations outside of the cooling core is low, indicating velocities smaller than ˜100 km s-1. The density fluctuations might be damped by thermal conduction in the hot and remarkably isothermal ICM, resulting in our underestimate of gas velocities. We find a surprising, sharp surface brightness discontinuity, that is curved away from the core, at r ˜ 120 kpc to the south-east of the cluster centre. We conclude that this feature is most likely due to gas dynamics associated with a merger. The cooling core lacks any observable X-ray cavities and the active galactic nucleus (AGN) only displays weak, point-like radio emission, lacking lobes or jets. The lack of strong AGN activity may be due to the bulk of the cooling taking place offset from the central supermassive black hole.

DeepSurveyCam--A Deep Ocean Optical Mapping System.

PubMed

Kwasnitschka, Tom; Köser, Kevin; Sticklus, Jan; Rothenbeck, Marcel; Weiß, Tim; Wenzlaff, Emanuel; Schoening, Timm; Triebe, Lars; Steinführer, Anja; Devey, Colin; Greinert, Jens

2016-01-28

Underwater photogrammetry and in particular systematic visual surveys of the deep sea are by far less developed than similar techniques on land or in space. The main challenges are the rough conditions with extremely high pressure, the accessibility of target areas (container and ship deployment of robust sensors, then diving for hours to the ocean floor), and the limitations of localization technologies (no GPS). The absence of natural light complicates energy budget considerations for deep diving flash-equipped drones. Refraction effects influence geometric image formation considerations with respect to field of view and focus, while attenuation and scattering degrade the radiometric image quality and limit the effective visibility. As an improvement on the stated issues, we present an AUV-based optical system intended for autonomous visual mapping of large areas of the seafloor (square kilometers) in up to 6000 m water depth. We compare it to existing systems and discuss tradeoffs such as resolution vs. mapped area and show results from a recent deployment with 90,000 mapped square meters of deep ocean floor.

DeepSurveyCam—A Deep Ocean Optical Mapping System

PubMed Central

Kwasnitschka, Tom; Köser, Kevin; Sticklus, Jan; Rothenbeck, Marcel; Weiß, Tim; Wenzlaff, Emanuel; Schoening, Timm; Triebe, Lars; Steinführer, Anja; Devey, Colin; Greinert, Jens

2016-01-01

Underwater photogrammetry and in particular systematic visual surveys of the deep sea are by far less developed than similar techniques on land or in space. The main challenges are the rough conditions with extremely high pressure, the accessibility of target areas (container and ship deployment of robust sensors, then diving for hours to the ocean floor), and the limitations of localization technologies (no GPS). The absence of natural light complicates energy budget considerations for deep diving flash-equipped drones. Refraction effects influence geometric image formation considerations with respect to field of view and focus, while attenuation and scattering degrade the radiometric image quality and limit the effective visibility. As an improvement on the stated issues, we present an AUV-based optical system intended for autonomous visual mapping of large areas of the seafloor (square kilometers) in up to 6000 m water depth. We compare it to existing systems and discuss tradeoffs such as resolution vs. mapped area and show results from a recent deployment with 90,000 mapped square meters of deep ocean floor. PMID:26828495

Deep-convection events foster carbonate ion reduction in deep coral reefs

NASA Astrophysics Data System (ADS)

Perez, Fiz F.; Fontela, Marcos; Garcia-Ibañez, Maribel I.; Lherminier, Pascale; Zunino, Patricia; de la Paz, Mercedes; Padín, Xose A.; Alonso-Pérez, Fernando; Velo, Anton; Guallart, Elisa F.; Mercier, Herle

2017-04-01

Since millennial times, water mass circulation and deep-convection events have been transforming warm upper waters at high latitudes into cold and well-oxygenated deep waters. These processes have filled the deep North Atlantic Ocean with waters moderately saturated in calcium carbonate, thus promoting the growth of stony corals, which are hotspots of biodiversity. During the Anthropocene, the meridional circulation has been conveying cumulative amounts of more acidified waters with lower calcium carbonate saturation levels due to the incorporation of anthropogenic carbon dioxide, with very harsh conditions for deep cold-water corals projected by 2100. We evaluate the diminution of calcium carbonate saturation levels (aragonite form) due to the increase in anthropogenic carbon dioxide during the last two decades (2002-2016). We observe a strong decrease in the aragonite saturation levels concomitant with the reduction in the volume transport of aragonite-saturated waters. We estimate a 30-35% reduction in the transport of ion carbonate excess over the saturation levels with respect to the natural carbon cycle for the period 2002-2016. This reduction is associated with an increase in the downward transport of hydrogen ions. We also observe a heaving of the aragonite saturation horizons during the last 25 years, which is estimated at 6 m year-1 for the deep waters and 12-14 m year-1 for the intermediated waters. The harsh winters of 2015 and 2016 have fostered the fast addition of more acidified water into the lower layers of the North Atlantic through deep-convection events. In the future scenario of 2oC warming, the anthropogenic carbon dioxide in the water column would be double than today and the associated transport of hydrogen ions towards the bottom water would reduce the aragonite saturation levels to 60-80% with respect to preindustrial levels. This reduction in the aragonite saturation levels would suppose a strong diminution of the North Atlantic habitats

Temperature impacts on deep-sea biodiversity.

PubMed

Yasuhara, Moriaki; Danovaro, Roberto

2016-05-01

Temperature is considered to be a fundamental factor controlling biodiversity in marine ecosystems, but precisely what role temperature plays in modulating diversity is still not clear. The deep ocean, lacking light and in situ photosynthetic primary production, is an ideal model system to test the effects of temperature changes on biodiversity. Here we synthesize current knowledge on temperature-diversity relationships in the deep sea. Our results from both present and past deep-sea assemblages suggest that, when a wide range of deep-sea bottom-water temperatures is considered, a unimodal relationship exists between temperature and diversity (that may be right skewed). It is possible that temperature is important only when at relatively high and low levels but does not play a major role in the intermediate temperature range. Possible mechanisms explaining the temperature-biodiversity relationship include the physiological-tolerance hypothesis, the metabolic hypothesis, island biogeography theory, or some combination of these. The possible unimodal relationship discussed here may allow us to identify tipping points at which on-going global change and deep-water warming may increase or decrease deep-sea biodiversity. Predicted changes in deep-sea temperatures due to human-induced climate change may have more adverse consequences than expected considering the sensitivity of deep-sea ecosystems to temperature changes. © 2014 Cambridge Philosophical Society.

[Search for life in deep biospheres].

PubMed

Naganuma, Takeshi

2003-12-01

The life in deep biospheres bridges conventional biology and future exobiology. This review focuses the microbiological studies from the selected deep biospheres, i.e., deep-sea hydrothermal vents, sub-hydrothermal vents, terrestrial subsurface and a sub-glacier lake. The dark biospheres facilitate the emergence of organisms and communities dependent on chemolithoautotrophy, which are overwhelmed by photoautotrophy (photosynthesis) in the surface biospheres. The life at deep-sea hydrothermal vents owes much to chemolithoautotrophy based on the oxidation of sulfide emitted from the vents. It is likely that similarly active bodies such as the Jovian satellite Europa may have hydrothermal vents and associated biological communities. Anoxic or anaerobic condition is characteristic of deep subsurface biospheres. Subsurface microorganisms exploit available oxidants, or terminal electron acceptors (TEA), for anaerobic respiration. Sulfate, nitrate, iron (III) and CO2 are the representative TEAs in the deep subsurface. Below the 3000-4000 m-thick glacier on Antarctica, there have been >70 lakes with liquid water located. One of such sub-glacial lakes, Lake Vostok, is about to be drill-penetrated for microbiological studies. These deep biosphere "platforms" provide new knowledge about the diversity and potential of the Earth's life. The expertise obtained from the deep biosphere expeditions will facilitate the capability of exobiologial exploration.

deepNF: Deep network fusion for protein function prediction.

PubMed

Gligorijevic, Vladimir; Barot, Meet; Bonneau, Richard

2018-06-01

The prevalence of high-throughput experimental methods has resulted in an abundance of large-scale molecular and functional interaction networks. The connectivity of these networks provides a rich source of information for inferring functional annotations for genes and proteins. An important challenge has been to develop methods for combining these heterogeneous networks to extract useful protein feature representations for function prediction. Most of the existing approaches for network integration use shallow models that encounter difficulty in capturing complex and highly-nonlinear network structures. Thus, we propose deepNF, a network fusion method based on Multimodal Deep Autoencoders to extract high-level features of proteins from multiple heterogeneous interaction networks. We apply this method to combine STRING networks to construct a common low-dimensional representation containing high-level protein features. We use separate layers for different network types in the early stages of the multimodal autoencoder, later connecting all the layers into a single bottleneck layer from which we extract features to predict protein function. We compare the cross-validation and temporal holdout predictive performance of our method with state-of-the-art methods, including the recently proposed method Mashup. Our results show that our method outperforms previous methods for both human and yeast STRING networks. We also show substantial improvement in the performance of our method in predicting GO terms of varying type and specificity. deepNF is freely available at: https://github.com/VGligorijevic/deepNF. vgligorijevic@flatironinstitute.org, rb133@nyu.edu. Supplementary data are available at Bioinformatics online.

The Deep Space Network: A Radio Communications Instrument for Deep Space Exploration

NASA Technical Reports Server (NTRS)

Renzetti, N. A.; Stelzried, C. T.; Noreen, G. K.; Slobin, S. D.; Petty, S. M.; Trowbridge, D. L.; Donnelly, H.; Kinman, P. W.; Armstrong, J. W.; Burow, N. A.

1983-01-01

The primary purpose of the Deep Space Network (DSN) is to serve as a communications instrument for deep space exploration, providing communications between the spacecraft and the ground facilities. The uplink communications channel provides instructions or commands to the spacecraft. The downlink communications channel provides command verification and spacecraft engineering and science instrument payload data.

Exposure of harbour seals Phoca vitulina to Brucella in declining populations across Scotland.

PubMed

Kershaw, Joanna L; Stubberfield, Emma J; Foster, Geoffrey; Brownlow, Andrew; Hall, Ailsa J; Perrett, Lorraine L

2017-09-20

Since 2000 there has been a major decline in the abundance of Scottish harbour seals Phoca vitulina. The causes of the decline remain uncertain. The aim of this study was to establish the extent to which the seals in the regions of greatest decline have been exposed to Brucella, a bacterial pathogen that causes reproductive failure in terrestrial mammalian hosts. Tissues from dead seals collected between 1992 and 2013 were cultured for Brucella (n = 150). Serum samples collected from live capture-released seals (n = 343) between 1997 and 2012 were tested for Brucella antibodies using the Rose Bengal plate agglutination test (RBT) and a competitive enzyme-linked immunosorbent assay (cELISA). In total, 16% of seals cultured had Brucella isolated from one or more tissues, but there were no pathological signs of infection. The cELISA results were more sensitive than the RBT results, showing that overall 25.4% of seals were seropositive, with the highest seroprevalence in juveniles. As there was no evidence of either a higher seroprevalence or higher circulating antibody levels in seropositive animals in the areas with the greatest declines, it was concluded that Brucella infection is likely not a major contributing factor to recent declines. However, the consistently high proportion of seals exposed to Brucella indicates possible endemicity in these populations, likely due to B. pinnipedialis, which has demonstrated a preference for pinniped hosts. Importantly, given the close proximity between seals, humans and livestock in many areas, there is the potential for cross-species infections.

The Deep Space Network

NASA Technical Reports Server (NTRS)

1979-01-01

Deep Space Network progress in flight project support, tracking and data acquisition, research and technology, network engineering, hardware and software implementation, and operations is cited. Topics covered include: tracking and ground based navigation; spacecraft/ground communication; station control and operations technology; ground communications; and deep space stations.

DeepMirTar: a deep-learning approach for predicting human miRNA targets.

PubMed

Wen, Ming; Cong, Peisheng; Zhang, Zhimin; Lu, Hongmei; Li, Tonghua

2018-06-01

MicroRNAs (miRNAs) are small noncoding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression by targeting messenger RNAs (mRNAs). Because the underlying mechanisms associated with miRNA binding to mRNA are not fully understood, a major challenge of miRNA studies involves the identification of miRNA-target sites on mRNA. In silico prediction of miRNA-target sites can expedite costly and time-consuming experimental work by providing the most promising miRNA-target-site candidates. In this study, we reported the design and implementation of DeepMirTar, a deep-learning-based approach for accurately predicting human miRNA targets at the site level. The predicted miRNA-target sites are those having canonical or non-canonical seed, and features, including high-level expert-designed, low-level expert-designed, and raw-data-level, were used to represent the miRNA-target site. Comparison with other state-of-the-art machine-learning methods and existing miRNA-target-prediction tools indicated that DeepMirTar improved overall predictive performance. DeepMirTar is freely available at https://github.com/Bjoux2/DeepMirTar_SdA. lith@tongji.edu.cn, hongmeilu@csu.edu.cn. Supplementary data are available at Bioinformatics online.

The deep space network

NASA Technical Reports Server (NTRS)

1974-01-01

The progress is reported of Deep Space Network (DSN) research in the following areas: (1) flight project support, (2) spacecraft/ground communications, (3) station control and operations technology, (4) network control and processing, and (5) deep space stations. A description of the DSN functions and facilities is included.

Extreme Longevity in Proteinaceous Deep-Sea Corals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roark, E B; Guilderson, T P; Dunbar, R B

2009-02-09

Deep-sea corals are found on hard substrates on seamounts and continental margins world-wide at depths of 300 to {approx}3000 meters. Deep-sea coral communities are hotspots of deep ocean biomass and biodiversity, providing critical habitat for fish and invertebrates. Newly applied radiocarbon age date from the deep water proteinaceous corals Gerardia sp. and Leiopathes glaberrima show that radial growth rates are as low as 4 to 35 {micro}m yr{sup -1} and that individual colony longevities are on the order of thousands of years. The management and conservation of deep sea coral communities is challenged by their commercial harvest for the jewelrymore » trade and damage caused by deep water fishing practices. In light of their unusual longevity, a better understanding of deep sea coral ecology and their interrelationships with associated benthic communities is needed to inform coherent international conservation strategies for these important deep-sea ecosystems.« less

Temporal and spatial patterns of habitat use by juveniles of a small coastal shark (Mustelus lenticulatus) in an estuarine nursery.

PubMed

Francis, Malcolm P

2013-01-01

Juvenile rig (Mustelus lenticulatus) were internally tagged with acoustic transmitters and tracked with acoustic receivers deployed throughout two arms of Porirua Harbour, a small (7 km(2)) estuary in New Zealand. Ten rig were tracked for up to four months during summer-autumn to determine their spatial and temporal use of the habitat. The overall goal was to estimate the size of Marine Protected Areas required to protect rig nursery areas from direct human impacts. Rig showed clear site preferences, but those preferences varied among rig and over time. They spent most of their time in large basins and on shallow sand and mud flats around the margins, and avoided deep channels. Habitat range increased during autumn for many of the rig. Only one shark spent time in both harbour arms, indicating that there was little movement between the two. Rig home ranges were 2-7 km(2), suggesting that an effective MPA would need to cover the entire Porirua Harbour. They moved to outer harbour sites following some high river flow rates, and most left the harbour permanently during or soon after a river spike, suggesting that they were avoiding low salinity water. Rig showed strong diel movements during summer, although the diel pattern weakened in autumn. Persistent use of the same day and night sites indicates that diel movements are directed rather than random. Further research is required to determine the sizes of rig home ranges in larger harbours where nursery habitat is more extensive. Marine Protected Areas do not control land-based impacts such as accelerated sedimentation and heavy metal pollution, so integration of marine and terrestrial management tools across a range of government agencies is essential to fully protect nursery areas.

Temporal and Spatial Patterns of Habitat Use by Juveniles of a Small Coastal Shark (Mustelus lenticulatus) in an Estuarine Nursery

PubMed Central

Francis, Malcolm P.

2013-01-01

Juvenile rig (Mustelus lenticulatus) were internally tagged with acoustic transmitters and tracked with acoustic receivers deployed throughout two arms of Porirua Harbour, a small (7 km2) estuary in New Zealand. Ten rig were tracked for up to four months during summer–autumn to determine their spatial and temporal use of the habitat. The overall goal was to estimate the size of Marine Protected Areas required to protect rig nursery areas from direct human impacts. Rig showed clear site preferences, but those preferences varied among rig and over time. They spent most of their time in large basins and on shallow sand and mud flats around the margins, and avoided deep channels. Habitat range increased during autumn for many of the rig. Only one shark spent time in both harbour arms, indicating that there was little movement between the two. Rig home ranges were 2–7 km2, suggesting that an effective MPA would need to cover the entire Porirua Harbour. They moved to outer harbour sites following some high river flow rates, and most left the harbour permanently during or soon after a river spike, suggesting that they were avoiding low salinity water. Rig showed strong diel movements during summer, although the diel pattern weakened in autumn. Persistent use of the same day and night sites indicates that diel movements are directed rather than random. Further research is required to determine the sizes of rig home ranges in larger harbours where nursery habitat is more extensive. Marine Protected Areas do not control land-based impacts such as accelerated sedimentation and heavy metal pollution, so integration of marine and terrestrial management tools across a range of government agencies is essential to fully protect nursery areas. PMID:23437298

Deep Unfolding for Topic Models.

PubMed

Chien, Jen-Tzung; Lee, Chao-Hsi

2018-02-01

Deep unfolding provides an approach to integrate the probabilistic generative models and the deterministic neural networks. Such an approach is benefited by deep representation, easy interpretation, flexible learning and stochastic modeling. This study develops the unsupervised and supervised learning of deep unfolded topic models for document representation and classification. Conventionally, the unsupervised and supervised topic models are inferred via the variational inference algorithm where the model parameters are estimated by maximizing the lower bound of logarithm of marginal likelihood using input documents without and with class labels, respectively. The representation capability or classification accuracy is constrained by the variational lower bound and the tied model parameters across inference procedure. This paper aims to relax these constraints by directly maximizing the end performance criterion and continuously untying the parameters in learning process via deep unfolding inference (DUI). The inference procedure is treated as the layer-wise learning in a deep neural network. The end performance is iteratively improved by using the estimated topic parameters according to the exponentiated updates. Deep learning of topic models is therefore implemented through a back-propagation procedure. Experimental results show the merits of DUI with increasing number of layers compared with variational inference in unsupervised as well as supervised topic models.

Crop response to deep tillage - a meta-analysis

NASA Astrophysics Data System (ADS)

Schneider, Florian; Don, Axel; Hennings, Inga; Schmittmann, Oliver; Seidel, Sabine J.

2017-04-01

Subsoil, i.e. the soil layer below the topsoil, stores tremendous stocks of nutrients and can keep water even under drought conditions. Deep tillage may be a method to enhance the plant-availability of subsoil resources. However, in field trials, deep tillage effects on crop yields were inconsistent. Therefore, we conducted a meta-analysis of crop yield response to subsoiling, deep ploughing and deep mixing of soil profiles. Our search resulted in 1530 yield comparisons following deep and conventional control tillage on 67 experimental cropping sites. The vast majority of the data derived from temperate latitudes, from trials conducted in the USA (679 observations) and Germany (630 observations). On average, crop yield response to deep tillage was slightly positive (6% increase). However, individual deep tillage effects were highly scattered including about 40% yield depressions after deep tillage. Deep tillage on soils with root restrictive layers increased crop yields about 20%, while soils containing >70% silt increased the risk of yield depressions following deep tillage. Generally, deep tillage effects increased with drought intensity indicating deep tillage as climate adaptation measure at certain sites. Our results suggest that deep tillage can facilitate the plant-availability of subsoil nutrients, which increases crop yields if (i) nutrients in the topsoil are growth limiting, and (ii) deep tillage does not come at the cost of impairing topsoil fertility. On sites with root restrictive soil layers, deep tillage can be an effective measure to mitigate drought stress and improve the resilience of crops. However, deep tillage should only be performed on soils with a stable structure, i.e. <70% silt content. We will discuss the contribution of deep tillage options to enhance the sustainability of agricultural production by facilitating the uptake of nutrients and water from the subsoil.

Complete sequences of a novel blaNDM-1-harbouring plasmid from Providencia rettgeri and an FII-type plasmid from Klebsiella pneumoniae identified in Canada.

PubMed

Mataseje, L F; Boyd, D A; Lefebvre, B; Bryce, E; Embree, J; Gravel, D; Katz, K; Kibsey, P; Kuhn, M; Langley, J; Mitchell, R; Roscoe, D; Simor, A; Taylor, G; Thomas, E; Turgeon, N; Mulvey, M R

2014-03-01

Emergence of plasmids harbouring bla(NDM-1) is a major public health concern due to their association with multidrug resistance and their potential mobility. PCR was used to detect bla(NDM-1) from clinical isolates of Providencia rettgeri (PR) and Klebsiella pneumoniae (KP). Antimicrobial susceptibilities were determined using Vitek 2. The complete DNA sequence of two bla(NDM-1) plasmids (pPrY2001 and pKp11-42) was obtained using a 454-Genome Sequencer FLX. Contig assembly and gap closures were confirmed by PCR-based sequencing. Comparative analysis was done using BLASTn and BLASTp algorithms. Both clinical isolates were resistant to all β-lactams, carbapenems, aminoglycosides, ciprofloxacin and trimethoprim/sulfamethoxazole, and susceptible to tigecycline. Plasmid pPrY2001 (113 295 bp) was isolated from PR. It did not show significant homology to any known plasmid backbone and contained a truncated repA and novel repB. Two bla(NDM-1)-harbouring plasmids from Acinetobacter lwoffii (JQ001791 and JQ060896) shared 100% similarity to a 15 kb region that contained bla(NDM-1). pPrY2001 also contained a type II toxin/antitoxin system. pKp11-42 (146 695 bp) was isolated from KP. It contained multiple repA genes. The plasmid backbone had the highest homology to the IncFIIk plasmid type (51% coverage, 100% nucleotide identity). The bla(NDM-1) region was unique in that it was flanked upstream by IS3000 and downstream by a novel transposon designated Tn6229. pKp11-42 also contained a number of mutagenesis and plasmid stability proteins. pPrY2001 differed from all known plasmids due to its novel backbone and repB. pKp11-42 was similar to IncFIIk plasmids and contained a number of genes that aid in plasmid persistence.

Ensuring very shallow-water sediment properties: case study from Capo Granitola harbour, Sicily (Italy)

NASA Astrophysics Data System (ADS)

Punzo, Michele; Cavuoto, Giuseppe; Tarallo, Daniela; Di Fiore, Vincenzo

2017-09-01

We present high-resolution Vp models of the Capo Granitola harbor, Sicily (Italy) obtained by first arrival traveltime tomography. Seismic data were collected along four hydrophone arrays on the sea-bottom and via a Watergun as seismic source, in order to plan dredging operations in the harbor. Using a hydrophone spacing of 2.5 m and shot spacing of 5 m, very high resolution quality data were recorded. Seismic tomography expands existing knowledge of the harbour subsoil with a penetration of about 20 m, illuminating the Lower Pleistocene bedrock (Marsala calcarenites) that corresponds to high-Vp regions (Vp > 4.5 km/s). Low Vp (1.8-4.5 km/s) deposits belonging to terraced calcarenites (Upper Pleistocene in age) are also well imaged; they are about 8 m thick and lie below loose sand deposits (Vp = 1.5 km/s). The substratum has an articulated morphology; Vp images unravel small steps in the basement probably related to structural discontinuities (e.g., faults). Processing data with 3D techniques enables images of the structure and the thickness of the lithotypes to be reconstructed, thus leading to large-scale, realistic estimates of the total quantity of material to be excavated or dredged. Tomographic profiles permit clear discrimination of the soft sediment above the basement and thus allow the determination of the total volume of sediment above the seismic bedrock, estimated at about 265,000 m3.

The Making of Deep Impact

NASA Image and Video Library

2006-10-19

This image shows NASA Deep Impact spacecraft being built at Ball Aerospace & Technologies Corporation, Boulder, Colo. on July 2, 2005. The spacecraft impactor was released from Deep Impact flyby spacecraft.

Summer School in Deep Ecology.

ERIC Educational Resources Information Center

Macmillan, Catherine Hume

1995-01-01

Describes one teacher's experiences at the Institute for Deep Ecology Education (IDEE) Summer School in Applied Deep Ecology. Reviews the program offered and the focus on interactive, experiential activities. (LZ)

Mobile measurements of ship emissions in two harbour areas in Finland

NASA Astrophysics Data System (ADS)

Pirjola, L.; Pajunoja, A.; Walden, J.; Jalkanen, J.-P.; Rönkkö, T.; Kousa, A.; Koskentalo, T.

2014-01-01

Four measurement campaigns were performed in two different environments - inside the harbour areas in the city centre of Helsinki, and along the narrow shipping channel near the city of Turku, Finland - using a mobile laboratory van during winter and summer conditions in 2010-2011. The characteristics of gaseous (CO, CO2, SO2, NO, NO2, NOx) and particulate (number and volume size distributions as well as PM2.5) emissions for 11 ships regularly operating on the Baltic Sea were studied to determine the emission parameters. The highest particle concentrations were 1.5 × 106 and 1.6 × 105 cm-3 in Helsinki and Turku, respectively, and the particle number size distributions had two modes. The dominating mode peaked at 20-30 nm, and the accumulation mode at 80-100 nm. The majority of the particle mass was volatile, since after heating the sample to 265 °C, the particle volume of the studied ship decreased by around 70%. The emission factors for NOx varied in the range of 25-100 g (kg fuel)-1, for SO2 in the range of 2.5-17.0 g (kg fuel)-1, for particle number in the range of (0.32-2.26) × 1016 # (kg fuel)-1, and for PM2.5 between 1.0-4.9 g (kg fuel)-1. The ships equipped with SCR (selective catalytic reduction) had the lowest NOx emissions, whereas the ships with DWI (direct water injection) and HAMs (humid air motors) had the lowest SO2 emissions but the highest particulate emissions. For all ships, the averaged fuel sulphur contents (FSCs) were less than 1% (by mass) but none of them was below 0.1% which will be the new EU directive starting 1 January 2015 in the SOx emission control areas; this indicates that ships operating on the Baltic Sea will face large challenges.

Characterization of trh2 Harbouring Vibrio parahaemolyticus Strains Isolated in Germany

PubMed Central

Bechlars, Silke; Jäckel, Claudia; Diescher, Susanne; Wüstenhagen, Doreen A.; Kubick, Stefan; Dieckmann, Ralf; Strauch, Eckhard

2015-01-01

Background Vibrio parahaemolyticus is a recognized human enteropathogen. Thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) as well as the type III secretion system 2 (T3SS2) are considered as major virulence factors. As tdh positive strains are not detected in coastal waters of Germany, we focused on the characterization of trh positive strains, which were isolated from mussels, seawater and patients in Germany. Results Ten trh harbouring V. parahaemolyticus strains from Germany were compared to twenty-one trh positive strains from other countries. The complete trh sequences revealed clustering into three different types: trh1 and trh2 genes and a pseudogene Ψtrh. All German isolates possessed alleles of the trh2 gene. MLST analysis indicated a close relationship to Norwegian isolates suggesting that these strains belong to the autochthonous microflora of Northern Europe seawaters. Strains carrying the pseudogene Ψtrh were negative for T3SS2β effector vopC. Transcription of trh and vopC genes was analyzed under different growth conditions. Trh2 gene expression was not altered by bile while trh1 genes were inducible. VopC could be induced by urea in trh2 bearing strains. Most trh1 carrying strains were hemolytic against sheep erythrocytes while all trh2 positive strains did not show any hemolytic activity. TRH variants were synthesized in a prokaryotic cell-free system and their hemolytic activity was analyzed. TRH1 was active against sheep erythrocytes while TRH2 variants were not active at all. Conclusion Our study reveals a high diversity among trh positive V. parahaemolyticus strains. The function of TRH2 hemolysins and the role of the pseudogene Ψtrh as pathogenicity factors are questionable. To assess the pathogenic potential of V. parahaemolyticus strains a differentiation of trh variants and the detection of T3SS2β components like vopC would improve the V. parahaemolyticus diagnostics and could lead to a refinement of the risk

Characterization of trh2 harbouring Vibrio parahaemolyticus strains isolated in Germany.

PubMed

Bechlars, Silke; Jäckel, Claudia; Diescher, Susanne; Wüstenhagen, Doreen A; Kubick, Stefan; Dieckmann, Ralf; Strauch, Eckhard

2015-01-01

Vibrio parahaemolyticus is a recognized human enteropathogen. Thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) as well as the type III secretion system 2 (T3SS2) are considered as major virulence factors. As tdh positive strains are not detected in coastal waters of Germany, we focused on the characterization of trh positive strains, which were isolated from mussels, seawater and patients in Germany. Ten trh harbouring V. parahaemolyticus strains from Germany were compared to twenty-one trh positive strains from other countries. The complete trh sequences revealed clustering into three different types: trh1 and trh2 genes and a pseudogene Ψtrh. All German isolates possessed alleles of the trh2 gene. MLST analysis indicated a close relationship to Norwegian isolates suggesting that these strains belong to the autochthonous microflora of Northern Europe seawaters. Strains carrying the pseudogene Ψtrh were negative for T3SS2β effector vopC. Transcription of trh and vopC genes was analyzed under different growth conditions. Trh2 gene expression was not altered by bile while trh1 genes were inducible. VopC could be induced by urea in trh2 bearing strains. Most trh1 carrying strains were hemolytic against sheep erythrocytes while all trh2 positive strains did not show any hemolytic activity. TRH variants were synthesized in a prokaryotic cell-free system and their hemolytic activity was analyzed. TRH1 was active against sheep erythrocytes while TRH2 variants were not active at all. Our study reveals a high diversity among trh positive V. parahaemolyticus strains. The function of TRH2 hemolysins and the role of the pseudogene Ψtrh as pathogenicity factors are questionable. To assess the pathogenic potential of V. parahaemolyticus strains a differentiation of trh variants and the detection of T3SS2β components like vopC would improve the V. parahaemolyticus diagnostics and could lead to a refinement of the risk assessment in food analyses and

Wolves Recolonizing Islands: Genetic Consequences and Implications for Conservation and Management.

PubMed

Plumer, Liivi; Keis, Marju; Remm, Jaanus; Hindrikson, Maris; Jõgisalu, Inga; Männil, Peep; Kübarsepp, Marko; Saarma, Urmas

2016-01-01

After a long and deliberate persecution, the grey wolf (Canis lupus) is slowly recolonizing its former areas in Europe, and the genetic consequences of this process are of particular interest. Wolves, though present in mainland Estonia for a long time, have only recently started to recolonize the country's two largest islands, Saaremaa and Hiiumaa. The main objective of this study was to analyse wolf population structure and processes in Estonia, with particular attention to the recolonization of islands. Fifteen microsatellite loci were genotyped for 185 individuals across Estonia. As a methodological novelty, all putative wolf-dog hybrids were identified and removed (n = 17) from the dataset beforehand to avoid interference of dog alleles in wolf population analysis. After the preliminary filtering, our final dataset comprised of 168 "pure" wolves. We recommend using hybrid-removal step as a standard precautionary procedure not only for wolf population studies, but also for other taxa prone to hybridization. STRUCTURE indicated four genetic groups in Estonia. Spatially explicit DResD analysis identified two areas, one of them on Saaremaa island and the other in southwestern Estonia, where neighbouring individuals were genetically more similar than expected from an isolation-by-distance null model. Three blending areas and two contrasting transition zones were identified in central Estonia, where the sampled individuals exhibited strong local differentiation over relatively short distance. Wolves on the largest Estonian islands are part of human-wildlife conflict due to livestock depredation. Negative public attitude, especially on Saaremaa where sheep herding is widespread, poses a significant threat for island wolves. To maintain the long-term viability of the wolf population on Estonian islands, not only wolf hunting quota should be targeted with extreme care, but effective measures should be applied to avoid inbreeding and minimize conflicts with local

Wolves Recolonizing Islands: Genetic Consequences and Implications for Conservation and Management

PubMed Central

Remm, Jaanus; Hindrikson, Maris; Jõgisalu, Inga; Männil, Peep; Kübarsepp, Marko; Saarma, Urmas

2016-01-01

After a long and deliberate persecution, the grey wolf (Canis lupus) is slowly recolonizing its former areas in Europe, and the genetic consequences of this process are of particular interest. Wolves, though present in mainland Estonia for a long time, have only recently started to recolonize the country’s two largest islands, Saaremaa and Hiiumaa. The main objective of this study was to analyse wolf population structure and processes in Estonia, with particular attention to the recolonization of islands. Fifteen microsatellite loci were genotyped for 185 individuals across Estonia. As a methodological novelty, all putative wolf-dog hybrids were identified and removed (n = 17) from the dataset beforehand to avoid interference of dog alleles in wolf population analysis. After the preliminary filtering, our final dataset comprised of 168 “pure” wolves. We recommend using hybrid-removal step as a standard precautionary procedure not only for wolf population studies, but also for other taxa prone to hybridization. STRUCTURE indicated four genetic groups in Estonia. Spatially explicit DResD analysis identified two areas, one of them on Saaremaa island and the other in southwestern Estonia, where neighbouring individuals were genetically more similar than expected from an isolation-by-distance null model. Three blending areas and two contrasting transition zones were identified in central Estonia, where the sampled individuals exhibited strong local differentiation over relatively short distance. Wolves on the largest Estonian islands are part of human-wildlife conflict due to livestock depredation. Negative public attitude, especially on Saaremaa where sheep herding is widespread, poses a significant threat for island wolves. To maintain the long-term viability of the wolf population on Estonian islands, not only wolf hunting quota should be targeted with extreme care, but effective measures should be applied to avoid inbreeding and minimize conflicts with local

Deep RNNs for video denoising

NASA Astrophysics Data System (ADS)

Chen, Xinyuan; Song, Li; Yang, Xiaokang

2016-09-01

Video denoising can be described as the problem of mapping from a specific length of noisy frames to clean one. We propose a deep architecture based on Recurrent Neural Network (RNN) for video denoising. The model learns a patch-based end-to-end mapping between the clean and noisy video sequences. It takes the corrupted video sequences as the input and outputs the clean one. Our deep network, which we refer to as deep Recurrent Neural Networks (deep RNNs or DRNNs), stacks RNN layers where each layer receives the hidden state of the previous layer as input. Experiment shows (i) the recurrent architecture through temporal domain extracts motion information and does favor to video denoising, and (ii) deep architecture have large enough capacity for expressing mapping relation between corrupted videos as input and clean videos as output, furthermore, (iii) the model has generality to learned different mappings from videos corrupted by different types of noise (e.g., Poisson-Gaussian noise). By training on large video databases, we are able to compete with some existing video denoising methods.

Deep Water Cooling | Climate Neutral Research Campuses | NREL

Science.gov Websites

the Cornell website. Additional examples of research campus geothermal cooling projects include Deep Water Cooling Deep Water Cooling Research campuses that are located near a deep lake or deep plan for your research campus. Considerations Sample Project Related Links Deep water cooling involves

Parasites in harbour seals ( Phoca vitulina) from the German Wadden Sea between two Phocine Distemper Virus epidemics

NASA Astrophysics Data System (ADS)

Lehnert, K.; Raga, J. A.; Siebert, U.

2007-12-01

Parasites were collected from 107 harbour seals ( Phoca vitulina) found on the coasts of Schleswig-Holstein, Germany, between 1997 and 2000. The prevalence of the parasites and their associated pathology were investigated. Eight species of parasites, primarily nematodes, were identified from the examined organs: two anisakid nematodes ( Pseudoterranova decipiens (sensu lato) , Contracaecum osculatum (sensu lato)) from the stomach, Otostrongylus circumlitus (Crenosomatidae) and Parafilaroides gymnurus (Filaroididae) from the respiratory tract, one filarioid nematode ( Acanthocheilonema spirocauda) from the heart, two acanthocephalans, Corynosoma strumosum and C. semerme (Polymorphidae), from the intestine and an ectoparasite, Echinophthirius horridus (Anoplura, Insecta). Lungworm infection was the most prominent parasitological finding and secondary bacterial bronchopneumonia the most pathogenic lesion correlated with the parasites. Heavy nematode burdens in the respiratory tract were highly age-related and more frequent in young seals. A positive correlation was observed between high levels of pulmonary infection and severity of bronchopneumonia. The prevalence of lungworms in this study was higher than in seals that died during the 1988/1989 Phocine Distemper Virus epidemic, and the prevalence of acanthocephalans and heartworms had decreased compared to findings from the first die-off.

How Stressful Is "Deep Bubbling"?

PubMed

Tyrmi, Jaana; Laukkanen, Anne-Maria

2017-03-01

Water resistance therapy by phonating through a tube into the water is used to treat dysphonia. Deep submersion (≥10 cm in water, "deep bubbling") is used for hypofunctional voice disorders. Using it with caution is recommended to avoid vocal overloading. This experimental study aimed to investigate how strenuous "deep bubbling" is. Fourteen subjects, half of them with voice training, repeated the syllable [pa:] in comfortable speaking pitch and loudness, loudly, and in strained voice. Thereafter, they phonated a vowel-like sound both in comfortable loudness and loudly into a glass resonance tube immersed 10 cm into the water. Oral pressure, contact quotient (CQ, calculated from electroglottographic signal), and sound pressure level were studied. The peak oral pressure P(oral) during [p] and shuttering of the outer end of the tube was measured to estimate the subglottic pressure P(sub) and the mean P(oral) during vowel portions to enable calculation of transglottic pressure P(trans). Sensations during phonation were reported with an open-ended interview. P(sub) and P(oral) were higher in "deep bubbling" and P(trans) lower than in loud syllable phonation, but the CQ did not differ significantly. Similar results were obtained for the comparison between loud "deep bubbling" and strained phonation, although P(sub) did not differ significantly. Most of the subjects reported "deep bubbling" to be stressful only for respiratory and lip muscles. No big differences were found between trained and untrained subjects. The CQ values suggest that "deep bubbling" may increase vocal fold loading. Further studies should address impact stress during water resistance exercises. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Simulator Studies of the Deep Stall

NASA Technical Reports Server (NTRS)

White, Maurice D.; Cooper, George E.

1965-01-01

Simulator studies of the deep-stall problem encountered with modern airplanes are discussed. The results indicate that the basic deep-stall tendencies produced by aerodynamic characteristics are augmented by operational considerations. Because of control difficulties to be anticipated in the deep stall, it is desirable that adequate safeguards be provided against inadvertent penetrations.

HPLC pigment analysis of marine phytoplankton during a red tide occurrence in Tolo Harbour, Hong Kong.

PubMed

Wong, C Kwan; Wong, C Kim

2003-09-01

A red tide was detected in the inner parts of Tolo Harbour, Hong Kong, in November 2000. Water samples were collected from a fixed station at the centre of the red tide patch for microscopic analysis of phytoplankton community composition and high performance liquid chromatography (HPLC) analysis of phytoplankton pigments. At the peak of the red tide on 24 November 2000, phytoplankton was dominated by the dinoflagellate Scrippsiella trochoidea. The red tide began to decline at the end of November and, by 1 December 2000, the phytoplankton was dominated by diatoms. Chlorophylls and carotenoids in water samples were analysed using HPLC pigment separation technique. Dinoflagellates were indicated by the signature pigment peridinin. Significant correlation (r=0.999) was found between the peridinin concentration and dinoflagellate density. A decrease in peridinin and an increase in fucoxanthin, a major carotenoid in diatoms, marked the shift in phytoplankton composition at the end of the red tide. HPLC analysis also revealed the occurrence of minor phytoplankton groups that are difficult to identify by light microscopy. Red tide monitoring and study of red tide dynamics in Hong Kong have been based on cell counting and spectrophotometric or fluorometric measurement of chlorophyll a. HPLC pigment analysis provides an effective alternative for investigating phytoplankton dynamics during red tide and other algal blooms.

Deep Extragalactic X-Ray Surveys

NASA Astrophysics Data System (ADS)

Brandt, W. N.; Hasinger, G.

2005-09-01

Deep surveys of the cosmic X-ray background are reviewed in the context of observational progress enabled by the Chandra X-Ray Observatory and the X-Ray Multi-Mirror Mission-Newton. The sources found by deep surveys are described along with their redshift and luminosity distributions, and the effectiveness of such surveys at selecting active galactic nuclei (AGN) is assessed. Some key results from deep surveys are highlighted, including (a) measurements of AGN evolution and the growth of supermassive black holes, (b) constraints on the demography and physics of high-redshift AGN, (c) the X-ray AGN content of infrared and submillimeter galaxies, and (d) X-ray emission from distant starburst and normal galaxies. We also describe some outstanding problems and future prospects for deep extragalactic X-ray surveys.

MR Anatomy of Deep Brain Nuclei with Special Reference to Specific Diseases and Deep Brain Stimulation Localization

PubMed Central

Telford, Ryan; Vattoth, Surjith

2014-01-01

Summary Diseases affecting the basal ganglia and deep brain structures vary widely in etiology and include metabolic, infectious, ischemic, and neurodegenerative conditions. Some neurologic diseases, such as Wernicke encephalopathy or pseudohypoparathyroidism, require specific treatments, which if unrecognized could lead to further complications. Other pathologies, such as hypertrophic olivary degeneration, if not properly diagnosed may be mistaken for a primary medullary neoplasm and create unnecessary concern. The deep brain structures are complex and can be difficult to distinguish on routine imaging. It is imperative that radiologists first understand the intrinsic anatomic relationships between the different basal ganglia nuclei and deep brain structures with magnetic resonance (MR) imaging. It is important to understand the "normal" MR signal characteristics, locations, and appearances of these structures. This is essential to recognizing diseases affecting the basal ganglia and deep brain structures, especially since most of these diseases result in symmetrical, and therefore less noticeable, abnormalities. It is also crucial that neurosurgeons correctly identify the deep brain nuclei presurgically for positioning deep brain stimulator leads, the most important being the subthalamic nucleus for Parkinson syndromes and the thalamic ventral intermediate nucleus for essential tremor. Radiologists will be able to better assist clinicians in diagnosis and treatment once they are able to accurately localize specific deep brain structures. PMID:24571832

DeepNAT: Deep convolutional neural network for segmenting neuroanatomy.

PubMed

Wachinger, Christian; Reuter, Martin; Klein, Tassilo

2018-04-15

We introduce DeepNAT, a 3D Deep convolutional neural network for the automatic segmentation of NeuroAnaTomy in T1-weighted magnetic resonance images. DeepNAT is an end-to-end learning-based approach to brain segmentation that jointly learns an abstract feature representation and a multi-class classification. We propose a 3D patch-based approach, where we do not only predict the center voxel of the patch but also neighbors, which is formulated as multi-task learning. To address a class imbalance problem, we arrange two networks hierarchically, where the first one separates foreground from background, and the second one identifies 25 brain structures on the foreground. Since patches lack spatial context, we augment them with coordinates. To this end, we introduce a novel intrinsic parameterization of the brain volume, formed by eigenfunctions of the Laplace-Beltrami operator. As network architecture, we use three convolutional layers with pooling, batch normalization, and non-linearities, followed by fully connected layers with dropout. The final segmentation is inferred from the probabilistic output of the network with a 3D fully connected conditional random field, which ensures label agreement between close voxels. The roughly 2.7million parameters in the network are learned with stochastic gradient descent. Our results show that DeepNAT compares favorably to state-of-the-art methods. Finally, the purely learning-based method may have a high potential for the adaptation to young, old, or diseased brains by fine-tuning the pre-trained network with a small training sample on the target application, where the availability of larger datasets with manual annotations may boost the overall segmentation accuracy in the future. Copyright © 2017 Elsevier Inc. All rights reserved.

Deep Learning and Its Applications in Biomedicine.

PubMed

Cao, Chensi; Liu, Feng; Tan, Hai; Song, Deshou; Shu, Wenjie; Li, Weizhong; Zhou, Yiming; Bo, Xiaochen; Xie, Zhi

2018-02-01

Advances in biological and medical technologies have been providing us explosive volumes of biological and physiological data, such as medical images, electroencephalography, genomic and protein sequences. Learning from these data facilitates the understanding of human health and disease. Developed from artificial neural networks, deep learning-based algorithms show great promise in extracting features and learning patterns from complex data. The aim of this paper is to provide an overview of deep learning techniques and some of the state-of-the-art applications in the biomedical field. We first introduce the development of artificial neural network and deep learning. We then describe two main components of deep learning, i.e., deep learning architectures and model optimization. Subsequently, some examples are demonstrated for deep learning applications, including medical image classification, genomic sequence analysis, as well as protein structure classification and prediction. Finally, we offer our perspectives for the future directions in the field of deep learning. Copyright © 2018. Production and hosting by Elsevier B.V.

Deep learning applications in ophthalmology.

PubMed

Rahimy, Ehsan

2018-05-01

To describe the emerging applications of deep learning in ophthalmology. Recent studies have shown that various deep learning models are capable of detecting and diagnosing various diseases afflicting the posterior segment of the eye with high accuracy. Most of the initial studies have centered around detection of referable diabetic retinopathy, age-related macular degeneration, and glaucoma. Deep learning has shown promising results in automated image analysis of fundus photographs and optical coherence tomography images. Additional testing and research is required to clinically validate this technology.

Overview of North Ecliptic Pole Deep Multi-Wavelength Survey Nep-Deep

NASA Astrophysics Data System (ADS)

Matsuhara, H.; Wada, T.; Oi, N.; Takagi, T.; Nakagawa, T.; Murata, K.; Goto, T.; Oyabu, S.; Takeuchi, T. T.; Malek, K.; Solarz, A.; Ohyama, Y.; Miyaji, T.; Krumpe, M.; Lee, H. M.; Im, M.; Serjeant, S.; Pearson, C. P.; White, G. J.; Malkan, M. A.; Hanami, H.; Ishigaki, T.; Burgarella, D.; Buat, V.; Pollo, A.

2017-03-01

The recent updates of the North Ecliptic Pole deep (0.5~deg$^2$, NEP-Deep) multi-wavelength survey covering from X-ray to radio-wave is presented. The NEP-Deep provides us with several thousands of 15~$\\mu$m or 18~$\\mu$m selected sample of galaxies, which is the largest sample ever made at this wavelengths. A continuous filter coverage in the mid-infrared wavelength (7, 9, 11, 15, 18, and 24~$\\mu$m) is unique and vital to diagnose the contributions from starbursts and AGNs in the galaxies out to $z$=2.The new goal of the project is to resolve the nature of the cosmic star formation history at the violent epoch (e.g. $z$=1--2), and to find a clue to understand its decline from $z$=1 to present universe by utilizing the unique power of the multi-wavelength survey. The progress in this context is briefly mentioned.

Overview of deep learning in medical imaging.

PubMed

Suzuki, Kenji

2017-09-01

The use of machine learning (ML) has been increasing rapidly in the medical imaging field, including computer-aided diagnosis (CAD), radiomics, and medical image analysis. Recently, an ML area called deep learning emerged in the computer vision field and became very popular in many fields. It started from an event in late 2012, when a deep-learning approach based on a convolutional neural network (CNN) won an overwhelming victory in the best-known worldwide computer vision competition, ImageNet Classification. Since then, researchers in virtually all fields, including medical imaging, have started actively participating in the explosively growing field of deep learning. In this paper, the area of deep learning in medical imaging is overviewed, including (1) what was changed in machine learning before and after the introduction of deep learning, (2) what is the source of the power of deep learning, (3) two major deep-learning models: a massive-training artificial neural network (MTANN) and a convolutional neural network (CNN), (4) similarities and differences between the two models, and (5) their applications to medical imaging. This review shows that ML with feature input (or feature-based ML) was dominant before the introduction of deep learning, and that the major and essential difference between ML before and after deep learning is the learning of image data directly without object segmentation or feature extraction; thus, it is the source of the power of deep learning, although the depth of the model is an important attribute. The class of ML with image input (or image-based ML) including deep learning has a long history, but recently gained popularity due to the use of the new terminology, deep learning. There are two major models in this class of ML in medical imaging, MTANN and CNN, which have similarities as well as several differences. In our experience, MTANNs were substantially more efficient in their development, had a higher performance, and required a

Making sense of deep sequencing

PubMed Central

Goldman, D.; Domschke, K.

2016-01-01

This review, the first of an occasional series, tries to make sense of the concepts and uses of deep sequencing of polynucleic acids (DNA and RNA). Deep sequencing, synonymous with next-generation sequencing, high-throughput sequencing and massively parallel sequencing, includes whole genome sequencing but is more often and diversely applied to specific parts of the genome captured in different ways, for example the highly expressed portion of the genome known as the exome and portions of the genome that are epigenetically marked either by DNA methylation, the binding of proteins including histones, or that are in different configurations and thus more or less accessible to enzymes that cleave DNA. Deep sequencing of RNA (RNASeq) reverse-transcribed to complementary DNA is invaluable for measuring RNA expression and detecting changes in RNA structure. Important concepts in deep sequencing include the length and depth of sequence reads, mapping and assembly of reads, sequencing error, haplotypes, and the propensity of deep sequencing, as with other types of ‘big data’, to generate large numbers of errors, requiring monitoring for methodologic biases and strategies for replication and validation. Deep sequencing yields a unique genetic fingerprint that can be used to identify a person, and a trove of predictors of genetic medical diseases. Deep sequencing to identify epigenetic events including changes in DNA methylation and RNA expression can reveal the history and impact of environmental exposures. Because of the power of sequencing to identify and deliver biomedically significant information about a person and their blood relatives, it creates ethical dilemmas and practical challenges in research and clinical care, for example the decision and procedures to report incidental findings that will increasingly and frequently be discovered. PMID:24925306

Identification of Deep Earthquakes

DTIC Science & Technology

2010-09-01

discriminants that will reliably separate small, crustal earthquakes (magnitudes less than about 4 and depths less than about 40 to 50 km) from small...characteristics on discrimination plots designed to separate nuclear explosions from crustal earthquakes. Thus, reliably flagging these small, deep events is...Further, reliably identifying subcrustal earthquakes will allow us to eliminate deep events (previously misidentified as crustal earthquakes) from

Deep Impact Spots Quarry

NASA Technical Reports Server (NTRS)

2005-01-01

Sixty-nine days before it gets up-close-and-personal with a comet, NASA's Deep Impact spacecraft successfully photographed its quarry, comet Tempel 1, at a distance of 39.7 million miles. The image, taken on April 25, 2005, is the first of many comet portraits Deep Impact will take leading up to its historic comet encounter on July 4.

WFIRST: Science from Deep Field Surveys

NASA Astrophysics Data System (ADS)

Koekemoer, Anton M.; Foley, Ryan; WFIRST Deep Field Working Group

2018-06-01

WFIRST will enable deep field imaging across much larger areas than those previously obtained with Hubble, opening up completely new areas of parameter space for extragalactic deep fields including cosmology, supernova and galaxy evolution science. The instantaneous field of view of the Wide Field Instrument (WFI) is about 0.3 square degrees, which would for example yield an Ultra Deep Field (UDF) reaching similar depths at visible and near-infrared wavelengths to that obtained with Hubble, over an area about 100-200 times larger, for a comparable investment in time. Moreover, wider fields on scales of 10-20 square degrees could achieve depths comparable to large HST surveys at medium depths such as GOODS and CANDELS, and would enable multi-epoch supernova science that could be matched in area to LSST Deep Drilling fields or other large survey areas. Such fields may benefit from being placed on locations in the sky that have ancillary multi-band imaging or spectroscopy from other facilities, from the ground or in space. The WFIRST Deep Fields Working Group has been examining the science considerations for various types of deep fields that may be obtained with WFIRST, and present here a summary of the various properties of different locations in the sky that may be considered for future deep fields with WFIRST.

WFIRST: Science from Deep Field Surveys

NASA Astrophysics Data System (ADS)

Koekemoer, Anton; Foley, Ryan; WFIRST Deep Field Working Group

2018-01-01

WFIRST will enable deep field imaging across much larger areas than those previously obtained with Hubble, opening up completely new areas of parameter space for extragalactic deep fields including cosmology, supernova and galaxy evolution science. The instantaneous field of view of the Wide Field Instrument (WFI) is about 0.3 square degrees, which would for example yield an Ultra Deep Field (UDF) reaching similar depths at visible and near-infrared wavelengths to that obtained with Hubble, over an area about 100-200 times larger, for a comparable investment in time. Moreover, wider fields on scales of 10-20 square degrees could achieve depths comparable to large HST surveys at medium depths such as GOODS and CANDELS, and would enable multi-epoch supernova science that could be matched in area to LSST Deep Drilling fields or other large survey areas. Such fields may benefit from being placed on locations in the sky that have ancillary multi-band imaging or spectroscopy from other facilities, from the ground or in space. The WFIRST Deep Fields Working Group has been examining the science considerations for various types of deep fields that may be obtained with WFIRST, and present here a summary of the various properties of different locations in the sky that may be considered for future deep fields with WFIRST.

Deep dysgraphia in Turkish.

PubMed

Raman, Ilhan; Weekes, Brendan Stuart

2005-01-01

Deep dysgraphic patients make semantic errors when writing to dictation and they cannot write nonwords. Extant reports of deep dysgraphia come from languages with relatively opaque orthographies. Turkish is a transparent orthography because the bidirectional mappings between phonology and orthography are completely predictable. We report BRB, a biscriptal Turkish-English speaker who has acquired dysgraphia characterised by semantic errors as well as effects of grammatical class and imageability on writing in Turkish. Nonword spelling is abolished. A similar pattern of errors is observed in English. BRB is the first report of acquired dysgraphia in a truly transparent writing system. We argue that deep dysgraphia results from damage to the mappings that are common to both languages between word meanings and orthographic representations.

Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS.

PubMed

Sabirova, Julia S; Xavier, Basil Britto; Coppens, Jasmine; Zarkotou, Olympia; Lammens, Christine; Janssens, Lore; Burggrave, Ronald; Wagner, Trevor; Goossens, Herman; Malhotra-Kumar, Surbhi

2016-06-01

We utilized whole-genome mapping (WGM) and WGS to characterize 12 clinical carbapenem-resistant Klebsiella pneumoniae strains (TGH1-TGH12). All strains were screened for carbapenemase genes by PCR, and typed by MLST, PFGE (XbaI) and WGM (AflII) (OpGen, USA). WGS (Illumina) was performed on TGH8 and TGH10. Reads were de novo assembled and annotated [SPAdes, Rapid Annotation Subsystem Technology (RAST)]. Contigs were aligned directly, and after in silico AflII restriction, with corresponding WGMs (MapSolver, OpGen; BioNumerics, Applied Maths). All 12 strains were ST383. Of the 12 strains, 11 were carbapenem resistant, 7 harboured blaKPC-2 and 11 harboured blaVIM-19. Varying the parameters for assigning WGM clusters showed that these were comparable to STs and to the eight PFGE types or subtypes (difference of three or more bands). A 95% similarity coefficient assigned all 12 WGMs to a single cluster, whereas a 99% similarity coefficient (or ≥10 unmatched-fragment difference) assigned the 12 WGMs to eight (sub)clusters. Based on a difference of three or more bands between PFGE profiles, the Simpson's diversity indices (SDIs) of WGM (0.94, Jackknife pseudo-values CI: 0.883-0.996) and PFGE (0.93, Jackknife pseudo-values CI: 0.828-1.000) were similar (P = 0.649). However, the discriminatory power of WGM was significantly higher (SDI: 0.94, Jackknife pseudo-values CI: 0.883-0.996) than that of PFGE profiles typed on a difference of seven or more bands (SDI: 0.53, Jackknife pseudo-values CI: 0.212-0.849) (P = 0.007). This study demonstrates the application of WGM to understanding the epidemiology of hospital-associated K. pneumoniae. Utilizing a combination of WGM and WGS, we also present here the first longitudinal genomic characterization of the highly dynamic carbapenem-resistant ST383 K. pneumoniae clone that is rapidly gaining importance in Europe. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial

Eco-Philosophy and Deep Ecology.

ERIC Educational Resources Information Center

Skolimowski, Henryk

1988-01-01

Criticizes the Deep Ecology Movement as a new ecological world view. Discusses the limits of this philosophy including its views of destiny, evolution and cosmology. Concludes that although its intentions are admirable, Deep Ecology leaves too much unanswered. (CW)

[Deep vein thrombosis prophylaxis.

PubMed

Sandoval-Chagoya, Gloria Alejandra; Laniado-Laborín, Rafael

2013-01-01

Background: despite the proven effectiveness of preventive therapy for deep vein thrombosis, a significant proportion of patients at risk for thromboembolism do not receive prophylaxis during hospitalization. Our objective was to determine the adherence to thrombosis prophylaxis guidelines in a general hospital as a quality control strategy. Methods: a random audit of clinical charts was conducted at the Tijuana General Hospital, Baja California, Mexico, to determine the degree of adherence to deep vein thrombosis prophylaxis guidelines. The instrument used was the Caprini's checklist for thrombosis risk assessment in adult patients. Results: the sample included 300 patient charts; 182 (60.7 %) were surgical patients and 118 were medical patients. Forty six patients (15.3 %) received deep vein thrombosis pharmacologic prophylaxis; 27.1 % of medical patients received deep vein thrombosis prophylaxis versus 8.3 % of surgical patients (p < 0.0001). Conclusions: our results show that adherence to DVT prophylaxis at our hospital is extremely low. Only 15.3 % of our patients at risk received treatment, and even patients with very high risk received treatment in less than 25 % of the cases. We have implemented strategies to increase compliance with clinical guidelines.

Deep-Sea Coral Image Catalog: Northeast Pacific

NASA Astrophysics Data System (ADS)

Freed, J. C.

2016-02-01

In recent years, deep-sea exploration in the Northeast Pacific ocean has been on the rise using submersibles and remotely operated vehicles (ROVs), acquiring a plethora of underwater videos and photographs. Analysis of deep-sea fauna revealed by this research has been hampered by the lack of catalogs or guides that allow identification of species in the field. Deep-sea corals are of particular conservation concern, but currently, there are few catalogs which describe and provide detailed information on deep-sea corals from the Northeast Pacific and those that exist are focused on small, specific areas. This project, in collaboration with NOAA's Deep-Sea Coral Ecology Laboratory at the Center for Coastal Environmental Health and Biomolecular Research (CCEHBR) and the Southwest Fisheries Science Center (SWFSC), developed pages for a deep-sea coral identification guide that provides photos and information on the visual identification, distributions, and habitats of species found in the Northeast Pacific. Using online databases, photo galleries, and literature, this catalog has been developed to be a living document open to future additions. This project produced 12 entries for the catalog on a variety of different deep-sea corals. The catalog is intended to be used during underwater surveys in the Northeast Pacific, but will also assist in identification of deep-sea coral by-catch by fishing vessels, and for general educational use. These uses will advance NOAA's ability to identify and protect sensitive deep-sea habitats that act as biological hotspots. The catalog is intended to be further developed into an online resource with greater interactive features with links to other resources and featured on NOAA's Deep-Sea Coral Data Portal.

The Deep Space Network. An instrument for radio navigation of deep space probes

NASA Technical Reports Server (NTRS)

Renzetti, N. A.; Jordan, J. F.; Berman, A. L.; Wackley, J. A.; Yunck, T. P.

1982-01-01

The Deep Space Network (DSN) network configurations used to generate the navigation observables and the basic process of deep space spacecraft navigation, from data generation through flight path determination and correction are described. Special emphasis is placed on the DSN Systems which generate the navigation data: the DSN Tracking and VLBI Systems. In addition, auxiliary navigational support functions are described.

Towards deep learning with segregated dendrites.

PubMed

Guerguiev, Jordan; Lillicrap, Timothy P; Richards, Blake A

2017-12-05

Deep learning has led to significant advances in artificial intelligence, in part, by adopting strategies motivated by neurophysiology. However, it is unclear whether deep learning could occur in the real brain. Here, we show that a deep learning algorithm that utilizes multi-compartment neurons might help us to understand how the neocortex optimizes cost functions. Like neocortical pyramidal neurons, neurons in our model receive sensory information and higher-order feedback in electrotonically segregated compartments. Thanks to this segregation, neurons in different layers of the network can coordinate synaptic weight updates. As a result, the network learns to categorize images better than a single layer network. Furthermore, we show that our algorithm takes advantage of multilayer architectures to identify useful higher-order representations-the hallmark of deep learning. This work demonstrates that deep learning can be achieved using segregated dendritic compartments, which may help to explain the morphology of neocortical pyramidal neurons.

Deep space communication - A one billion mile noisy channel

NASA Technical Reports Server (NTRS)

Smith, J. G.

1982-01-01

Deep space exploration is concerned with the study of natural phenomena in the solar system with the aid of measurements made at spacecraft on deep space missions. Deep space communication refers to communication between earth and spacecraft in deep space. The Deep Space Network is an earth-based facility employed for deep space communication. It includes a network of large tracking antennas located at various positions around the earth. The goals and achievements of deep space exploration over the past 20 years are discussed along with the broad functional requirements of deep space missions. Attention is given to the differences in space loss between communication satellites and deep space vehicles, effects of the long round-trip light time on spacecraft autonomy, requirements for the use of massive nuclear power plants on spacecraft at large distances from the sun, and the kinds of scientific return provided by a deep space mission. Problems concerning a deep space link of one billion miles are also explored.

The deep ocean under climate change

NASA Astrophysics Data System (ADS)

Levin, Lisa A.; Le Bris, Nadine

2015-11-01

The deep ocean absorbs vast amounts of heat and carbon dioxide, providing a critical buffer to climate change but exposing vulnerable ecosystems to combined stresses of warming, ocean acidification, deoxygenation, and altered food inputs. Resulting changes may threaten biodiversity and compromise key ocean services that maintain a healthy planet and human livelihoods. There exist large gaps in understanding of the physical and ecological feedbacks that will occur. Explicit recognition of deep-ocean climate mitigation and inclusion in adaptation planning by the United Nations Framework Convention on Climate Change (UNFCCC) could help to expand deep-ocean research and observation and to protect the integrity and functions of deep-ocean ecosystems.

Deep smarts.

PubMed

Leonard, Dorothy; Swap, Walter

2004-09-01

When a person sizes up a complex situation and rapidly comes to a decision that proves to be not just good but brilliant, you think, "That was smart." After you watch him do this a few times, you realize you're in the presence of something special. It's not raw brainpower, though that helps. It's not emotional intelligence, either, though that, too, is often involved. It's deep smarts. Deep smarts are not philosophical--they're not"wisdom" in that sense, but they're as close to wisdom as business gets. You see them in the manager who understands when and how to move into a new international market, in the executive who knows just what kind of talk to give when her organization is in crisis, in the technician who can track a product failure back to an interaction between independently produced elements. These are people whose knowledge would be hard to purchase on the open market. Their insight is based on know-how more than on know-what; it comprises a system view as well as expertise in individual areas. Because deep smarts are experienced based and often context specific, they can't be produced overnight or readily imported into an organization. It takes years for an individual to develop them--and no time at all for an organization to lose them when a valued veteran walks out the door. They can be taught, however, with the right techniques. Drawing on their forthcoming book Deep Smarts, Dorothy Leonard and Walter Swap say the best way to transfer such expertise to novices--and, on a larger scale, to make individual knowledge institutional--isn't through PowerPoint slides, a Web site of best practices, online training, project reports, or lectures. Rather, the sage needs to teach the neophyte individually how to draw wisdom from experience. Companies have to be willing to dedicate time and effort to such extensive training, but the investment more than pays for itself.

Deep Learning and Developmental Learning: Emergence of Fine-to-Coarse Conceptual Categories at Layers of Deep Belief Network.

PubMed

Sadeghi, Zahra

2016-09-01

In this paper, I investigate conceptual categories derived from developmental processing in a deep neural network. The similarity matrices of deep representation at each layer of neural network are computed and compared with their raw representation. While the clusters generated by raw representation stand at the basic level of abstraction, conceptual categories obtained from deep representation shows a bottom-up transition procedure. Results demonstrate a developmental course of learning from specific to general level of abstraction through learned layers of representations in a deep belief network. © The Author(s) 2016.

Towards deep learning with segregated dendrites

PubMed Central

Guerguiev, Jordan; Lillicrap, Timothy P

2017-01-01

Deep learning has led to significant advances in artificial intelligence, in part, by adopting strategies motivated by neurophysiology. However, it is unclear whether deep learning could occur in the real brain. Here, we show that a deep learning algorithm that utilizes multi-compartment neurons might help us to understand how the neocortex optimizes cost functions. Like neocortical pyramidal neurons, neurons in our model receive sensory information and higher-order feedback in electrotonically segregated compartments. Thanks to this segregation, neurons in different layers of the network can coordinate synaptic weight updates. As a result, the network learns to categorize images better than a single layer network. Furthermore, we show that our algorithm takes advantage of multilayer architectures to identify useful higher-order representations—the hallmark of deep learning. This work demonstrates that deep learning can be achieved using segregated dendritic compartments, which may help to explain the morphology of neocortical pyramidal neurons. PMID:29205151

Microplastic pollution in deep-sea sediments.

PubMed

Van Cauwenberghe, Lisbeth; Vanreusel, Ann; Mees, Jan; Janssen, Colin R

2013-11-01

Microplastics are small plastic particles (<1 mm) originating from the degradation of larger plastic debris. These microplastics have been accumulating in the marine environment for decades and have been detected throughout the water column and in sublittoral and beach sediments worldwide. However, up to now, it has never been established whether microplastic presence in sediments is limited to accumulation hot spots such as the continental shelf, or whether they are also present in deep-sea sediments. Here we show, for the first time ever, that microplastics have indeed reached the most remote of marine environments: the deep sea. We found plastic particles sized in the micrometre range in deep-sea sediments collected at four locations representing different deep-sea habitats ranging in depth from 1100 to 5000 m. Our results demonstrate that microplastic pollution has spread throughout the world's seas and oceans, into the remote and largely unknown deep sea. Copyright © 2013. Published by Elsevier Ltd.

The deep space network, volume 13

NASA Technical Reports Server (NTRS)

1973-01-01

The objectives, functions, and organization of the Deep Space Network are summarized. The deep space instrumentation facility, the ground communications facility, and the network control system are described. Other areas reported include: Helios Mission support, DSN support of the Mariner Mars 1971 extended mission, Mariner Venus/Mercury 1973 mission support, Viking mission support, radio science, tracking and ground-based navigation, network control and data processing, and deep space stations.

Climate, carbon cycling, and deep-ocean ecosystems.

PubMed

Smith, K L; Ruhl, H A; Bett, B J; Billett, D S M; Lampitt, R S; Kaufmann, R S

2009-11-17

Climate variation affects surface ocean processes and the production of organic carbon, which ultimately comprises the primary food supply to the deep-sea ecosystems that occupy approximately 60% of the Earth's surface. Warming trends in atmospheric and upper ocean temperatures, attributed to anthropogenic influence, have occurred over the past four decades. Changes in upper ocean temperature influence stratification and can affect the availability of nutrients for phytoplankton production. Global warming has been predicted to intensify stratification and reduce vertical mixing. Research also suggests that such reduced mixing will enhance variability in primary production and carbon export flux to the deep sea. The dependence of deep-sea communities on surface water production has raised important questions about how climate change will affect carbon cycling and deep-ocean ecosystem function. Recently, unprecedented time-series studies conducted over the past two decades in the North Pacific and the North Atlantic at >4,000-m depth have revealed unexpectedly large changes in deep-ocean ecosystems significantly correlated to climate-driven changes in the surface ocean that can impact the global carbon cycle. Climate-driven variation affects oceanic communities from surface waters to the much-overlooked deep sea and will have impacts on the global carbon cycle. Data from these two widely separated areas of the deep ocean provide compelling evidence that changes in climate can readily influence deep-sea processes. However, the limited geographic coverage of these existing time-series studies stresses the importance of developing a more global effort to monitor deep-sea ecosystems under modern conditions of rapidly changing climate.

The deep ocean under climate change.

PubMed

Levin, Lisa A; Le Bris, Nadine

2015-11-13

The deep ocean absorbs vast amounts of heat and carbon dioxide, providing a critical buffer to climate change but exposing vulnerable ecosystems to combined stresses of warming, ocean acidification, deoxygenation, and altered food inputs. Resulting changes may threaten biodiversity and compromise key ocean services that maintain a healthy planet and human livelihoods. There exist large gaps in understanding of the physical and ecological feedbacks that will occur. Explicit recognition of deep-ocean climate mitigation and inclusion in adaptation planning by the United Nations Framework Convention on Climate Change (UNFCCC) could help to expand deep-ocean research and observation and to protect the integrity and functions of deep-ocean ecosystems. Copyright © 2015, American Association for the Advancement of Science.

SEDS: The Spitzer Extended Deep Survey. Survey Design, Photometry, and Deep IRAC Source Counts

NASA Technical Reports Server (NTRS)

Ashby, M. L. N.; Willner, S. P.; Fazio, G. G.; Huang, J.-S.; Arendt, A.; Barmby, P.; Barro, G; Bell, E. F.; Bouwens, R.; Cattaneo, A.;

The deep lymphatic anatomy of the hand.

PubMed

Ma, Chuan-Xiang; Pan, Wei-Ren; Liu, Zhi-An; Zeng, Fan-Qiang; Qiu, Zhi-Qiang

2018-07-01

The deep lymphatic anatomy of the hand still remains the least described in medical literature. Eight hands were harvested from four nonembalmed human cadavers amputated above the wrist. A small amount of 6% hydrogen peroxide was employed to detect the lymphatic vessels around the superficial and deep palmar vascular arches, in webs from the index to little fingers, the thenar and hypothenar areas. A 30-gauge needle was inserted into the vessels and injected with a barium sulphate compound. Each specimen was dissected, photographed and radiographed to demonstrate deep lymphatic distribution of the hand. Five groups of deep collecting lymph vessels were found in the hand: superficial palmar arch lymph vessel (SPALV); deep palmar arch lymph vessel (DPALV); thenar lymph vessel (TLV); hypothenar lymph vessel (HTLV); deep finger web lymph vessel (DFWLV). Each group of vessels drained in different directions first, then all turned and ran towards the wrist in different layers. The deep lymphatic drainage of the hand has been presented. The results will provide an anatomical basis for clinical management, educational reference and scientific research. Copyright © 2018 Elsevier GmbH. All rights reserved.

Deep Reconditioning Testing for near Earth Orbits

NASA Technical Reports Server (NTRS)

Betz, F. E.; Barnes, W. L.

1984-01-01

The problems and benefits of deep reconditioning to near Earth orbit missions with high cycle life and shallow discharge depth requirements is discussed. A simple battery level approach to deep reconditioning of nickel cadmium batteries in near Earth orbit is considered. A test plan was developed to perform deep reconditioning in direct comparison with an alternative trickle charge approach. The results demonstrate that the deep reconditioning procedure described for near Earth orbit application is inferior to the alternative of trickle charging.

Biological effects of rice harbouring Bph14 and Bph15 on brown planthopper, Nilaparvata lugens.

PubMed

Li, Jie; Chen, Qiuhong; Wang, Liangquan; Liu, Jia; Shang, Keke; Hua, Hongxia

2011-05-01

Brown planthopper (Nilaparvata lugens Stål; BPH) resistance genes Bph14 and Bph15 have been introgressed singly or pyramided into rice variety Minghui 63 (MH63). The antibiosis and antixenosis effects of these rice lines on BPH and the expression of five P450 genes of BPH regulated by these rice lines were investigated in this study. The resistance level of rice lines harbouring resistance genes was improved compared with MH63. MH63::14 (carrying Bph14) had negative effects on the development of males, honeydew excretion of females, the female ratio and the copulation rate compared with MH63. MH63::14 also exhibited antixenosis action against BPH nymphs, female adults and oviposition. Besides these negative effects, MH63::15 (carrying Bph15) could also retard the development of females, lower the fecundity and shorten the lifespan of females. The antixenosis action of MH63::15 was stronger than that of MH63::14. When Bph14 and Bph15 were pyramided, antibiosis and antixenosis effects were significantly enhanced relative to single-introgression lines. Among the five P450 genes of BPH, expression of three genes was upregulated, one gene was downregulated and one gene was unchanged by resistant hosts. Both Bph14 and Bph15 could improve resistance levels of MH63. MH63::15 and MH63::14&15 had greater potential to control BPH infestations than MH63::14. Copyright © 2011 Society of Chemical Industry.

47 CFR 32.2424 - Submarine & deep sea cable.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 2 2011-10-01 2011-10-01 false Submarine & deep sea cable. 32.2424 Section 32... Submarine & deep sea cable. (a) This account shall include the original cost of submarine cable and deep sea... defined below, are to be maintained for nonmetallic submarine and deep sea cable and metallic submarine...

47 CFR 32.2424 - Submarine & deep sea cable.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 2 2014-10-01 2014-10-01 false Submarine & deep sea cable. 32.2424 Section 32... Submarine & deep sea cable. (a) This account shall include the original cost of submarine cable and deep sea... defined below, are to be maintained for nonmetallic submarine and deep sea cable and metallic submarine...

47 CFR 32.2424 - Submarine & deep sea cable.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 2 2010-10-01 2010-10-01 false Submarine & deep sea cable. 32.2424 Section 32... Submarine & deep sea cable. (a) This account shall include the original cost of submarine cable and deep sea... defined below, are to be maintained for nonmetallic submarine and deep sea cable and metallic submarine...

47 CFR 32.2424 - Submarine & deep sea cable.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 2 2013-10-01 2013-10-01 false Submarine & deep sea cable. 32.2424 Section 32... Submarine & deep sea cable. (a) This account shall include the original cost of submarine cable and deep sea... defined below, are to be maintained for nonmetallic submarine and deep sea cable and metallic submarine...

47 CFR 32.2424 - Submarine & deep sea cable.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 2 2012-10-01 2012-10-01 false Submarine & deep sea cable. 32.2424 Section 32... Submarine & deep sea cable. (a) This account shall include the original cost of submarine cable and deep sea... defined below, are to be maintained for nonmetallic submarine and deep sea cable and metallic submarine...

Deep ECGNet: An Optimal Deep Learning Framework for Monitoring Mental Stress Using Ultra Short-Term ECG Signals.

PubMed

Hwang, Bosun; You, Jiwoo; Vaessen, Thomas; Myin-Germeys, Inez; Park, Cheolsoo; Zhang, Byoung-Tak

2018-02-08

Stress recognition using electrocardiogram (ECG) signals requires the intractable long-term heart rate variability (HRV) parameter extraction process. This study proposes a novel deep learning framework to recognize the stressful states, the Deep ECGNet, using ultra short-term raw ECG signals without any feature engineering methods. The Deep ECGNet was developed through various experiments and analysis of ECG waveforms. We proposed the optimal recurrent and convolutional neural networks architecture, and also the optimal convolution filter length (related to the P, Q, R, S, and T wave durations of ECG) and pooling length (related to the heart beat period) based on the optimization experiments and analysis on the waveform characteristics of ECG signals. The experiments were also conducted with conventional methods using HRV parameters and frequency features as a benchmark test. The data used in this study were obtained from Kwangwoon University in Korea (13 subjects, Case 1) and KU Leuven University in Belgium (9 subjects, Case 2). Experiments were designed according to various experimental protocols to elicit stressful conditions. The proposed framework to recognize stress conditions, the Deep ECGNet, outperformed the conventional approaches with the highest accuracy of 87.39% for Case 1 and 73.96% for Case 2, respectively, that is, 16.22% and 10.98% improvements compared with those of the conventional HRV method. We proposed an optimal deep learning architecture and its parameters for stress recognition, and the theoretical consideration on how to design the deep learning structure based on the periodic patterns of the raw ECG data. Experimental results in this study have proved that the proposed deep learning model, the Deep ECGNet, is an optimal structure to recognize the stress conditions using ultra short-term ECG data.

The Deep Space Network, volume 17

NASA Technical Reports Server (NTRS)

1973-01-01

The objectives, functions, and organization of the Deep Space Network are summarized. The Deep Space Instrumentation Facility, the Ground Communications Facility, and the Network Control System are described.

Holography as deep learning

NASA Astrophysics Data System (ADS)

Gan, Wen-Cong; Shu, Fu-Wen

Quantum many-body problem with exponentially large degrees of freedom can be reduced to a tractable computational form by neural network method [G. Carleo and M. Troyer, Science 355 (2017) 602, arXiv:1606.02318.] The power of deep neural network (DNN) based on deep learning is clarified by mapping it to renormalization group (RG), which may shed lights on holographic principle by identifying a sequence of RG transformations to the AdS geometry. In this paper, we show that any network which reflects RG process has intrinsic hyperbolic geometry, and discuss the structure of entanglement encoded in the graph of DNN. We find the entanglement structure of DNN is of Ryu-Takayanagi form. Based on these facts, we argue that the emergence of holographic gravitational theory is related to deep learning process of the quantum-field theory.

Mass extinctions in the deep sea

NASA Technical Reports Server (NTRS)

Thomas, E.

1988-01-01

The character of mass extinctions can be assessed by studying extinction patterns of organisms, the fabric of the extinction, and assessing the environmental niche and mode of life of survivors. Deep-sea benthic foraminifera have been listed as little affected by the Cretaceous-Tertiary (K-T) mass extinction, but very few quantitative data are available. New data on deep-sea Late Maestrichtian-Eocene benthic foraminifera from Maud Rise (Antractica) indicate that about 10 percent of the species living at depths of 2000 to 2500 m had last appearances within 1 my of the Cretaceous-Tertiary (K-T) boundary, versus about 25 percent of species at 1000 to 1500 m. Many survivors from the Cretaceous became extinct in a period of global deep-sea benthic foraminiferal extinction at the end of the Paleocene, a time otherwise marked by very few extinctions. Preliminary conclusions suggest that the deep oceanic environment is essentially decoupled from the shallow marine and terrestrial environment, and that even major disturbances of one of these will not greatly affect the other. This gives deep-sea benthic faunas a good opportunity to recolonize shallow environments from greater depths and vice versa after massive extinctions. The decoupling means that data on deep-sea benthic boundary was caused by the environmental effects of asteriod impact or excessive volcanism. The benthic foraminiferal data strongly suggest, however, that the environmental results were strongest at the Earth's surface, and that there was no major disturbance of the deep ocean; this pattern might result both from excessive volcanism and from an impact on land.

Nucleic acid based quantitative microbial community analysis in different marine and terrestrial sediments

NASA Astrophysics Data System (ADS)

Schippers, A.; Blazejak, A.; Köweker, G.

2009-12-01

Sub-seafloor sediments harbour over half of all prokaryotic cells on Earth. This immense cell number is calculated from numerous microscopic cell counts (AODC) in ODP sediment cores. Since AODC can not differentiate between living or dead cells, the population size of living microorganisms and the abundance of different prokaryotic groups are unknown. Recent molecular nucleic acid and biomarker analyses showed that a high proportion of the cells are alive and that the microbial communities of deep marine sediments harbour members of distinct, uncultured bacterial and archaeal lineages. The main objective of our project is the quantification of living prokaryotes in various sediments. Deep sediment samples from the Pacific and the Atlantic Oceans (ODP Legs 201 and 207, IODP Exp. 307 and 308), sediments from the Indian Ocean (RV Sonne 189-2) and the Black Sea (RV Meteor 51/4) as well as terrestrial Chesapeake Bay Sediments (ICDP) were analyzed using Catalyzed Reporter Deposition - Fluorescence In Situ Hybridisation (CARD - FISH) and quantitative, real-time PCR (Q-PCR), targeting either the 16S rRNA gene or the functional genes dsrA, mcrA and aprA to quantify microorganisms of various phylogenetic or physiological groups (e.g. JS1 cluster and Chloroflexi). At all sediment sites, cell numbers decreased with depth, however, the abundance of particular microbial groups varied at different sites and depths. The results indicate that global estimates of the deep biosphere should be reconsidered.

Deep learning methods for protein torsion angle prediction.

PubMed

Li, Haiou; Hou, Jie; Adhikari, Badri; Lyu, Qiang; Cheng, Jianlin

2017-09-18

Deep learning is one of the most powerful machine learning methods that has achieved the state-of-the-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012, it has achieved success in a number of areas such as protein residue-residue contact prediction, secondary structure prediction, and fold recognition. In this work, we developed deep learning methods to improve the prediction of torsion (dihedral) angles of proteins. We design four different deep learning architectures to predict protein torsion angles. The architectures including deep neural network (DNN) and deep restricted Boltzmann machine (DRBN), deep recurrent neural network (DRNN) and deep recurrent restricted Boltzmann machine (DReRBM) since the protein torsion angle prediction is a sequence related problem. In addition to existing protein features, two new features (predicted residue contact number and the error distribution of torsion angles extracted from sequence fragments) are used as input to each of the four deep learning architectures to predict phi and psi angles of protein backbone. The mean absolute error (MAE) of phi and psi angles predicted by DRNN, DReRBM, DRBM and DNN is about 20-21° and 29-30° on an independent dataset. The MAE of phi angle is comparable to the existing methods, but the MAE of psi angle is 29°, 2° lower than the existing methods. On the latest CASP12 targets, our methods also achieved the performance better than or comparable to a state-of-the art method. Our experiment demonstrates that deep learning is a valuable method for predicting protein torsion angles. The deep recurrent network architecture performs slightly better than deep feed-forward architecture, and the predicted residue contact number and the error distribution of torsion angles extracted from sequence fragments are useful features for improving prediction accuracy.

Deep tissue massage: What are we talking about?

PubMed

Koren, Yogev; Kalichman, Leonid

2018-04-01

Massage is a common treatment in complementary and integrative medicine. Deep tissue massage, a form of therapeutic massage, has become more and more popular in recent years. Hence, the use of massage generally and deep tissue massage specifically, should be evaluated as any other modality of therapy to establish its efficacy and safety. To determine the definitions used for deep tissue massage in the scientific literature and to review the current scientific evidence for its efficacy and safety. Narrative review. There is no commonly accepted definition of deep tissue massage in the literature. The definition most frequently used is the intention of the therapist. We suggest separating the definitions of deep massage and deep tissue massage as follows: deep massage should be used to describe the intention of the therapist to treat deep tissue by using any form of massage and deep tissue massage should be used to describe a specific and independent method of massage therapy, utilizing the specific set of principles and techniques as defined by Riggs: "The understanding of the layers of the body, and the ability to work with tissue in these layers to relax, lengthen, and release holding patterns in the most effective and energy efficient way possible within the client's parameters of comfort". Heterogeneity of techniques and protocols used in published studies have made it difficult to draw any clear conclusions. Favorable outcomes may result from deep tissue massage in pain populations and patients with decreased range of motion. In addition, several rare serious adverse events were found related to deep tissue massage, probably as a result of the forceful application of massage therapy. Future research of deep tissue massage should be based on a common definition, classification system and the use of common comparators as controls. Copyright © 2017 Elsevier Ltd. All rights reserved.

Deep Learning in Gastrointestinal Endoscopy.

PubMed

Patel, Vivek; Armstrong, David; Ganguli, Malika; Roopra, Sandeep; Kantipudi, Neha; Albashir, Siwar; Kamath, Markad V

2016-01-01

Gastrointestinal (GI) endoscopy is used to inspect the lumen or interior of the GI tract for several purposes, including, (1) making a clinical diagnosis, in real time, based on the visual appearances; (2) taking targeted tissue samples for subsequent histopathological examination; and (3) in some cases, performing therapeutic interventions targeted at specific lesions. GI endoscopy is therefore predicated on the assumption that the operator-the endoscopist-is able to identify and characterize abnormalities or lesions accurately and reproducibly. However, as in other areas of clinical medicine, such as histopathology and radiology, many studies have documented marked interobserver and intraobserver variability in lesion recognition. Thus, there is a clear need and opportunity for techniques or methodologies that will enhance the quality of lesion recognition and diagnosis and improve the outcomes of GI endoscopy. Deep learning models provide a basis to make better clinical decisions in medical image analysis. Biomedical image segmentation, classification, and registration can be improved with deep learning. Recent evidence suggests that the application of deep learning methods to medical image analysis can contribute significantly to computer-aided diagnosis. Deep learning models are usually considered to be more flexible and provide reliable solutions for image analysis problems compared to conventional computer vision models. The use of fast computers offers the possibility of real-time support that is important for endoscopic diagnosis, which has to be made in real time. Advanced graphics processing units and cloud computing have also favored the use of machine learning, and more particularly, deep learning for patient care. This paper reviews the rapidly evolving literature on the feasibility of applying deep learning algorithms to endoscopic imaging.

The deep space network, volume 7

NASA Technical Reports Server (NTRS)

1972-01-01

The objectives, functions, and organization of the Deep Space Network are summarized. The Deep Space Instrumentation Facility, the Ground Communications Facility, and the Space Flight Operations Facility are described.

The deep space network

NASA Technical Reports Server (NTRS)

1975-01-01

The objectives, functions, and organization of the Deep Space Network are summarized along with deep space station, ground communication, and network operations control capabilities. Mission support of ongoing planetary/interplanetary flight projects is discussed with emphasis on Viking orbiter radio frequency compatibility tests, the Pioneer Venus orbiter mission, and Helios-1 mission status and operations. Progress is also reported in tracking and data acquisition research and technology, network engineering, hardware and software implementation, and operations.

The Deep Space Network

NASA Technical Reports Server (NTRS)

1974-01-01

The objectives, functions, and organization, of the Deep Space Network are summarized. Deep Space stations, ground communications, and network operations control capabilities are described. The network is designed for two-way communications with unmanned spacecraft traveling approximately 1600 km from earth to the farthest planets in the solar system. It has provided tracking and data acquisition support for the following projects: Ranger, Surveyor, Mariner, Pioneer, Apollo, Helios, Viking, and the Lunar Orbiter.

Rapid emergence of high-level tigecycline resistance in Escherichia coli strains harbouring blaNDM-5 in vivo.

PubMed

Li, Xi; Mu, Xinli; Yang, Yunxing; Hua, Xiaoting; Yang, Qing; Wang, Nanfei; Du, Xiaoxing; Ruan, Zhi; Shen, Xiaoqiang; Yu, Yunsong

2016-04-01

Tigecycline (TIG) resistance is a growing concern because this antibiotic is regarded as one of the last resorts to treat infections caused by multidrug-resistant and extensively drug-resistant (XDR) bacteria. Information regarding TIG-resistant Escherichia coli isolates is scarce. In this study, we report the emergence of high-level TIG resistance in a longitudinal series of XDR E. coli isolates collected during TIG treatment. Whole-genome sequencing was performed for six E. coli strains harbouring bla(NDM-5) and genomic comparison revealed two amino acid substitutions. Mutation in rpsJ could be a significant factor conferring TIG resistance in these isolates. The fitness cost of TIG resistance in resistant strains was evaluated by determining the relative growth rate, indicating that TIG resistance reduced fitness by ca. 7%. This study is the first report to demonstrate high-level TIG resistance in E. coli in vivo. In addition, we report the first treatment-emergent minimum inhibitory concentration (MIC) development of TIG from 1mg/L to 64 mg/L in E. coli. Clinicians should be aware of the risk of an increase in the MIC of TIG under therapy. Copyright © 2016 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Deep Restricted Kernel Machines Using Conjugate Feature Duality.

PubMed

Suykens, Johan A K

2017-08-01

The aim of this letter is to propose a theory of deep restricted kernel machines offering new foundations for deep learning with kernel machines. From the viewpoint of deep learning, it is partially related to restricted Boltzmann machines, which are characterized by visible and hidden units in a bipartite graph without hidden-to-hidden connections and deep learning extensions as deep belief networks and deep Boltzmann machines. From the viewpoint of kernel machines, it includes least squares support vector machines for classification and regression, kernel principal component analysis (PCA), matrix singular value decomposition, and Parzen-type models. A key element is to first characterize these kernel machines in terms of so-called conjugate feature duality, yielding a representation with visible and hidden units. It is shown how this is related to the energy form in restricted Boltzmann machines, with continuous variables in a nonprobabilistic setting. In this new framework of so-called restricted kernel machine (RKM) representations, the dual variables correspond to hidden features. Deep RKM are obtained by coupling the RKMs. The method is illustrated for deep RKM, consisting of three levels with a least squares support vector machine regression level and two kernel PCA levels. In its primal form also deep feedforward neural networks can be trained within this framework.

The deep space network, volume 18. [Deep Space Instrumentation Facility, Ground Communication Facility, and Network Control System

NASA Technical Reports Server (NTRS)

1973-01-01

The objectives, functions, and organization of the Deep Space Network are summarized. The Deep Space Instrumentation Facility, the Ground Communications Facility, and the Network Control System are described.

Toolkits and Libraries for Deep Learning.

PubMed

Erickson, Bradley J; Korfiatis, Panagiotis; Akkus, Zeynettin; Kline, Timothy; Philbrick, Kenneth

2017-08-01

Deep learning is an important new area of machine learning which encompasses a wide range of neural network architectures designed to complete various tasks. In the medical imaging domain, example tasks include organ segmentation, lesion detection, and tumor classification. The most popular network architecture for deep learning for images is the convolutional neural network (CNN). Whereas traditional machine learning requires determination and calculation of features from which the algorithm learns, deep learning approaches learn the important features as well as the proper weighting of those features to make predictions for new data. In this paper, we will describe some of the libraries and tools that are available to aid in the construction and efficient execution of deep learning as applied to medical images.

De novo peptide sequencing by deep learning

PubMed Central

Tran, Ngoc Hieu; Zhang, Xianglilan; Xin, Lei; Shan, Baozhen; Li, Ming

2017-01-01

De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing. We evaluated the method on a wide variety of species and found that DeepNovo considerably outperformed state of the art methods, achieving 7.7–22.9% higher accuracy at the amino acid level and 38.1–64.0% higher accuracy at the peptide level. We further used DeepNovo to automatically reconstruct the complete sequences of antibody light and heavy chains of mouse, achieving 97.5–100% coverage and 97.2–99.5% accuracy, without assisting databases. Moreover, DeepNovo is retrainable to adapt to any sources of data and provides a complete end-to-end training and prediction solution to the de novo sequencing problem. Not only does our study extend the deep learning revolution to a new field, but it also shows an innovative approach in solving optimization problems by using deep learning and dynamic programming. PMID:28720701

Deep-sea coral research and technology program: Alaska deep-sea coral and sponge initiative final report

USGS Publications Warehouse

Rooper, Chris; Stone, Robert P.; Etnoyer, Peter; Conrath, Christina; Reynolds, Jennifer; Greene, H. Gary; Williams, Branwen; Salgado, Enrique; Morrison, Cheryl L.; Waller, Rhian G.; Demopoulos, Amanda W.J.

2017-01-01

Deep-sea coral and sponge ecosystems are widespread throughout most of Alaska’s marine waters. In some places, such as the central and western Aleutian Islands, deep-sea coral and sponge resources can be extremely diverse and may rank among the most abundant deep-sea coral and sponge communities in the world. Many different species of fishes and invertebrates are associated with deep-sea coral and sponge communities in Alaska. Because of their biology, these benthic invertebrates are potentially impacted by climate change and ocean acidification. Deepsea coral and sponge ecosystems are also vulnerable to the effects of commercial fishing activities. Because of the size and scope of Alaska’s continental shelf and slope, the vast majority of the area has not been visually surveyed for deep-sea corals and sponges. NOAA’s Deep Sea Coral Research and Technology Program (DSCRTP) sponsored a field research program in the Alaska region between 2012–2015, referred to hereafter as the Alaska Initiative. The priorities for Alaska were derived from ongoing data needs and objectives identified by the DSCRTP, the North Pacific Fishery Management Council (NPFMC), and Essential Fish Habitat-Environmental Impact Statement (EFH-EIS) process.This report presents the results of 15 projects conducted using DSCRTP funds from 2012-2015. Three of the projects conducted as part of the Alaska deep-sea coral and sponge initiative included dedicated at-sea cruises and fieldwork spread across multiple years. These projects were the eastern Gulf of Alaska Primnoa pacifica study, the Aleutian Islands mapping study, and the Gulf of Alaska fish productivity study. In all, there were nine separate research cruises carried out with a total of 109 at-sea days conducting research. The remaining projects either used data and samples collected by the three major fieldwork projects or were piggy-backed onto existing research programs at the Alaska Fisheries Science Center (AFSC).

Colonization of the deep sea by fishes

PubMed Central

Priede, I G; Froese, R

2013-01-01

Analysis of maximum depth of occurrence of 11 952 marine fish species shows a global decrease in species number (N) with depth (x; m): log10N = −0·000422x + 3·610000 (r2 = 0·948). The rate of decrease is close to global estimates for change in pelagic and benthic biomass with depth (−0·000430), indicating that species richness of fishes may be limited by food energy availability in the deep sea. The slopes for the Classes Myxini (−0·000488) and Actinopterygii (−0·000413) follow this trend but Chondrichthyes decrease more rapidly (−0·000731) implying deficiency in ability to colonize the deep sea. Maximum depths attained are 2743, 4156 and 8370 m for Myxini, Chondrichthyes and Actinopterygii, respectively. Endemic species occur in abundance at 7–7800 m depth in hadal trenches but appear to be absent from the deepest parts of the oceans, >9000 m deep. There have been six global oceanic anoxic events (OAE) since the origin of the major fish taxa in the Devonian c. 400 million years ago (mya). Colonization of the deep sea has taken place largely since the most recent OAE in the Cretaceous 94 mya when the Atlantic Ocean opened up. Patterns of global oceanic circulation oxygenating the deep ocean basins became established coinciding with a period of teleost diversification and appearance of the Acanthopterygii. Within the Actinopterygii, there is a trend for greater invasion of the deep sea by the lower taxa in accordance with the Andriashev paradigm. Here, 31 deep-sea families of Actinopterygii were identified with mean maximum depth >1000 m and with >10 species. Those with most of their constituent species living shallower than 1000 m are proposed as invasive, with extinctions in the deep being continuously balanced by export of species from shallow seas. Specialized families with most species deeper than 1000 m are termed deep-sea endemics in this study; these appear to persist in the deep by virtue of global distribution enabling

The Future of the Deep Space Network: Technology Development for K2-Band Deep Space Communications

NASA Technical Reports Server (NTRS)

Bhanji, Alaudin M.

1999-01-01

Projections indicate that in the future the number of NASA's robotic deep space missions is likely to increase significantly. A launch rate of up to 4-6 launches per year is projected with up to 25 simultaneous missions active [I]. Future high resolution mapping missions to other planetary bodies as well as other experiments are likely to require increased downlink capacity. These future deep space communications requirements will, according to baseline loading analysis, exceed the capacity of NASA's Deep Space Network in its present form. There are essentially two approaches for increasing the channel capacity of the Deep Space Network. Given the near-optimum performance of the network at the two deep space communications bands, S-Band (uplink 2.025-2.120 GHz, downlink 2.2-2.3 GHz), and X-Band (uplink 7.145-7.19 GHz, downlink 8.48.5 GHz), additional improvements bring only marginal return for the investment. Thus the only way to increase channel capacity is simply to construct more antennas, receivers, transmitters and other hardware. This approach is relatively low-risk but involves increasing both the number of assets in the network and operational costs.

Ancient origin of the modern deep-sea fauna.

PubMed

Thuy, Ben; Gale, Andy S; Kroh, Andreas; Kucera, Michal; Numberger-Thuy, Lea D; Reich, Mike; Stöhr, Sabine

2012-01-01

The origin and possible antiquity of the spectacularly diverse modern deep-sea fauna has been debated since the beginning of deep-sea research in the mid-nineteenth century. Recent hypotheses, based on biogeographic patterns and molecular clock estimates, support a latest Mesozoic or early Cenozoic date for the origin of key groups of the present deep-sea fauna (echinoids, octopods). This relatively young age is consistent with hypotheses that argue for extensive extinction during Jurassic and Cretaceous Oceanic Anoxic Events (OAEs) and the mid-Cenozoic cooling of deep-water masses, implying repeated re-colonization by immigration of taxa from shallow-water habitats. Here we report on a well-preserved echinoderm assemblage from deep-sea (1000-1500 m paleodepth) sediments of the NE-Atlantic of Early Cretaceous age (114 Ma). The assemblage is strikingly similar to that of extant bathyal echinoderm communities in composition, including families and genera found exclusively in modern deep-sea habitats. A number of taxa found in the assemblage have no fossil record at shelf depths postdating the assemblage, which precludes the possibility of deep-sea recolonization from shallow habitats following episodic extinction at least for those groups. Our discovery provides the first key fossil evidence that a significant part of the modern deep-sea fauna is considerably older than previously assumed. As a consequence, most major paleoceanographic events had far less impact on the diversity of deep-sea faunas than has been implied. It also suggests that deep-sea biota are more resilient to extinction events than shallow-water forms, and that the unusual deep-sea environment, indeed, provides evolutionary stability which is very rarely punctuated on macroevolutionary time scales.

Deep space communication - Past, present, and future

NASA Technical Reports Server (NTRS)

Posner, E. C.; Stevens, R.

1984-01-01

This paper reviews the progress made in deep space communication from its beginnings until now, describes the development and applications of NASA's Deep Space Network, and indicates directions for the future. Limiting factors in deep space communication are examined using the upcoming Voyager encounter with Uranus, centered on the downlink telemetry from spacecraft to earth, as an example. A link calculation for Voyager at Uranus over Australia is exhibited. Seven basic deep space communication functions are discussed, and technical aspects of spacecraft communication equipment, ground antennas, and ground electronics and processing are considered.

Edge systems in the deep ocean

NASA Astrophysics Data System (ADS)

Coon, Andrew; Earp, Samuel L.

2010-04-01

DARPA has initiated a program to explore persistent presence in the deep ocean. The deep ocean is difficult to access and presents a hostile environment. Persistent operations in the deep ocean will require new technology for energy, communications and autonomous operations. Several fundamental characteristics of the deep ocean shape any potential system architecture. The deep sea presents acoustic sensing opportunities that may provide significantly enhanced sensing footprints relative to sensors deployed at traditional depths. Communication limitations drive solutions towards autonomous operation of the platforms and automation of data collection and processing. Access to the seabed presents an opportunity for fixed infrastructure with no important limitations on size and weight. Difficult access and persistence impose requirements for long-life energy sources and potentially energy harvesting. The ocean is immense, so there is a need to scale the system footprint for presence over tens of thousands and perhaps hundreds of thousands of square nautical miles. This paper focuses on the aspect of distributed sensing, and the engineering of networks of sensors to cover the required footprint.

Research Possibilities Beyond Deep Space Gateway

NASA Astrophysics Data System (ADS)

Smitherman, D. V.; Needham, D. H.; Lewis, R.

2018-02-01

This abstract explores the possibilities for a large research facilities module attached to the Deep Space Gateway, using the same large module design and basic layout planned for the Deep Space Transport.

After Superficial Ablation for Superficial Reflux Associated with Primary Deep Axial Reflux, Can Variable Outcomes be Caused by Deep Venous Valve Anomalies?

PubMed

Maleti, O; Lugli, M; Perrin, M

2017-02-01

To identify which deep anatomical anomalies can explain variable hemodynamic outcomes in patients with superficial reflux associated with primary deep axial reflux who underwent isolated superficial vein ablation without improvement. This is a retrospective study of deep venous valve anomalies in patients who underwent superficial vein ablation for superficial and associated deep reflux. A group of 21 patients who were diagnosed with saphenous reflux associated with primary deep axial reflux, were submitted to great saphenous vein ablation. In 17 patients the deep reflux was not abolished. In this subgroup, surgical exploration of the deep valve was carried out using venotomy for possible valve repair. Among the 17 subgroup patients, four post-thrombotic lesions were discovered intra-operatively in four patients; they underwent different surgical procedures. In 13 of the subgroup patients, primary valve incompetence was confirmed intra-operatively. In 11 cases the leaflets were asymmetrical and in only two were they symmetrical. After valvuloplasty, deep reflux was abolished in all 13 patients. Clinical improvement was obtained in 12/13 patients (92%). It is noteworthy that abolition of deep reflux was associated with significant improvement in air plethysmography data as well as with improvement in clinical status measured on CEAP class, VCSS and the SF-36 questionnaire. Failure to correct deep axial reflux by superficial ablation in patients with superficial and associated primary deep axial reflux may be related to asymmetry in the leaflets of the incompetent deep venous valve. Copyright © 2016 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

Deep space network energy program

NASA Technical Reports Server (NTRS)

Friesema, S. E.

1980-01-01

If the Deep Space Network is to exist in a cost effective and reliable manner in the next decade, the problems presented by international energy cost increases and energy availability must be addressed. The Deep Space Network Energy Program was established to implement solutions compatible with the ongoing development of the total network.

Deep crustal earthquakes associated with continental rifts

NASA Astrophysics Data System (ADS)

Doser, Diane I.; Yarwood, Dennis R.

1994-01-01

Deep (> 20 km) crustal earthquakes have occurred within or along the margins of at least four continental rift zones. The largest of these deep crustal earthquakes ( M ⩾ 5.0) have strike-slip or oblique-slip mechanisms with T-axes oriented similarly to those associated with shallow normal faulting within the rift zones. The majority of deep crustal earthquakes occur along the rift margins in regions that have cooler, thicker crust. Several deep crustal events, however, occur in regions of high heat flow. These regions also appear to be regions of high strain, a factor that could account for the observed depths. We believe the deep crustal earthquakes represent either the relative motion of rift zones with respect to adjacent stable regions or the propagation of rifting into stable regions.

DeepVel: Deep learning for the estimation of horizontal velocities at the solar surface

NASA Astrophysics Data System (ADS)

Asensio Ramos, A.; Requerey, I. S.; Vitas, N.

2017-07-01

Many phenomena taking place in the solar photosphere are controlled by plasma motions. Although the line-of-sight component of the velocity can be estimated using the Doppler effect, we do not have direct spectroscopic access to the components that are perpendicular to the line of sight. These components are typically estimated using methods based on local correlation tracking. We have designed DeepVel, an end-to-end deep neural network that produces an estimation of the velocity at every single pixel, every time step, and at three different heights in the atmosphere from just two consecutive continuum images. We confront DeepVel with local correlation tracking, pointing out that they give very similar results in the time and spatially averaged cases. We use the network to study the evolution in height of the horizontal velocity field in fragmenting granules, supporting the buoyancy-braking mechanism for the formation of integranular lanes in these granules. We also show that DeepVel can capture very small vortices, so that we can potentially expand the scaling cascade of vortices to very small sizes and durations. The movie attached to Fig. 3 is available at http://www.aanda.org

How to study deep roots—and why it matters

PubMed Central

Maeght, Jean-Luc; Rewald, Boris; Pierret, Alain

2013-01-01

The drivers underlying the development of deep root systems, whether genetic or environmental, are poorly understood but evidence has accumulated that deep rooting could be a more widespread and important trait among plants than commonly anticipated from their share of root biomass. Even though a distinct classification of “deep roots” is missing to date, deep roots provide important functions for individual plants such as nutrient and water uptake but can also shape plant communities by hydraulic lift (HL). Subterranean fauna and microbial communities are highly influenced by resources provided in the deep rhizosphere and deep roots can influence soil pedogenesis and carbon storage.Despite recent technological advances, the study of deep roots and their rhizosphere remains inherently time-consuming, technically demanding and costly, which explains why deep roots have yet to be given the attention they deserve. While state-of-the-art technologies are promising for laboratory studies involving relatively small soil volumes, they remain of limited use for the in situ observation of deep roots. Thus, basic techniques such as destructive sampling or observations at transparent interfaces with the soil (e.g., root windows) which have been known and used for decades to observe roots near the soil surface, must be adapted to the specific requirements of deep root observation. In this review, we successively address major physical, biogeochemical and ecological functions of deep roots to emphasize the significance of deep roots and to illustrate the yet limited knowledge. In the second part we describe the main methodological options to observe and measure deep roots, providing researchers interested in the field of deep root/rhizosphere studies with a comprehensive overview. Addressed methodologies are: excavations, trenches and soil coring approaches, minirhizotrons (MR), access shafts, caves and mines, and indirect approaches such as tracer-based techniques. PMID

Deep-sea piezosphere and piezophiles: geomicrobiology and biogeochemistry.

PubMed

Fang, Jiasong; Zhang, Li; Bazylinski, Dennis A

2010-09-01

The deep-sea piezosphere accounts for approximately 75% of the total ocean volume and hosts active and diverse biological communities. Evidence obtained thus far suggests that the microbial biomass present in the piezosphere is significant. Continued international interest in exploring the deep ocean provides impetus to increase our understanding of the deep-sea piezosphere and of the influence of piezophilic microbial communities on the global ocean environment and on biogeochemical cycling occurring in the deep sea. Here, we review the diversity, metabolic characteristics, geomicrobiology and biogeochemistry of the deep-sea piezophiles. Copyright 2010 Elsevier Ltd. All rights reserved.

Iris Transponder-Communications and Navigation for Deep Space

NASA Technical Reports Server (NTRS)

Duncan, Courtney B.; Smith, Amy E.; Aguirre, Fernando H.

2014-01-01

The Jet Propulsion Laboratory has developed the Iris CubeSat compatible deep space transponder for INSPIRE, the first CubeSat to deep space. Iris is 0.4 U, 0.4 kg, consumes 12.8 W, and interoperates with NASA's Deep Space Network (DSN) on X-Band frequencies (7.2 GHz uplink, 8.4 GHz downlink) for command, telemetry, and navigation. This talk discusses the Iris for INSPIRE, it's features and requirements; future developments and improvements underway; deep space and proximity operations applications for Iris; high rate earth orbit variants; and ground requirements, such as are implemented in the DSN, for deep space operations.

Numerical investigation of deep-crust behavior under lithospheric extension

NASA Astrophysics Data System (ADS)

Korchinski, Megan; Rey, Patrice F.; Mondy, Luke; Teyssier, Christian; Whitney, Donna L.

2018-02-01

What are the conditions under which lithospheric extension drives exhumation of the deep orogenic crust during the formation of gneiss domes? The mechanical link between extension of shallow crust and flow of deep crust is investigated using two-dimensional numerical experiments of lithospheric extension in which the crust is 60 km thick and the deep-crust viscosity and density parameter space is explored. Results indicate that the style of extension of the shallow crust and the path, magnitude, and rate of flow of deep crust are dynamically linked through the deep-crust viscosity, with density playing an important role in experiments with a high-viscosity deep crust. Three main groups of domes are defined based on their mechanisms of exhumation across the viscosity-density parameter space. In the first group (low-viscosity, low-density deep crust), domes develop by lateral and upward flow of the deep crust at km m.y-1 velocity rates (i.e. rate of experiment boundary extension). In this case, extension in the shallow crust is localized on a single interface, and the deep crust traverses the entire thickness of the crust to the Earth's near-surface in 5 m.y. This high exhuming power relies on the dynamic feedback between the flow of deep crust and the localization of extension in the shallow crust. The second group (intermediate-viscosity, low-density deep crust) has less exhuming power because the stronger deep crust flows less readily and instead accommodates more uniform extension, which imparts distributed extension to the shallow crust. The third group represents the upper limits of viscosity and density for the deep crust; in this case the low buoyancy of the deep crust results in localized thinning of the crust with large upward motion of the Moho and lithosphere-asthenosphere boundary. These numerical experiments test the exhuming power of the deep crust in the formation of extensional gneiss domes.

Context and Deep Learning Design

ERIC Educational Resources Information Center

Boyle, Tom; Ravenscroft, Andrew

2012-01-01

Conceptual clarification is essential if we are to establish a stable and deep discipline of technology enhanced learning. The technology is alluring; this can distract from deep design in a surface rush to exploit the affordances of the new technology. We need a basis for design, and a conceptual unit of organization, that are applicable across…

Anomalies of rupture velocity in deep earthquakes

NASA Astrophysics Data System (ADS)

Suzuki, M.; Yagi, Y.

2010-12-01

Explaining deep seismicity is a long-standing challenge in earth science. Deeper than 300 km, the occurrence rate of earthquakes with depth remains at a low level until ~530 km depth, then rises until ~600 km, finally terminate near 700 km. Given the difficulty of estimating fracture properties and observing the stress field in the mantle transition zone (410-660 km), the seismic source processes of deep earthquakes are the most important information for understanding the distribution of deep seismicity. However, in a compilation of seismic source models of deep earthquakes, the source parameters for individual deep earthquakes are quite varied [Frohlich, 2006]. Rupture velocities for deep earthquakes estimated using seismic waveforms range from 0.3 to 0.9Vs, where Vs is the shear wave velocity, a considerably wider range than the velocities for shallow earthquakes. The uncertainty of seismic source models prevents us from determining the main characteristics of the rupture process and understanding the physical mechanisms of deep earthquakes. Recently, the back projection method has been used to derive a detailed and stable seismic source image from dense seismic network observations [e.g., Ishii et al., 2005; Walker et al., 2005]. Using this method, we can obtain an image of the seismic source process from the observed data without a priori constraints or discarding parameters. We applied the back projection method to teleseismic P-waveforms of 24 large, deep earthquakes (moment magnitude Mw ≥ 7.0, depth ≥ 300 km) recorded since 1994 by the Data Management Center of the Incorporated Research Institutions for Seismology (IRIS-DMC) and reported in the U.S. Geological Survey (USGS) catalog, and constructed seismic source models of deep earthquakes. By imaging the seismic rupture process for a set of recent deep earthquakes, we found that the rupture velocities are less than about 0.6Vs except in the depth range of 530 to 600 km. This is consistent with the depth

Too Deep or Not Too Deep?: A Propensity-Matched Comparison of the Analgesic Effects of a Superficial Versus Deep Serratus Fascial Plane Block for Ambulatory Breast Cancer Surgery.

PubMed

Abdallah, Faraj W; Cil, Tulin; MacLean, David; Madjdpour, Caveh; Escallon, Jaime; Semple, John; Brull, Richard

2018-07-01

Serratus fascial plane block can reduce pain following breast surgery, but the question of whether to inject the local anesthetic superficial or deep to the serratus muscle has not been answered. This cohort study compares the analgesic benefits of superficial versus deep serratus plane blocks in ambulatory breast cancer surgery patients at Women's College Hospital between February 2014 and December 2016. We tested the joint hypothesis that deep serratus block is noninferior to superficial serratus block for postoperative in-hospital (pre-discharge) opioid consumption and pain severity. One hundred sixty-six patients were propensity matched among 2 groups (83/group): superficial and deep serratus blocks. The cohort was used to evaluate the effect of blocks on postoperative oral morphine equivalent consumption and area under the curve for rest pain scores. We considered deep serratus block to be noninferior to superficial serratus block if it were noninferior for both outcomes, within 15 mg morphine and 4 cm·h units margins. Other outcomes included intraoperative fentanyl requirements, time to first analgesic request, recovery room stay, and incidence of postoperative nausea and vomiting. Deep serratus block was associated with postoperative morphine consumption and pain scores area under the curve that were noninferior to those of the superficial serratus block. Intraoperative fentanyl requirements, time to first analgesic request, recovery room stay, and postoperative nausea and vomiting were not different between blocks. The postoperative in-hospital analgesia associated with deep serratus block is as effective (within an acceptable margin) as superficial serratus block following ambulatory breast cancer surgery. These new findings are important to inform both current clinical practices and future prospective studies.

Deep Lysimeter

DOEpatents

Hubbell, Joel M.; Sisson, James B.

2004-06-01

A deep lysimeter including a hollow vessel having a chamber, a fill conduit extending into the chamber through apertures, a semi-permeable member mounted on the vessel and in fluid communication with the fill conduit, and a line connection for retrieving the lysimeter.

The deep plantar arch in humans: constitution and topography.

PubMed

Gabrielli, C; Olave, E; Mandiola, E; Rodrigues, C F; Prates, J C

2001-01-01

The integrity of the various structures within the feet depends on their blood supply. Lesions of the feet often require revascularization, which if successful avoids the need for amputation. To provide greater anatomical detail to aid vascular surgery and imaging, the anatomy and constitution of the deep plantar arch was studied in 50 adult cadaveric feet. The arteries of the foot were injected with red neoprene latex and dissected under magnification. The deep plantar arch, present in all feet, was the result of anastomosis between the deep plantar artery and the deep branch of the lateral plantar artery. The deep plantar artery was predominant in 72% of specimens (Type I arches) and the lateral plantar artery in 22% (Type II), with the contribution being equal in 6% (Type III). The medial plantar artery contributed to the medial segment of the deep plantar arch by its deep branch in 12% of specimens. The distance between the deep plantar arch and each interdigital commissure was generally constant, averaging 29% of total foot length. The deep plantar arch was located in the middle third of the foot in all specimens, being in the distal part of this third in 90%. The deep plantar arch is, therefore formed mainly by the deep plantar artery, a branch of the dorsal artery of foot; its location can be estimated if foot length is known.

Deep learning architecture for iris recognition based on optimal Gabor filters and deep belief network

NASA Astrophysics Data System (ADS)

He, Fei; Han, Ye; Wang, Han; Ji, Jinchao; Liu, Yuanning; Ma, Zhiqiang

2017-03-01

Gabor filters are widely utilized to detect iris texture information in several state-of-the-art iris recognition systems. However, the proper Gabor kernels and the generative pattern of iris Gabor features need to be predetermined in application. The traditional empirical Gabor filters and shallow iris encoding ways are incapable of dealing with such complex variations in iris imaging including illumination, aging, deformation, and device variations. Thereby, an adaptive Gabor filter selection strategy and deep learning architecture are presented. We first employ particle swarm optimization approach and its binary version to define a set of data-driven Gabor kernels for fitting the most informative filtering bands, and then capture complex pattern from the optimal Gabor filtered coefficients by a trained deep belief network. A succession of comparative experiments validate that our optimal Gabor filters may produce more distinctive Gabor coefficients and our iris deep representations be more robust and stable than traditional iris Gabor codes. Furthermore, the depth and scales of the deep learning architecture are also discussed.

Climate Influence on Deep Sea Populations

PubMed Central

Company, Joan B.; Puig, Pere; Sardà, Francesc; Palanques, Albert; Latasa, Mikel; Scharek, Renate

2008-01-01

Dynamics of biological processes on the deep-sea floor are traditionally thought to be controlled by vertical sinking of particles from the euphotic zone at a seasonal scale. However, little is known about the influence of lateral particle transport from continental margins to deep-sea ecosystems. To address this question, we report here how the formation of dense shelf waters and their subsequent downslope cascade, a climate induced phenomenon, affects the population of the deep-sea shrimp Aristeus antennatus. We found evidence that strong currents associated with intense cascading events correlates with the disappearance of this species from its fishing grounds, producing a temporary fishery collapse. Despite this initial negative effect, landings increase between 3 and 5 years after these major events, preceded by an increase of juveniles. The transport of particulate organic matter associated with cascading appears to enhance the recruitment of this deep-sea living resource, apparently mitigating the general trend of overexploitation. Because cascade of dense water from continental shelves is a global phenomenon, we anticipate that its influence on deep-sea ecosystems and fisheries worldwide should be larger than previously thought. PMID:18197243

Development of deep eutectic solvents applied in extraction and separation.

PubMed

Li, Xiaoxia; Row, Kyung Ho

2016-09-01

Deep eutectic solvents, as an alternative to ionic liquids, have greener credentials than ionic liquids, and have attracted considerable attention in related chemical research. Deep eutectic solvents have attracted increasing attention in chemistry for the extraction and separation of various target compounds from natural products. This review highlights the preparation of deep eutectic solvents, unique properties of deep eutectic solvents, and synthesis of deep-eutectic-solvent-based materials. On the other hand, application in the extraction and separation of deep eutectic solvents is also included in this report. In this paper, the available data and references in this field are reviewed to summarize the applications and developments of deep eutectic solvents. Based on the development of deep eutectic solvents, an exploitation of new deep eutectic solvents and deep eutectic solvents-based materials is expected to diversify into extraction and separation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DEEP UNDERGROUND NEUTRINO EXPERIMENT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, Robert J.

2016-03-03

The Deep Underground Neutrino Experiment (DUNE) collaboration will perform an experiment centered on accelerator-based long-baseline neutrino studies along with nucleon decay and topics in neutrino astrophysics. It will consist of a modular 40-kt (fiducial) mass liquid argon TPC detector located deep underground at the Sanford Underground Research Facility in South Dakota and a high-resolution near detector at Fermilab in Illinois. This conguration provides a 1300-km baseline in a megawatt-scale neutrino beam provided by the Fermilab- hosted international Long-Baseline Neutrino Facility.

Implementation Experience with Deep Discount Fares

DOT National Transportation Integrated Search

1994-09-01

This report reviews the experiences of transit agencies across the country with Deep Discount fares, a new public transit pricing strategy, between 1988 and 1993. Based on new market research findings, Deep Discounting has shown that it is possible t...

Pre-cementation of deep shaft

NASA Astrophysics Data System (ADS)

Heinz, W. F.

1988-12-01

Pre-cementation or pre-grouting of deep shafts in South Africa is an established technique to improve safety and reduce water ingress during shaft sinking. The recent completion of several pre-cementation projects for shafts deeper than 1000m has once again highlighted the effectiveness of pre-grouting of shafts utilizing deep slimline boreholes and incorporating wireline technique for drilling and conventional deep borehole grouting techniques for pre-cementation. Pre-cementation of deep shaft will: (i) Increase the safety of shaft sinking operation (ii) Minimize water and gas inflow during shaft sinking (iii) Minimize the time lost due to additional grouting operations during sinking of the shaft and hence minimize costly delays and standing time of shaft sinking crews and equipment. (iv) Provide detailed information of the geology of the proposed shaft site. Informations on anomalies, dykes, faults as well as reef (gold bearing conglomerates) intersections can be obtained from the evaluation of cores of the pre-cementation boreholes. (v) Provide improved rock strength for excavations in the immediate vicinity of the shaft area. The paper describes pre-cementation techniques recently applied successfully from surface and some conclusions drawn for further considerations.

Deep Space 1 Ion Engine

NASA Image and Video Library

2002-12-21

Kennedy Space Center, Florida. - Deep Space 1 is lifted from its work platform, giving a closeup view of the experimental solar-powered ion propulsion engine. The ion propulsion engine is the first non-chemical propulsion to be used as the primary means of propelling a spacecraft. The first flight in NASA's New Millennium Program, Deep Space 1 is designed to validate 12 new technologies for scientific space missions of the next century. Another onboard experiment includes software that tracks celestial bodies so the spacecraft can make its own navigation decisions without the intervention of ground controllers. Deep Space 1 will complete most of its mission objectives within the first two months, but may also do a flyby of a near-Earth asteroid, 1992 KD, in July 1999. Deep Space 1 will be launched aboard a Boeing Delta 7326 rocket from Launch Pad 17A, Cape Canaveral Air Station, in October. Delta II rockets are medium capacity expendable launch vehicles derived from the Delta family of rockets built and launched since 1960. Since then there have been more than 245 Delta launches. http://photojournal.jpl.nasa.gov/catalog/PIA04232

Deep Pyriform Space: Anatomical Clarifications and Clinical Implications.

PubMed

Surek, Christopher K; Vargo, James; Lamb, Jerome

2016-07-01

The purpose of this study was to define the anatomical boundaries, transformation in the aging face, and clinical implications of the Ristow space. The authors propose a title of deep pyriform space for anatomical continuity. The deep pyriform space was dissected in 12 hemifacial fresh cadaver dissections. Specimens were divided into three separate groups. For group 1, dimensions were measured and plaster molds were fashioned to evaluate shape and contour. For group 2, the space was injected percutaneously with dyed hyaluronic acid to examine proximity relationships to adjacent structures. For group 3, the space was pneumatized to evaluate its cephalic extension. The average dimensions of the deep pyriform space are 1.1 × 0.9 cm. It is bounded medially by the depressor septi nasi and cradled laterally and superficially in a "half-moon" shape by the deep medial cheek fat and lip elevators. The angular artery courses on the roof of the space within a septum between the space and deep medial cheek fat. Pneumatization of the space traverses cephalic to the level of the tear trough ligament in a plane deep to the premaxillary space. The deep pyriform space is a midface cavity cradled by the pyriform aperture and deep medial cheek compartment. Bony recession of the maxilla with age predisposes this space for use as a potential area of deep volumization to support overlying cheek fat and draping lip elevators. The position of the angular artery in the roof of the space allows safe injection on the bone without concern for vascular injury.

Applications of Deep Learning in Biomedicine.

PubMed

Mamoshina, Polina; Vieira, Armando; Putin, Evgeny; Zhavoronkov, Alex

2016-05-02

Increases in throughput and installed base of biomedical research equipment led to a massive accumulation of -omics data known to be highly variable, high-dimensional, and sourced from multiple often incompatible data platforms. While this data may be useful for biomarker identification and drug discovery, the bulk of it remains underutilized. Deep neural networks (DNNs) are efficient algorithms based on the use of compositional layers of neurons, with advantages well matched to the challenges -omics data presents. While achieving state-of-the-art results and even surpassing human accuracy in many challenging tasks, the adoption of deep learning in biomedicine has been comparatively slow. Here, we discuss key features of deep learning that may give this approach an edge over other machine learning methods. We then consider limitations and review a number of applications of deep learning in biomedical studies demonstrating proof of concept and practical utility.

Microbial Life in the Deep Subsurface: Deep, Hot and Radioactive

NASA Technical Reports Server (NTRS)

DeStefano, Andrea L.; Ford, Jill C.; Winsor, Seana K.; Allen, Carlton C.; Miller, Judith; McNamara, Karen M.; Gibson, Everett K., Jr.

2000-01-01

Recent studies, motivated in part by the search for extraterrestrial life, continue to expand the recognized limits of Earth's biosphere. This work explored evidence for life a high-temperature, radioactive environment in the deep subsurface.

Possible seasonality in large deep-focus earthquakes

NASA Astrophysics Data System (ADS)

Zhan, Zhongwen; Shearer, Peter M.

2015-09-01

Large deep-focus earthquakes (magnitude > 7.0, depth > 500 km) have exhibited strong seasonality in their occurrence times since the beginning of global earthquake catalogs. Of 60 such events from 1900 to the present, 42 have occurred in the middle half of each year. The seasonality appears strongest in the northwest Pacific subduction zones and weakest in the Tonga region. Taken at face value, the surplus of northern hemisphere summer events is statistically significant, but due to the ex post facto hypothesis testing, the absence of seasonality in smaller deep earthquakes, and the lack of a known physical triggering mechanism, we cannot rule out that the observed seasonality is just random chance. However, we can make a testable prediction of seasonality in future large deep-focus earthquakes, which, given likely earthquake occurrence rates, should be verified or falsified within a few decades. If confirmed, deep earthquake seasonality would challenge our current understanding of deep earthquakes.

Deep learning for neuroimaging: a validation study.

PubMed

Plis, Sergey M; Hjelm, Devon R; Salakhutdinov, Ruslan; Allen, Elena A; Bockholt, Henry J; Long, Jeffrey D; Johnson, Hans J; Paulsen, Jane S; Turner, Jessica A; Calhoun, Vince D

2014-01-01

Deep learning methods have recently made notable advances in the tasks of classification and representation learning. These tasks are important for brain imaging and neuroscience discovery, making the methods attractive for porting to a neuroimager's toolbox. Success of these methods is, in part, explained by the flexibility of deep learning models. However, this flexibility makes the process of porting to new areas a difficult parameter optimization problem. In this work we demonstrate our results (and feasible parameter ranges) in application of deep learning methods to structural and functional brain imaging data. These methods include deep belief networks and their building block the restricted Boltzmann machine. We also describe a novel constraint-based approach to visualizing high dimensional data. We use it to analyze the effect of parameter choices on data transformations. Our results show that deep learning methods are able to learn physiologically important representations and detect latent relations in neuroimaging data.

46 CFR 167.40-20 - Deep-sea sounding apparatus.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 7 2014-10-01 2014-10-01 false Deep-sea sounding apparatus. 167.40-20 Section 167.40-20... SHIPS Certain Equipment Requirements § 167.40-20 Deep-sea sounding apparatus. Nautical school ships shall be equipped with an efficient or electronic deep-sea sounding apparatus. The electronic deep-sea...

46 CFR 167.40-20 - Deep-sea sounding apparatus.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 7 2012-10-01 2012-10-01 false Deep-sea sounding apparatus. 167.40-20 Section 167.40-20... SHIPS Certain Equipment Requirements § 167.40-20 Deep-sea sounding apparatus. Nautical school ships shall be equipped with an efficient or electronic deep-sea sounding apparatus. The electronic deep-sea...

46 CFR 167.40-20 - Deep-sea sounding apparatus.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 7 2013-10-01 2013-10-01 false Deep-sea sounding apparatus. 167.40-20 Section 167.40-20... SHIPS Certain Equipment Requirements § 167.40-20 Deep-sea sounding apparatus. Nautical school ships shall be equipped with an efficient or electronic deep-sea sounding apparatus. The electronic deep-sea...

46 CFR 167.40-20 - Deep-sea sounding apparatus.

Code of Federal Regulations, 2011 CFR

2011-10-01

... SHIPS Certain Equipment Requirements § 167.40-20 Deep-sea sounding apparatus. Nautical school ships shall be equipped with an efficient or electronic deep-sea sounding apparatus. The electronic deep-sea... 46 Shipping 7 2011-10-01 2011-10-01 false Deep-sea sounding apparatus. 167.40-20 Section 167.40-20...

46 CFR 167.40-20 - Deep-sea sounding apparatus.

Code of Federal Regulations, 2010 CFR

2010-10-01

... SHIPS Certain Equipment Requirements § 167.40-20 Deep-sea sounding apparatus. Nautical school ships shall be equipped with an efficient or electronic deep-sea sounding apparatus. The electronic deep-sea... 46 Shipping 7 2010-10-01 2010-10-01 false Deep-sea sounding apparatus. 167.40-20 Section 167.40-20...

The study of deep-sea cephalopods.

PubMed

Hoving, Henk-Jan T; Perez, Jose Angel A; Bolstad, Kathrin S R; Braid, Heather E; Evans, Aaron B; Fuchs, Dirk; Judkins, Heather; Kelly, Jesse T; Marian, José E A R; Nakajima, Ryuta; Piatkowski, Uwe; Reid, Amanda; Vecchione, Michael; Xavier, José C C

2014-01-01

"Deep-sea" cephalopods are here defined as cephalopods that spend a significant part of their life cycles outside the euphotic zone. In this chapter, the state of knowledge in several aspects of deep-sea cephalopod research are summarized, including information sources for these animals, diversity and general biogeography and life cycles, including reproduction. Recommendations are made for addressing some of the remaining knowledge deficiencies using a variety of traditional and more recently developed methods. The types of oceanic gear that are suitable for collecting cephalopod specimens and images are reviewed. Many groups of deep-sea cephalopods require taxonomic reviews, ideally based on both morphological and molecular characters. Museum collections play a vital role in these revisions, and novel (molecular) techniques may facilitate new use of old museum specimens. Fundamental life-cycle parameters remain unknown for many species; techniques developed for neritic species that could potentially be applied to deep-sea cephalopods are discussed. Reproductive tactics and strategies in deep-sea cephalopods are very diverse and call for comparative evolutionary and experimental studies, but even in the twenty-first century, mature individuals are still unknown for many species. New insights into diet and trophic position have begun to reveal a more diverse range of feeding strategies than the typically voracious predatory lifestyle known for many cephalopods. Regular standardized deep-sea cephalopod surveys are necessary to provide insight into temporal changes in oceanic cephalopod populations and to forecast, verify and monitor the impacts of global marine changes and human impacts on these populations. © 2014 Elsevier Ltd All rights reserved.

Life Support for Deep Space and Mars

NASA Technical Reports Server (NTRS)

Jones, Harry W.; Hodgson, Edward W.; Kliss, Mark H.

2014-01-01

How should life support for deep space be developed? The International Space Station (ISS) life support system is the operational result of many decades of research and development. Long duration deep space missions such as Mars have been expected to use matured and upgraded versions of ISS life support. Deep space life support must use the knowledge base incorporated in ISS but it must also meet much more difficult requirements. The primary new requirement is that life support in deep space must be considerably more reliable than on ISS or anywhere in the Earth-Moon system, where emergency resupply and a quick return are possible. Due to the great distance from Earth and the long duration of deep space missions, if life support systems fail, the traditional approaches for emergency supply of oxygen and water, emergency supply of parts, and crew return to Earth or escape to a safe haven are likely infeasible. The Orbital Replacement Unit (ORU) maintenance approach used by ISS is unsuitable for deep space with ORU's as large and complex as those originally provided in ISS designs because it minimizes opportunities for commonality of spares, requires replacement of many functional parts with each failure, and results in substantial launch mass and volume penalties. It has become impractical even for ISS after the shuttle era, resulting in the need for ad hoc repair activity at lower assembly levels with consequent crew time penalties and extended repair timelines. Less complex, more robust technical approaches may be needed to meet the difficult deep space requirements for reliability, maintainability, and reparability. Developing an entirely new life support system would neglect what has been achieved. The suggested approach is use the ISS life support technologies as a platform to build on and to continue to improve ISS subsystems while also developing new subsystems where needed to meet deep space requirements.

Effect of flow rate, duty cycle, amplitude, and treatment Time of ultrasonic regimens towards Escherichia coli harbouring lipase

NASA Astrophysics Data System (ADS)

Omar, W. S. A. W.; Sulaiman, A. Z.; Ajit, A.; Chisti, Y.; Chor, A. L. T.

2017-06-01

A full factorial design (FFD) approach was conducted to assess the effect of four factors, namely flow rate, duty cycle, amplitude, and treatment time of ultrasonic regimens towards Escherichia coli harbouring lipase. The 22 experiments were performed as the following values with six replicates of centre point: flow rate (0.1, 0.2, and 0.3 L/min), duty cycle (0, 20, and 40 ), amplitude (2, 6, and 10), and treatment time (10, 35, and 60 min). The FFD was employed as preliminary screening in shake flask cultivation to choose the significant factors (P< 0.05) for further optimisation process. In this study, zero duty cycle signified non-sonication of amplitude and no treatment time effect to the E. coli culture. Also, the designated flow rate and amplitude accordingly showed no effect towards the amount of dry cells weight (DCW). DCW1 was found significantly degraded after the exposure of high duty cycle and treatment time as other factors remained constant. Whereas for the lipase activity, no significant difference was observed in any main factors or interactions. Paired samples t-test confirms the result at a p-value of 0.625. This experimental study suggests the direct and continuous approach of sonication caused an adverse effect on the cells culture density.

Practice It: Deep Conscious Breathing Exercise

Cancer.gov

No time to sit and breathe? No problem; take your breathing practice with you! Deep conscious breathing can also be done with the eyes open wherever you happen to be—simply pause and take two to three full deep breaths (inhale deeply and exhale completely).

Deep Sea Actinomycetes and Their Secondary Metabolites

PubMed Central

Kamjam, Manita; Sivalingam, Periyasamy; Deng, Zinxin; Hong, Kui

2017-01-01

Deep sea is a unique and extreme environment. It is a hot spot for hunting marine actinomycetes resources and secondary metabolites. The novel deep sea actinomycete species reported from 2006 to 2016 including 21 species under 13 genera with the maximum number from Microbacterium, followed by Dermacoccus, Streptomyces and Verrucosispora, and one novel species for the other 9 genera. Eight genera of actinomycetes were reported to produce secondary metabolites, among which Streptomyces is the richest producer. Most of the compounds produced by the deep sea actinomycetes presented antimicrobial and anti-cancer cell activities. Gene clusters related to biosynthesis of desotamide, heronamide, and lobophorin have been identified from the deep sea derived Streptomyces. PMID:28507537

DeepMeSH: deep semantic representation for improving large-scale MeSH indexing

PubMed Central

Peng, Shengwen; You, Ronghui; Wang, Hongning; Zhai, Chengxiang; Mamitsuka, Hiroshi; Zhu, Shanfeng

2016-01-01

Motivation: Medical Subject Headings (MeSH) indexing, which is to assign a set of MeSH main headings to citations, is crucial for many important tasks in biomedical text mining and information retrieval. Large-scale MeSH indexing has two challenging aspects: the citation side and MeSH side. For the citation side, all existing methods, including Medical Text Indexer (MTI) by National Library of Medicine and the state-of-the-art method, MeSHLabeler, deal with text by bag-of-words, which cannot capture semantic and context-dependent information well. Methods: We propose DeepMeSH that incorporates deep semantic information for large-scale MeSH indexing. It addresses the two challenges in both citation and MeSH sides. The citation side challenge is solved by a new deep semantic representation, D2V-TFIDF, which concatenates both sparse and dense semantic representations. The MeSH side challenge is solved by using the ‘learning to rank’ framework of MeSHLabeler, which integrates various types of evidence generated from the new semantic representation. Results: DeepMeSH achieved a Micro F-measure of 0.6323, 2% higher than 0.6218 of MeSHLabeler and 12% higher than 0.5637 of MTI, for BioASQ3 challenge data with 6000 citations. Availability and Implementation: The software is available upon request. Contact: zhusf@fudan.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307646

DeepMeSH: deep semantic representation for improving large-scale MeSH indexing.

PubMed

Peng, Shengwen; You, Ronghui; Wang, Hongning; Zhai, Chengxiang; Mamitsuka, Hiroshi; Zhu, Shanfeng

2016-06-15

Medical Subject Headings (MeSH) indexing, which is to assign a set of MeSH main headings to citations, is crucial for many important tasks in biomedical text mining and information retrieval. Large-scale MeSH indexing has two challenging aspects: the citation side and MeSH side. For the citation side, all existing methods, including Medical Text Indexer (MTI) by National Library of Medicine and the state-of-the-art method, MeSHLabeler, deal with text by bag-of-words, which cannot capture semantic and context-dependent information well. We propose DeepMeSH that incorporates deep semantic information for large-scale MeSH indexing. It addresses the two challenges in both citation and MeSH sides. The citation side challenge is solved by a new deep semantic representation, D2V-TFIDF, which concatenates both sparse and dense semantic representations. The MeSH side challenge is solved by using the 'learning to rank' framework of MeSHLabeler, which integrates various types of evidence generated from the new semantic representation. DeepMeSH achieved a Micro F-measure of 0.6323, 2% higher than 0.6218 of MeSHLabeler and 12% higher than 0.5637 of MTI, for BioASQ3 challenge data with 6000 citations. The software is available upon request. zhusf@fudan.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Deep Learning: A Primer for Radiologists.

PubMed

Chartrand, Gabriel; Cheng, Phillip M; Vorontsov, Eugene; Drozdzal, Michal; Turcotte, Simon; Pal, Christopher J; Kadoury, Samuel; Tang, An

2017-01-01

Deep learning is a class of machine learning methods that are gaining success and attracting interest in many domains, including computer vision, speech recognition, natural language processing, and playing games. Deep learning methods produce a mapping from raw inputs to desired outputs (eg, image classes). Unlike traditional machine learning methods, which require hand-engineered feature extraction from inputs, deep learning methods learn these features directly from data. With the advent of large datasets and increased computing power, these methods can produce models with exceptional performance. These models are multilayer artificial neural networks, loosely inspired by biologic neural systems. Weighted connections between nodes (neurons) in the network are iteratively adjusted based on example pairs of inputs and target outputs by back-propagating a corrective error signal through the network. For computer vision tasks, convolutional neural networks (CNNs) have proven to be effective. Recently, several clinical applications of CNNs have been proposed and studied in radiology for classification, detection, and segmentation tasks. This article reviews the key concepts of deep learning for clinical radiologists, discusses technical requirements, describes emerging applications in clinical radiology, and outlines limitations and future directions in this field. Radiologists should become familiar with the principles and potential applications of deep learning in medical imaging. © RSNA, 2017.

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.

PubMed

Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

2016-01-11

Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

NASA Astrophysics Data System (ADS)

Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

2016-01-01

Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.

Stratification-Based Outlier Detection over the Deep Web.

PubMed

Xian, Xuefeng; Zhao, Pengpeng; Sheng, Victor S; Fang, Ligang; Gu, Caidong; Yang, Yuanfeng; Cui, Zhiming

2016-01-01

For many applications, finding rare instances or outliers can be more interesting than finding common patterns. Existing work in outlier detection never considers the context of deep web. In this paper, we argue that, for many scenarios, it is more meaningful to detect outliers over deep web. In the context of deep web, users must submit queries through a query interface to retrieve corresponding data. Therefore, traditional data mining methods cannot be directly applied. The primary contribution of this paper is to develop a new data mining method for outlier detection over deep web. In our approach, the query space of a deep web data source is stratified based on a pilot sample. Neighborhood sampling and uncertainty sampling are developed in this paper with the goal of improving recall and precision based on stratification. Finally, a careful performance evaluation of our algorithm confirms that our approach can effectively detect outliers in deep web.

Stratification-Based Outlier Detection over the Deep Web

PubMed Central

Xian, Xuefeng; Zhao, Pengpeng; Sheng, Victor S.; Fang, Ligang; Gu, Caidong; Yang, Yuanfeng; Cui, Zhiming

2016-01-01

For many applications, finding rare instances or outliers can be more interesting than finding common patterns. Existing work in outlier detection never considers the context of deep web. In this paper, we argue that, for many scenarios, it is more meaningful to detect outliers over deep web. In the context of deep web, users must submit queries through a query interface to retrieve corresponding data. Therefore, traditional data mining methods cannot be directly applied. The primary contribution of this paper is to develop a new data mining method for outlier detection over deep web. In our approach, the query space of a deep web data source is stratified based on a pilot sample. Neighborhood sampling and uncertainty sampling are developed in this paper with the goal of improving recall and precision based on stratification. Finally, a careful performance evaluation of our algorithm confirms that our approach can effectively detect outliers in deep web. PMID:27313603

Eric Davidson and deep time.

PubMed

Erwin, Douglas H

2017-10-13

Eric Davidson had a deep and abiding interest in the role developmental mechanisms played in generating evolutionary patterns documented in deep time, from the origin of the euechinoids to the processes responsible for the morphological architectures of major animal clades. Although not an evolutionary biologist, Davidson's interests long preceded the current excitement over comparative evolutionary developmental biology. Here I discuss three aspects at the intersection between his research and evolutionary patterns in deep time: First, understanding the mechanisms of body plan formation, particularly those associated with the early diversification of major metazoan clades. Second, a critique of early claims about ancestral metazoans based on the discoveries of highly conserved genes across bilaterian animals. Third, Davidson's own involvement in paleontology through a collaborative study of the fossil embryos from the Ediacaran Doushantuo Formation in south China.

Project DEEP STEAM

NASA Astrophysics Data System (ADS)

Aeschliman, D. P.; Clay, R. G.; Donaldson, A. B.; Eisenhawer, S. W.; Fox, R. L.; Johnson, D. R.; Mulac, A. J.

1982-01-01

The objective of Project DEEP STEAM is to develop the technology to economically produce heavy oils from deep reservoirs. The tasks included in this project are the development of thermally efficient delivery systems and downhole steam generation systems. During the period January 1-March 31, 1981, effort has continued on a low pressure combustion downhole generator (Rocketdyne), and on two high pressure designs (Foster-Miller Associates, Sandia National Laboratories). The Sandia design was prepared for deployment in the Wilmington Field at Long Beach, California. Progress continued on the Min-Stress II packer concept at L'Garde, Inc., and on the extruded metal packer at Foster-Miller. Initial bare string field data are reported on the insulated tubular test at Lloydminster, Saskatchewan, Canada.

Deep Crustal Melting and the Survival of Continental Crust

NASA Astrophysics Data System (ADS)

Whitney, D.; Teyssier, C. P.; Rey, P. F.; Korchinski, M.

2017-12-01

Plate convergence involving continental lithosphere leads to crustal melting, which ultimately stabilizes the crust because it drives rapid upward flow of hot deep crust, followed by rapid cooling at shallow levels. Collision drives partial melting during crustal thickening (at 40-75 km) and/or continental subduction (at 75-100 km). These depths are not typically exceeded by crustal rocks that are exhumed in each setting because partial melting significantly decreases viscosity, facilitating upward flow of deep crust. Results from numerical models and nature indicate that deep crust moves laterally and then vertically, crystallizing at depths as shallow as 2 km. Deep crust flows en masse, without significant segregation of melt into magmatic bodies, over 10s of kms of vertical transport. This is a major mechanism by which deep crust is exhumed and is therefore a significant process of heat and mass transfer in continental evolution. The result of vertical flow of deep, partially molten crust is a migmatite dome. When lithosphere is under extension or transtension, the deep crust is solicited by faulting of the brittle upper crust, and the flow of deep crust in migmatite domes traverses nearly the entire thickness of orogenic crust in <10 million years. This cycle of burial, partial melting, rapid ascent, and crystallization/cooling preserves the continents from being recycled into the mantle by convergent tectonic processes over geologic time. Migmatite domes commonly preserve a record of high-T - low-P metamorphism. Domes may also contain rocks or minerals that record high-T - high-P conditions, including high-P metamorphism broadly coeval with host migmatite, evidence for the deep crustal origin of migmatite. There exists a spectrum of domes, from entirely deep-sourced to mixtures of deep and shallow sources. Controlling factors in deep vs. shallow sources are relative densities of crustal layers and rate of extension: fast extension (cm/yr) promotes efficient

DeepAnomaly: Combining Background Subtraction and Deep Learning for Detecting Obstacles and Anomalies in an Agricultural Field.

PubMed

Christiansen, Peter; Nielsen, Lars N; Steen, Kim A; Jørgensen, Rasmus N; Karstoft, Henrik

2016-11-11

Convolutional neural network (CNN)-based systems are increasingly used in autonomous vehicles for detecting obstacles. CNN-based object detection and per-pixel classification (semantic segmentation) algorithms are trained for detecting and classifying a predefined set of object types. These algorithms have difficulties in detecting distant and heavily occluded objects and are, by definition, not capable of detecting unknown object types or unusual scenarios. The visual characteristics of an agriculture field is homogeneous, and obstacles, like people, animals and other obstacles, occur rarely and are of distinct appearance compared to the field. This paper introduces DeepAnomaly, an algorithm combining deep learning and anomaly detection to exploit the homogenous characteristics of a field to perform anomaly detection. We demonstrate DeepAnomaly as a fast state-of-the-art detector for obstacles that are distant, heavily occluded and unknown. DeepAnomaly is compared to state-of-the-art obstacle detectors including "Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks" (RCNN). In a human detector test case, we demonstrate that DeepAnomaly detects humans at longer ranges (45-90 m) than RCNN. RCNN has a similar performance at a short range (0-30 m). However, DeepAnomaly has much fewer model parameters and (182 ms/25 ms =) a 7.28-times faster processing time per image. Unlike most CNN-based methods, the high accuracy, the low computation time and the low memory footprint make it suitable for a real-time system running on a embedded GPU (Graphics Processing Unit).

DeepAnomaly: Combining Background Subtraction and Deep Learning for Detecting Obstacles and Anomalies in an Agricultural Field

PubMed Central

Christiansen, Peter; Nielsen, Lars N.; Steen, Kim A.; Jørgensen, Rasmus N.; Karstoft, Henrik

2016-01-01

Convolutional neural network (CNN)-based systems are increasingly used in autonomous vehicles for detecting obstacles. CNN-based object detection and per-pixel classification (semantic segmentation) algorithms are trained for detecting and classifying a predefined set of object types. These algorithms have difficulties in detecting distant and heavily occluded objects and are, by definition, not capable of detecting unknown object types or unusual scenarios. The visual characteristics of an agriculture field is homogeneous, and obstacles, like people, animals and other obstacles, occur rarely and are of distinct appearance compared to the field. This paper introduces DeepAnomaly, an algorithm combining deep learning and anomaly detection to exploit the homogenous characteristics of a field to perform anomaly detection. We demonstrate DeepAnomaly as a fast state-of-the-art detector for obstacles that are distant, heavily occluded and unknown. DeepAnomaly is compared to state-of-the-art obstacle detectors including “Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks” (RCNN). In a human detector test case, we demonstrate that DeepAnomaly detects humans at longer ranges (45–90 m) than RCNN. RCNN has a similar performance at a short range (0–30 m). However, DeepAnomaly has much fewer model parameters and (182 ms/25 ms =) a 7.28-times faster processing time per image. Unlike most CNN-based methods, the high accuracy, the low computation time and the low memory footprint make it suitable for a real-time system running on a embedded GPU (Graphics Processing Unit). PMID:27845717

Deep Space Earth Observations from DSCOVR

NASA Astrophysics Data System (ADS)

Marshak, A.; Herman, J.

2018-02-01

The Deep Space Climate Observatory (DSCOVR) at Sun-Earth L1 orbit observes the full sunlit disk of Earth. There are two Earth science instruments on board DSCOVR — EPIC and NISTAR. We discuss if EPIC and NISAR-like instruments can be used in Deep Space Gateway.

The Deep Space Atomic Clock Mission

NASA Technical Reports Server (NTRS)

Ely, Todd A.; Koch, Timothy; Kuang, Da; Lee, Karen; Murphy, David; Prestage, John; Tjoelker, Robert; Seubert, Jill

2012-01-01

The Deep Space Atomic Clock (DSAC) mission will demonstrate the space flight performance of a small, low-mass, high-stability mercury-ion atomic clock with long term stability and accuracy on par with that of the Deep Space Network. The timing stability introduced by DSAC allows for a 1-Way radiometric tracking paradigm for deep space navigation, with benefits including increased tracking via utilization of the DSN's Multiple Spacecraft Per Aperture (MSPA) capability and full ground station-spacecraft view periods, more accurate radio occultation signals, decreased single-frequency measurement noise, and the possibility for fully autonomous on-board navigation. Specific examples of navigation and radio science benefits to deep space missions are highlighted through simulations of Mars orbiter and Europa flyby missions. Additionally, this paper provides an overview of the mercury-ion trap technology behind DSAC, details of and options for the upcoming 2015/2016 space demonstration, and expected on-orbit clock performance.

Ubiquitous healthy diatoms in the deep sea confirms deep carbon injection by the biological pump

NASA Astrophysics Data System (ADS)

Agustí, Susana; González-Gordillo, Jose I.; Vaqué, Dolors; Estrada, Marta; Cerezo, Maria I.; Salazar, Guillem; Gasol, Josep M.; Duarte, Carlos M.

2016-04-01

The role of the ocean as a sink for CO2 is partially dependent on the downward transport of phytoplankton cells packaged within fast-sinking particles. However, whether such fast-sinking mechanisms deliver fresh organic carbon down to the deep bathypelagic sea and whether this mechanism is prevalent across the ocean awaits confirmation. Photosynthetic plankton, directly responsible for trapping CO2 in organic form in the surface layer, are a key constituent of the flux of sinking particles and are assumed to die and become detritus upon leaving the photic layer. Research in the 1960-70's reported the occasional presence of well-preserved phytoplankton cells in the deep ocean, but these observations, which could signal at rapid sinking rates, were considered anecdotal. Using new developments we tested the presence of healthy phytoplankton cells in the deep sea (2000 to 4000 m depth) along the Malaspina 2010 Circumnavigation Expedition, a global expedition sampling the bathypelagic zone of the Atlantic, Indian and Pacific Oceans. In particular, we used a new microplankton sampling device, the Bottle-Net, 16S rDNA sequences, flow cytometric counts, vital stains and experiments to explore the abundance and health status of photosynthetic plankton cells between 2,000 and 4,000 m depth along the Circumnavigation track. We described the community of microplankton (> 20μm) found at the deep ocean (2000-4000 m depth), surprisingly dominated by phytoplankton, and within this, by diatoms. Moreover, we report the ubiquitous presence of healthy photosynthetic cells, dominated by diatoms, down to 4,000 m in the deep dark sea. Decay experiments with surface phytoplankton suggested that the large proportion (18%) of healthy photosynthetic cells observed, on average, in the dark ocean, requires transport times from few days to few weeks, corresponding to sinking rates of 124 to 732 m d-1, comparable to those of fast sinking aggregates and faecal pellets. These results confirm the

1. Deep Creek Road, picnic pavilion Great Smoky Mountains ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. Deep Creek Road, picnic pavilion - Great Smoky Mountains National Park Roads & Bridges, Deep Creek Road, Between Park Boundary near Bryson City & Deep Creek Campground, Gatlinburg, Sevier County, TN

Challenging Oil Bioremediation at Deep-Sea Hydrostatic Pressure

PubMed Central

Scoma, Alberto; Yakimov, Michail M.; Boon, Nico

2016-01-01

The Deepwater Horizon accident has brought oil contamination of deep-sea environments to worldwide attention. The risk for new deep-sea spills is not expected to decrease in the future, as political pressure mounts to access deep-water fossil reserves, and poorly tested technologies are used to access oil. This also applies to the response to oil-contamination events, with bioremediation the only (bio)technology presently available to combat deep-sea spills. Many questions about the fate of petroleum-hydrocarbons within deep-sea environments remain unanswered, as well as the main constraints limiting bioremediation under increased hydrostatic pressures and low temperatures. The microbial pathways fueling oil bioassimilation are unclear, and the mild upregulation observed for beta-oxidation-related genes in both water and sediments contrasts with the high amount of alkanes present in the spilled oil. The fate of solid alkanes (tar), hydrocarbon degradation rates and the reason why the most predominant hydrocarbonoclastic genera were not enriched at deep-sea despite being present at hydrocarbon seeps at the Gulf of Mexico have been largely overlooked. This mini-review aims at highlighting the missing information in the field, proposing a holistic approach where in situ and ex situ studies are integrated to reveal the principal mechanisms accounting for deep-sea oil bioremediation. PMID:27536290

Text feature extraction based on deep learning: a review.

PubMed

Liang, Hong; Sun, Xiao; Sun, Yunlei; Gao, Yuan

2017-01-01

Selection of text feature item is a basic and important matter for text mining and information retrieval. Traditional methods of feature extraction require handcrafted features. To hand-design, an effective feature is a lengthy process, but aiming at new applications, deep learning enables to acquire new effective feature representation from training data. As a new feature extraction method, deep learning has made achievements in text mining. The major difference between deep learning and conventional methods is that deep learning automatically learns features from big data, instead of adopting handcrafted features, which mainly depends on priori knowledge of designers and is highly impossible to take the advantage of big data. Deep learning can automatically learn feature representation from big data, including millions of parameters. This thesis outlines the common methods used in text feature extraction first, and then expands frequently used deep learning methods in text feature extraction and its applications, and forecasts the application of deep learning in feature extraction.

Tractography patterns of subthalamic nucleus deep brain stimulation.

PubMed

Vanegas-Arroyave, Nora; Lauro, Peter M; Huang, Ling; Hallett, Mark; Horovitz, Silvina G; Zaghloul, Kareem A; Lungu, Codrin

2016-04-01

Deep brain stimulation therapy is an effective symptomatic treatment for Parkinson's disease, yet the precise mechanisms responsible for its therapeutic effects remain unclear. Although the targets of deep brain stimulation are grey matter structures, axonal modulation is known to play an important role in deep brain stimulation's therapeutic mechanism. Several white matter structures in proximity to the subthalamic nucleus have been implicated in the clinical benefits of deep brain stimulation for Parkinson's disease. We assessed the connectivity patterns that characterize clinically beneficial electrodes in Parkinson's disease patients, after deep brain stimulation of the subthalamic nucleus. We evaluated 22 patients with Parkinson's disease (11 females, age 57 ± 9.1 years, disease duration 13.3 ± 6.3 years) who received bilateral deep brain stimulation of the subthalamic nucleus at the National Institutes of Health. During an initial electrode screening session, one month after deep brain stimulation implantation, the clinical benefits of each contact were determined. The electrode was localized by coregistering preoperative magnetic resonance imaging and postoperative computer tomography images and the volume of tissue activated was estimated from stimulation voltage and impedance. Brain connectivity for the volume of tissue activated of deep brain stimulation contacts was assessed using probabilistic tractography with diffusion-tensor data. Areas most frequently connected to clinically effective contacts included the thalamus, substantia nigra, brainstem and superior frontal gyrus. A series of discriminant analyses demonstrated that the strength of connectivity to the superior frontal gyrus and the thalamus were positively associated with clinical effectiveness. The connectivity patterns observed in our study suggest that the modulation of white matter tracts directed to the superior frontal gyrus and the thalamus is associated with favourable clinical

2. Deep Creek Road, old bridge at campground entrance. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

2. Deep Creek Road, old bridge at campground entrance. - Great Smoky Mountains National Park Roads & Bridges, Deep Creek Road, Between Park Boundary near Bryson City & Deep Creek Campground, Gatlinburg, Sevier County, TN

Innovations in deep brain stimulation methodology.

PubMed

Kühn, Andrea A; Volkmann, Jens

2017-01-01

Deep brain stimulation is a powerful clinical method for movement disorders that no longer respond satisfactorily to pharmacological management, but its progress has been hampered by stagnation in technological procedure solutions and device development. Recently, the combined research efforts of bioengineers, neuroscientists, and clinicians have helped to better understand the mechanisms of deep brain stimulation, and solutions for the translational roadblock are emerging. Here, we define the needs for methodological advances in deep brain stimulation from a neurophysiological perspective and describe technological solutions that are currently evaluated for near-term clinical application. © 2016 International Parkinson and Movement Disorder Society. © 2016 International Parkinson and Movement Disorder Society.

In Brief: Deep-sea observatory

NASA Astrophysics Data System (ADS)

Showstack, Randy

2008-11-01

The first deep-sea ocean observatory offshore of the continental United States has begun operating in the waters off central California. The remotely operated Monterey Accelerated Research System (MARS) will allow scientists to monitor the deep sea continuously. Among the first devices to be hooked up to the observatory are instruments to monitor earthquakes, videotape deep-sea animals, and study the effects of acidification on seafloor animals. ``Some day we may look back at the first packets of data streaming in from the MARS observatory as the equivalent of those first words spoken by Alexander Graham Bell: `Watson, come here, I need you!','' commented Marcia McNutt, president and CEO of the Monterey Bay Aquarium Research Institute, which coordinated construction of the observatory. For more information, see http://www.mbari.org/news/news_releases/2008/mars-live/mars-live.html.

Deep Learning for Computer Vision: A Brief Review

PubMed Central

Doulamis, Nikolaos; Doulamis, Anastasios; Protopapadakis, Eftychios

2018-01-01

Over the last years deep learning methods have been shown to outperform previous state-of-the-art machine learning techniques in several fields, with computer vision being one of the most prominent cases. This review paper provides a brief overview of some of the most significant deep learning schemes used in computer vision problems, that is, Convolutional Neural Networks, Deep Boltzmann Machines and Deep Belief Networks, and Stacked Denoising Autoencoders. A brief account of their history, structure, advantages, and limitations is given, followed by a description of their applications in various computer vision tasks, such as object detection, face recognition, action and activity recognition, and human pose estimation. Finally, a brief overview is given of future directions in designing deep learning schemes for computer vision problems and the challenges involved therein. PMID:29487619

Is deep dreaming the new collage?

NASA Astrophysics Data System (ADS)

Boden, Margaret A.

2017-10-01

Deep dreaming (DD) can combine and transform images in surprising ways. But, being based in deep learning (DL), it is not analytically understood. Collage is an art form that is constrained along various dimensions. DD will not be able to generate collages until DL can be guided in a disciplined fashion.

Possible Causes of a Harbour Porpoise Mass Stranding in Danish Waters in 2005

PubMed Central

Wright, Andrew J.; Maar, Marie; Mohn, Christian; Nabe-Nielsen, Jacob; Siebert, Ursula; Jensen, Lasse Fast; Baagøe, Hans J.; Teilmann, Jonas

2013-01-01

An unprecedented 85 harbour porpoises stranded freshly dead along approximately 100 km of Danish coastline from 7–15 April, 2005. This total is considerably above the mean weekly stranding rate for the whole of Denmark, both for any time of year, 1.23 animals/week (ranging from 0 to 20 during 2003–2008, excluding April 2005), and specifically in April, 0.65 animals/week (0 to 4, same period). Bycatch was established as the cause of death for most of the individuals through typical indications of fisheries interactions, including net markings in the skin and around the flippers, and loss of tail flukes. Local fishermen confirmed unusually large porpoise bycatch in nets set for lumpfish (Cyclopterus lumpus) and the strandings were attributed to an early lumpfish season. However, lumpfish catches for 2005 were not unusual in terms of season onset, peak or total catch, when compared to 2003–2008. Consequently, human activity was combined with environmental factors and the variation in Danish fisheries landings (determined through a principal component analysis) in a two-part statistical model to assess the correlation of these factors with both the presence of fresh strandings and the numbers of strandings on the Danish west coast. The final statistical model (which was forward selected using Akaike information criterion; AIC) indicated that naval presence is correlated with higher rates of porpoise strandings, particularly in combination with certain fisheries, although it is not correlated with the actual presence of strandings. Military vessels from various countries were confirmed in the area from the 7th April, en route to the largest naval exercise in Danish waters to date (Loyal Mariner 2005, 11–28 April). Although sonar usage cannot be confirmed, it is likely that ships were testing various equipment prior to the main exercise. Thus naval activity cannot be ruled out as a possible contributing factor. PMID:23460787

Warming trend in the western Mediterranean deep water

NASA Astrophysics Data System (ADS)

Bethoux, J. P.; Gentili, B.; Raunet, J.; Tailliez, D.

1990-10-01

THE western Mediterranean Sea comprises three water masses: a surface layer (from 0 to ~150 m depth), an intermediate layer (~150-400 m) issuing from the eastern basin, and a deep water mass at depths below 400 m. The deep water is homogeneous and has maintained a more or less constant temperature and salinity from the start of the century until recently1. Here we report measurements from the Medatlante cruises of December 1988 and August 1989, which show the deep layer to be 0.12 °C warmer and ~0.03 p.s.u. more saline than in 1959. Taking these data together with those from earlier cruises, we find a trend of continuously increasing temperatures over the past three decades. These deep-water records reflect the averaged evolution of climate conditions at the surface during the winter, when the deep water is formed. Consideration of the heat budget and water flux in the Mediterranean2,3 leads to the possibility that the deep-water temperature trend may be the result of greenhouse-gas-induced local warming.

Deep-Plane Lipoabdominoplasty in East Asians

PubMed Central

Jang, Jun-Young; Hong, Yoon Gi; Sim, Hyung Bo; Sun, Sang Hoon

2016-01-01

Background The objective of this study was to develop a new surgical technique by combining traditional abdominoplasty with liposuction. This combination of operations permits simpler and more accurate management of various abdominal deformities. In lipoabdominoplasty, the combination of techniques is of paramount concern. Herein, we introduce a new combination of liposuction and abdominoplasty using deep-plane flap sliding to maximize the benefits of both techniques. Methods Deep-plane lipoabdominoplasty was performed in 143 patients between January 2007 and May 2014. We applied extensive liposuction on the entire abdomen followed by a sliding flap through the deep plane after repairing the diastasis recti. The abdominal wound closure was completed with repair of Scarpa's fascia. Results The average amount of liposuction aspirate was 1,400 mL (700–3,100 mL), and the size of the average excised skin ellipse was 21.78×12.81 cm (from 15×10 to 25×15 cm). There were no major complications such as deep-vein thrombosis or pulmonary embolism. We encountered 22 cases of minor complications: one wound infection, one case of skin necrosis, two cases of undercorrection, nine hypertrophic scars, and nine seromas. These complications were solved by conservative management or simple revision. Conclusions The use of deep-plane lipoabdominoplasty can correct abdominal deformities more effectively and with fewer complications than traditional abdominoplasty. PMID:27462568

Deep Carbon Observatory investigates Carbon from Crust to Core: An Academic Record of the History of Deep Carbon Science

NASA Astrophysics Data System (ADS)

Mitton, S. A.

2017-12-01

Carbon plays an unparalleled role in our lives: as the element of life, as the basis of most of society's energy, as the backbone of most new materials, and as the central focus in efforts to understand Earth's variable and uncertain climate. Yet in spite of carbon's importance, scientists remain largely ignorant of the physical, chemical, and biological behavior of many of Earth's carbon-bearing systems. The Deep Carbon Observatory (DCO) is a global research program to transform our understanding of carbon in Earth. At its heart, DCO is a community of scientists, from biologists to physicists, geoscientists to chemists, and many others whose work crosses these disciplinary lines, forging a new, integrative field of deep carbon science. As a historian of science, I specialise in the history of planetary science and astronomy since 1900. This is directed toward understanding of the history of the steps on the road to discovering the internal dynamics of our planet. Within a framework that describes the historical background to the new field of Earth System Science, I present the first history of deep carbon science. This project will identifies the key discoveries of deep carbon science. It will assess the impact of new knowledge on geochemistry, geodynamics, and geobiology. The project will lead to publication, in book form in 2019, of an illuminating narrative that will highlight the engaging human stories of many remarkable scientists and natural philosophers from whom we have learned about the complexity of Earth's internal world. On this journey of discovery we will encounter not just the pioneering researchers of deep carbon science, but also their institutions, their instrumental inventiveness, and their passion for exploration. The book is organised thematically around the four communities of the Deep Carbon Observatory: Deep Life, Extreme Physics and Chemistry, Reservoirs and Fluxes, and Deep Energy. The presentation has a gallery and list of Deep Carbon

Electron paramagnetic resonance of deep boron in silicon carbide

NASA Astrophysics Data System (ADS)

Baranov, P. G.; Mokhov, E. N.

1996-04-01

In this article we report the first EPR observation of deep boron centres in silicon carbide. A direct identification of the boron atom involved in the defect centre, considered as deep boron, has been established by the presence of a hyperfine interaction with 0268-1242/11/4/005/img1 and 0268-1242/11/4/005/img2 nuclei in isotope-enriched 6H-SiC:B crystals. Deep boron centres were shown from EPR spectra to have axial symmetry along the hexagonal axis. A correspondence between the EPR spectra and the luminescence, ODMR and DLTS spectra of deep boron centres has been indicated. The structural model for a deep boron centre as a boron - vacancy pair is presented and the evidence for bistable behaviour of deep boron centres is discussed.

DeepText2GO: Improving large-scale protein function prediction with deep semantic text representation.

PubMed

You, Ronghui; Huang, Xiaodi; Zhu, Shanfeng

2018-06-06

As of April 2018, UniProtKB has collected more than 115 million protein sequences. Less than 0.15% of these proteins, however, have been associated with experimental GO annotations. As such, the use of automatic protein function prediction (AFP) to reduce this huge gap becomes increasingly important. The previous studies conclude that sequence homology based methods are highly effective in AFP. In addition, mining motif, domain, and functional information from protein sequences has been found very helpful for AFP. Other than sequences, alternative information sources such as text, however, may be useful for AFP as well. Instead of using BOW (bag of words) representation in traditional text-based AFP, we propose a new method called DeepText2GO that relies on deep semantic text representation, together with different kinds of available protein information such as sequence homology, families, domains, and motifs, to improve large-scale AFP. Furthermore, DeepText2GO integrates text-based methods with sequence-based ones by means of a consensus approach. Extensive experiments on the benchmark dataset extracted from UniProt/SwissProt have demonstrated that DeepText2GO significantly outperformed both text-based and sequence-based methods, validating its superiority. Copyright © 2018 Elsevier Inc. All rights reserved.

DEEP: a general computational framework for predicting enhancers

PubMed Central

Kleftogiannis, Dimitrios; Kalnis, Panos; Bajic, Vladimir B.

2015-01-01

Transcription regulation in multicellular eukaryotes is orchestrated by a number of DNA functional elements located at gene regulatory regions. Some regulatory regions (e.g. enhancers) are located far away from the gene they affect. Identification of distal regulatory elements is a challenge for the bioinformatics research. Although existing methodologies increased the number of computationally predicted enhancers, performance inconsistency of computational models across different cell-lines, class imbalance within the learning sets and ad hoc rules for selecting enhancer candidates for supervised learning, are some key questions that require further examination. In this study we developed DEEP, a novel ensemble prediction framework. DEEP integrates three components with diverse characteristics that streamline the analysis of enhancer's properties in a great variety of cellular conditions. In our method we train many individual classification models that we combine to classify DNA regions as enhancers or non-enhancers. DEEP uses features derived from histone modification marks or attributes coming from sequence characteristics. Experimental results indicate that DEEP performs better than four state-of-the-art methods on the ENCODE data. We report the first computational enhancer prediction results on FANTOM5 data where DEEP achieves 90.2% accuracy and 90% geometric mean (GM) of specificity and sensitivity across 36 different tissues. We further present results derived using in vivo-derived enhancer data from VISTA database. DEEP-VISTA, when tested on an independent test set, achieved GM of 80.1% and accuracy of 89.64%. DEEP framework is publicly available at http://cbrc.kaust.edu.sa/deep/. PMID:25378307

Ultra-Deep Drilling Cost Reduction; Design and Fabrication of an Ultra-Deep Drilling Simulator (UDS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindstrom, Jason

2010-01-31

Ultra-deep drilling, below about 20,000 ft (6,096 m), is extremely expensive and limits the recovery of hydrocarbons at these depths. Unfortunately, rock breakage and cuttings removal under these conditions is not understood. To better understand and thus reduce cost at these conditions an ultra-deep single cutter drilling simulator (UDS) capable of drill cutter and mud tests to sustained pressure and temperature of 30,000 psi (207 MPa) and 482 °F (250 °C), respectively, was designed and manufactured at TerraTek, a Schlumberger company, in cooperation with the Department of Energy’s National Energy Technology Laboratory. UDS testing under ultra-deep drilling conditions offers anmore » economical alternative to high day rates and can prove or disprove the viability of a particular drilling technique or fluid to provide opportunity for future domestic energy needs.« less

30 CFR 203.42 - What conditions and limitations apply to royalty relief for deep wells and phase 1 ultra-deep wells?

Code of Federal Regulations, 2013 CFR

2013-07-01

... or deeper, your lease cannot earn an RSV under § 203.41 as a result of drilling any subsequent deep wells or phase 1 ultra-deep wells. (b) You determine RSV under § 203.41 for the first qualified deep... wells, that determination establishes the total RSV available for that drilling depth interval on your...

30 CFR 203.42 - What conditions and limitations apply to royalty relief for deep wells and phase 1 ultra-deep wells?

Code of Federal Regulations, 2014 CFR

2014-07-01

... or deeper, your lease cannot earn an RSV under § 203.41 as a result of drilling any subsequent deep wells or phase 1 ultra-deep wells. (b) You determine RSV under § 203.41 for the first qualified deep... wells, that determination establishes the total RSV available for that drilling depth interval on your...

30 CFR 203.42 - What conditions and limitations apply to royalty relief for deep wells and phase 1 ultra-deep wells?

Code of Federal Regulations, 2012 CFR

2012-07-01

... or deeper, your lease cannot earn an RSV under § 203.41 as a result of drilling any subsequent deep wells or phase 1 ultra-deep wells. (b) You determine RSV under § 203.41 for the first qualified deep... wells, that determination establishes the total RSV available for that drilling depth interval on your...

DEWS (DEep White matter hyperintensity Segmentation framework): A fully automated pipeline for detecting small deep white matter hyperintensities in migraineurs.

PubMed

Park, Bo-Yong; Lee, Mi Ji; Lee, Seung-Hak; Cha, Jihoon; Chung, Chin-Sang; Kim, Sung Tae; Park, Hyunjin

2018-01-01

Migraineurs show an increased load of white matter hyperintensities (WMHs) and more rapid deep WMH progression. Previous methods for WMH segmentation have limited efficacy to detect small deep WMHs. We developed a new fully automated detection pipeline, DEWS (DEep White matter hyperintensity Segmentation framework), for small and superficially-located deep WMHs. A total of 148 non-elderly subjects with migraine were included in this study. The pipeline consists of three components: 1) white matter (WM) extraction, 2) WMH detection, and 3) false positive reduction. In WM extraction, we adjusted the WM mask to re-assign misclassified WMHs back to WM using many sequential low-level image processing steps. In WMH detection, the potential WMH clusters were detected using an intensity based threshold and region growing approach. For false positive reduction, the detected WMH clusters were classified into final WMHs and non-WMHs using the random forest (RF) classifier. Size, texture, and multi-scale deep features were used to train the RF classifier. DEWS successfully detected small deep WMHs with a high positive predictive value (PPV) of 0.98 and true positive rate (TPR) of 0.70 in the training and test sets. Similar performance of PPV (0.96) and TPR (0.68) was attained in the validation set. DEWS showed a superior performance in comparison with other methods. Our proposed pipeline is freely available online to help the research community in quantifying deep WMHs in non-elderly adults.

Challenging the paradigms of deep-sea ecology.

PubMed

Danovaro, Roberto; Snelgrove, Paul V R; Tyler, Paul

2014-08-01

Deep-sea ecosystems represent Earth's major ecological research frontier. Focusing on seafloor ecosystems, we demonstrate how new technologies underpin discoveries that challenge major ecological hypotheses and paradigms, illuminating new deep-sea geosphere-biosphere interactions. We now recognize greater habitat complexity, new ecological interactions and the importance of 'dark energy', and chemosynthetic production in fuelling biodiversity. We also acknowledge functional hotspots that contradict a food-poor, metabolically inactive, and minor component of global carbon cycles. Symbioses appear widespread, revealing novel adaptations. Populations show complex spatial structure and evolutionary histories. These new findings redefine deep-sea ecology and the role of Earth's largest biome in global biosphere functioning. Indeed, deep-sea exploration can open new perspectives in ecological research to help mitigate exploitation impacts. Copyright © 2014 Elsevier Ltd. All rights reserved.

Hot and sour in the deep ocean

NASA Astrophysics Data System (ADS)

Sabine, Christopher L.

2017-12-01

Stable layering in the ocean limits the rate that human-derived carbon dioxide can acidify the deep ocean. Now observations show that ocean warming, however, can enhance deep-ocean acidification through increased organic matter decomposition.

DEEP: Database of Energy Efficiency Performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Tianzhen; Piette, Mary; Lee, Sang Hoon

A database of energy efficiency performance (DEEP) is a presimulated database to enable quick and accurate assessment of energy retrofit of commercial buildings. DEEP was compiled from results of about 10 million EnergyPlus simulations. DEEP provides energy savings for screening and evaluation of retrofit measures targeting the small and medium-sized office and retail buildings in California. The prototype building models are developed for a comprehensive assessment of building energy performance based on DOE commercial reference buildings and the California DEER [sic] prototype buildings. The prototype buildings represent seven building types across six vintages of constructions and 16 California climate zones.more » DEEP uses these prototypes to evaluate energy performance of about 100 energy conservation measures covering envelope, lighting, heating, ventilation, air conditioning, plug loads, and domestic hot war. DEEP consists the energy simulation results for individual retrofit measures as well as packages of measures to consider interactive effects between multiple measures. The large scale EnergyPlus simulations are being conducted on the super computers at the National Energy Research Scientific Computing Center (NERSC) of Lawrence Berkeley National Laboratory. The pre-simulation database is a part of the CEC PIER project to develop a web-based retrofit toolkit for small and medium-sized commercial buildings in California, which provides real-time energy retrofit feedback by querying DEEP with recommended measures, estimated energy savings and financial payback period based on users' decision criteria of maximizing energy savings, energy cost savings, carbon reduction, or payback of investment. The pre-simulated database and associated comprehensive measure analysis enhances the ability to performance assessments of retrofits to reduce energy use for small and medium buildings and business owners who typically do not have resources to conduct costly

30 CFR 203.42 - What conditions and limitations apply to royalty relief for deep wells and phase 1 ultra-deep wells?

Code of Federal Regulations, 2010 CFR

2010-07-01

... ROYALTY RATES OCS Oil, Gas, and Sulfur General Royalty Relief for Drilling Deep Gas Wells on Leases Not... royalty relief under § 203.41. If . . . Then . . . (a) Your lease has produced gas or oil from a well with... RSV under § 203.41 as a result of drilling any subsequent deep wells or phase 1 ultra-deep wells. (b...

The dynamics of biogeographic ranges in the deep sea.

PubMed

McClain, Craig R; Hardy, Sarah Mincks

2010-12-07

Anthropogenic disturbances such as fishing, mining, oil drilling, bioprospecting, warming, and acidification in the deep sea are increasing, yet generalities about deep-sea biogeography remain elusive. Owing to the lack of perceived environmental variability and geographical barriers, ranges of deep-sea species were traditionally assumed to be exceedingly large. In contrast, seamount and chemosynthetic habitats with reported high endemicity challenge the broad applicability of a single biogeographic paradigm for the deep sea. New research benefiting from higher resolution sampling, molecular methods and public databases can now more rigorously examine dispersal distances and species ranges on the vast ocean floor. Here, we explore the major outstanding questions in deep-sea biogeography. Based on current evidence, many taxa appear broadly distributed across the deep sea, a pattern replicated in both the abyssal plains and specialized environments such as hydrothermal vents. Cold waters may slow larval metabolism and development augmenting the great intrinsic ability for dispersal among many deep-sea species. Currents, environmental shifts, and topography can prove to be dispersal barriers but are often semipermeable. Evidence of historical events such as points of faunal origin and climatic fluctuations are also evident in contemporary biogeographic ranges. Continued synthetic analysis, database construction, theoretical advancement and field sampling will be required to further refine hypotheses regarding deep-sea biogeography.

Survey on deep learning for radiotherapy.

PubMed

Meyer, Philippe; Noblet, Vincent; Mazzara, Christophe; Lallement, Alex

2018-07-01

More than 50% of cancer patients are treated with radiotherapy, either exclusively or in combination with other methods. The planning and delivery of radiotherapy treatment is a complex process, but can now be greatly facilitated by artificial intelligence technology. Deep learning is the fastest-growing field in artificial intelligence and has been successfully used in recent years in many domains, including medicine. In this article, we first explain the concept of deep learning, addressing it in the broader context of machine learning. The most common network architectures are presented, with a more specific focus on convolutional neural networks. We then present a review of the published works on deep learning methods that can be applied to radiotherapy, which are classified into seven categories related to the patient workflow, and can provide some insights of potential future applications. We have attempted to make this paper accessible to both radiotherapy and deep learning communities, and hope that it will inspire new collaborations between these two communities to develop dedicated radiotherapy applications. Copyright © 2018 Elsevier Ltd. All rights reserved.

DeepLoc: prediction of protein subcellular localization using deep learning.

PubMed

Almagro Armenteros, José Juan; Sønderby, Casper Kaae; Sønderby, Søren Kaae; Nielsen, Henrik; Winther, Ole

2017-11-01

The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of them, predictions rely on annotation of homologues from knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effects of sequence variants, it is desirable to have methods for predicting protein properties from sequence information only. Here, we present a prediction algorithm using deep neural networks to predict protein subcellular localization relying only on sequence information. At its core, the prediction model uses a recurrent neural network that processes the entire protein sequence and an attention mechanism identifying protein regions important for the subcellular localization. The model was trained and tested on a protein dataset extracted from one of the latest UniProt releases, in which experimentally annotated proteins follow more stringent criteria than previously. We demonstrate that our model achieves a good accuracy (78% for 10 categories; 92% for membrane-bound or soluble), outperforming current state-of-the-art algorithms, including those relying on homology information. The method is available as a web server at http://www.cbs.dtu.dk/services/DeepLoc. Example code is available at https://github.com/JJAlmagro/subcellular_localization. The dataset is available at http://www.cbs.dtu.dk/services/DeepLoc/data.php. jjalma@dtu.dk. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance.

PubMed

Nakagawa, Satoshi; Takai, Ken

2008-07-01

Deep-sea vents support productive ecosystems driven primarily by chemoautotrophs. Chemoautotrophs are organisms that are able to fix inorganic carbon using a chemical energy obtained through the oxidation of reduced compounds. Following the discovery of deep-sea vent ecosystems in 1977, there has been an increasing knowledge that deep-sea vent chemoautotrophs display remarkable physiological and phylogenetic diversity. Cultivation-dependent and -independent studies have led to an emerging view that the majority of deep-sea vent chemoautotrophs have the ability to derive energy from a variety of redox couples other than the conventional sulfur-oxygen couple, and fix inorganic carbon via the reductive tricarboxylic acid cycle. In addition, recent genomic, metagenomic and postgenomic studies have considerably accelerated the comprehensive understanding of molecular mechanisms of deep-sea vent chemoautotrophy, even in yet uncultivable endosymbionts of vent fauna. Genomic analysis also suggested that there are previously unrecognized evolutionary links between deep-sea vent chemoautotrophs and important human/animal pathogens. This review summarizes chemoautotrophy in deep-sea vents, highlighting recent biochemical and genomic discoveries.

Imagining Deep Time (Invited)

NASA Astrophysics Data System (ADS)

Talasek, J.

2013-12-01

Imagining Deep Time '...the mind seemed to grow giddy by looking so far into the abyss of time.' John Playfair (1748 -1819), scientist and mathematician "Man cannot afford to conceive of nature and exclude himself." Emmit Gowin, photographer 'A person would have to take themselves out of the human context to begin to think in terms of geologic time. They would have to think like a rock.' Terry Falke, photographer The term Deep Time refers to the vastness of the geological time scale. First conceived in the 18th century, the development of this perspective on time has been pieced together like a jigsaw puzzle of information and observations drawn from the study of the earth's structure and discovered fossilized flora and fauna. Deep time may possibly be the greatest contribution made by the discipline of geology forever impacting our perception of earth and our relationship to it. How do we grasp such vast concepts as deep time which relates to the origins of the earth or cosmic time which relates to the origins of the universe - concepts that exist far beyond the realm of human experience? Further more how do we communicate this? The ability to visualize is a powerful tool of discovery and communication for the scientist and it is part and parcel of the work of visual artists. The scientific process provides evidence yet it is imagination on the part of the scientists and artists alike that is needed to interpret that information. This exhibition represents an area where both rational and intuitive thinking come together to explore this question of how we relate to the vastness of time. The answer suggested by the combination of art work assembled here suggests that we do so through a combination of visual metaphors (cycles, circles, arrows, trajectories) and visual evidence (rock formations, strata, fossils of fauna and flora) while being mediated through various technologies. One provides factual and empirical evidence while the other provides a way of grasping

Hello World Deep Learning in Medical Imaging.

PubMed

Lakhani, Paras; Gray, Daniel L; Pett, Carl R; Nagy, Paul; Shih, George

2018-05-03

There is recent popularity in applying machine learning to medical imaging, notably deep learning, which has achieved state-of-the-art performance in image analysis and processing. The rapid adoption of deep learning may be attributed to the availability of machine learning frameworks and libraries to simplify their use. In this tutorial, we provide a high-level overview of how to build a deep neural network for medical image classification, and provide code that can help those new to the field begin their informatics projects.

Deep Spitzer/IRAC Imaging of the Subaru Deep Field

NASA Astrophysics Data System (ADS)

Jiang, Linhua; Egami, Eiichi; Cohen, Seth; Fan, Xiaohui; Ly, Chun; Mechtley, Matthew; Windhorst, Rogier

2013-10-01

The last decade saw great progress in our understanding of the distant Universe as a number of objects at z > 6 were discovered. The Subaru Deep Field (SDF) project has played an important role on study of high-z galaxies. The SDF is unique: it covers a large area of 850 sq arcmin; it has extremely deep optical images in a series of broad and narrow bands; it has the largest sample of spectroscopically-confirmed galaxies known at z >= 6, including ~100 Lyman alpha emitters (LAEs) and ~50 Lyman break galaxies (LBGs). Here we propose to carry out deep IRAC imaging observations of the central 75% of the SDF. The proposed observations together with those from our previous Spitzer programs will reach a depth of ~10 hours, and enable the first complete census of physical properties and stellar populations of spectroscopically-confirmed galaxies at the end of cosmic reionization. IRAC data is the key to measure stellar masses and constrain stellar populations in high-z galaxies. From SED modeling with secure redshifts, we will characterize the physical properties of these galaxies, and trace their mass assembly and star formation history. In particular, it allows us, for the first time, to study stellar populations in a large sample of z >=6 LAEs. We will also address some critical questions, such as whether LAEs and LBGs represent physically different galaxy populations. All these will help us to understand the earliest galaxy formation and evolution, and better constrain the galaxy contribution to reionization. The IRAC data will also cover 10,000 emission-line selected galaxies at z < 1.5, 50,000 UV and mass selected LBGs at 1.5 < z < 3, and more than 5,000 LBGs at 3 < z < 6. It will have a legacy value for SDF-related programs.

Gating mass cytometry data by deep learning.

PubMed

Li, Huamin; Shaham, Uri; Stanton, Kelly P; Yao, Yi; Montgomery, Ruth R; Kluger, Yuval

2017-11-01

Mass cytometry or CyTOF is an emerging technology for high-dimensional multiparameter single cell analysis that overcomes many limitations of fluorescence-based flow cytometry. New methods for analyzing CyTOF data attempt to improve automation, scalability, performance and interpretation of data generated in large studies. Assigning individual cells into discrete groups of cell types (gating) involves time-consuming sequential manual steps, untenable for larger studies. We introduce DeepCyTOF, a standardization approach for gating, based on deep learning techniques. DeepCyTOF requires labeled cells from only a single sample. It is based on domain adaptation principles and is a generalization of previous work that allows us to calibrate between a target distribution and a source distribution in an unsupervised manner. We show that DeepCyTOF is highly concordant (98%) with cell classification obtained by individual manual gating of each sample when applied to a collection of 16 biological replicates of primary immune blood cells, even when measured across several instruments. Further, DeepCyTOF achieves very high accuracy on the semi-automated gating challenge of the FlowCAP-I competition as well as two CyTOF datasets generated from primary immune blood cells: (i) 14 subjects with a history of infection with West Nile virus (WNV), (ii) 34 healthy subjects of different ages. We conclude that deep learning in general, and DeepCyTOF specifically, offers a powerful computational approach for semi-automated gating of CyTOF and flow cytometry data. Our codes and data are publicly available at https://github.com/KlugerLab/deepcytof.git. yuval.kluger@yale.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Evolutionary process of deep-sea bathymodiolus mussels.

PubMed

Miyazaki, Jun-Ichi; de Oliveira Martins, Leonardo; Fujita, Yuko; Matsumoto, Hiroto; Fujiwara, Yoshihiro

2010-04-27

Since the discovery of deep-sea chemosynthesis-based communities, much work has been done to clarify their organismal and environmental aspects. However, major topics remain to be resolved, including when and how organisms invade and adapt to deep-sea environments; whether strategies for invasion and adaptation are shared by different taxa or unique to each taxon; how organisms extend their distribution and diversity; and how they become isolated to speciate in continuous waters. Deep-sea mussels are one of the dominant organisms in chemosynthesis-based communities, thus investigations of their origin and evolution contribute to resolving questions about life in those communities. We investigated worldwide phylogenetic relationships of deep-sea Bathymodiolus mussels and their mytilid relatives by analyzing nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4) genes. Phylogenetic analysis of the concatenated sequence data showed that mussels of the subfamily Bathymodiolinae from vents and seeps were divided into four groups, and that mussels of the subfamily Modiolinae from sunken wood and whale carcasses assumed the outgroup position and shallow-water modioline mussels were positioned more distantly to the bathymodioline mussels. We provisionally hypothesized the evolutionary history of Bathymodilolus mussels by estimating evolutionary time under a relaxed molecular clock model. Diversification of bathymodioline mussels was initiated in the early Miocene, and subsequently diversification of the groups occurred in the early to middle Miocene. The phylogenetic relationships support the "Evolutionary stepping stone hypothesis," in which mytilid ancestors exploited sunken wood and whale carcasses in their progressive adaptation to deep-sea environments. This hypothesis is also supported by the evolutionary transition of symbiosis in that nutritional adaptation to the deep sea proceeded from extracellular

Diabetic retinopathy screening using deep neural network.

PubMed

Ramachandran, Nishanthan; Hong, Sheng Chiong; Sime, Mary J; Wilson, Graham A

2017-09-07

There is a burgeoning interest in the use of deep neural network in diabetic retinal screening. To determine whether a deep neural network could satisfactorily detect diabetic retinopathy that requires referral to an ophthalmologist from a local diabetic retinal screening programme and an international database. Retrospective audit. Diabetic retinal photos from Otago database photographed during October 2016 (485 photos), and 1200 photos from Messidor international database. Receiver operating characteristic curve to illustrate the ability of a deep neural network to identify referable diabetic retinopathy (moderate or worse diabetic retinopathy or exudates within one disc diameter of the fovea). Area under the receiver operating characteristic curve, sensitivity and specificity. For detecting referable diabetic retinopathy, the deep neural network had an area under receiver operating characteristic curve of 0.901 (95% confidence interval 0.807-0.995), with 84.6% sensitivity and 79.7% specificity for Otago and 0.980 (95% confidence interval 0.973-0.986), with 96.0% sensitivity and 90.0% specificity for Messidor. This study has shown that a deep neural network can detect referable diabetic retinopathy with sensitivities and specificities close to or better than 80% from both an international and a domestic (New Zealand) database. We believe that deep neural networks can be integrated into community screening once they can successfully detect both diabetic retinopathy and diabetic macular oedema. © 2017 Royal Australian and New Zealand College of Ophthalmologists.

Extracting Databases from Dark Data with DeepDive

PubMed Central

Zhang, Ce; Shin, Jaeho; Ré, Christopher; Cafarella, Michael; Niu, Feng

2016-01-01

DeepDive is a system for extracting relational databases from dark data: the mass of text, tables, and images that are widely collected and stored but which cannot be exploited by standard relational tools. If the information in dark data — scientific papers, Web classified ads, customer service notes, and so on — were instead in a relational database, it would give analysts a massive and valuable new set of “big data.” DeepDive is distinctive when compared to previous information extraction systems in its ability to obtain very high precision and recall at reasonable engineering cost; in a number of applications, we have used DeepDive to create databases with accuracy that meets that of human annotators. To date we have successfully deployed DeepDive to create data-centric applications for insurance, materials science, genomics, paleontologists, law enforcement, and others. The data unlocked by DeepDive represents a massive opportunity for industry, government, and scientific researchers. DeepDive is enabled by an unusual design that combines large-scale probabilistic inference with a novel developer interaction cycle. This design is enabled by several core innovations around probabilistic training and inference. PMID:28316365

Extracting Databases from Dark Data with DeepDive.

PubMed

Zhang, Ce; Shin, Jaeho; Ré, Christopher; Cafarella, Michael; Niu, Feng

2016-01-01

DeepDive is a system for extracting relational databases from dark data : the mass of text, tables, and images that are widely collected and stored but which cannot be exploited by standard relational tools. If the information in dark data - scientific papers, Web classified ads, customer service notes, and so on - were instead in a relational database, it would give analysts a massive and valuable new set of "big data." DeepDive is distinctive when compared to previous information extraction systems in its ability to obtain very high precision and recall at reasonable engineering cost; in a number of applications, we have used DeepDive to create databases with accuracy that meets that of human annotators. To date we have successfully deployed DeepDive to create data-centric applications for insurance, materials science, genomics, paleontologists, law enforcement, and others. The data unlocked by DeepDive represents a massive opportunity for industry, government, and scientific researchers. DeepDive is enabled by an unusual design that combines large-scale probabilistic inference with a novel developer interaction cycle. This design is enabled by several core innovations around probabilistic training and inference.

Deep infection in total hip arthroplasty

PubMed Central

Hamilton, Henry; Jamieson, John

2008-01-01

Objective To report on a 30-year prospective study of deep infection in 1993 consecutive total hip arthroplasties performed by a single surgeon. Methods The relations of numerous variables to the incidence of deep infection were studied. Results The cumulative infection rate after the index total hip arthroplasties rose from 0.8% at 2 years to 1.4% at 20 years; 9.6% of the index operations required further surgery. When infections attributed to these secondary procedures were included, the infection rate rose from 0.9% at 2 years to 2% at 20 years. Although the usual variables increased the incidence of infection, the significant and most precise predictors of infection were radiologic diagnoses of upper pole grade III and protrusio acetabuli, an elevated erythrocyte sedimentation rate, alcoholism and units of blood transfused. Conclusion From 2–20 years, the incidence of deep infection doubled. Preoperative recognition of the first 4 risk factors permits the use of additional prophylactic measures. Spinal or epidural anesthesia reduced the units of blood transfused (the fifth risk factor) and, hence, the risk of infection. Although most deep infections are seeded while the wound is open, there are many possible postoperative causes. In this study, fewer than one-third of the infections that presented after 2 years were related to hematogenous spread. The efficacy of clean air technology was supported, and it is recommended that all measures that may reduce the incidence of deep infection be employed. PMID:18377751

Preface: Deep Slab and Mantle Dynamics

NASA Astrophysics Data System (ADS)

Suetsugu, Daisuke; Bina, Craig R.; Inoue, Toru; Wiens, Douglas A.

2010-11-01

We are pleased to publish this special issue of the journal Physics of the Earth and Planetary Interiors entitled "Deep Slab and Mantle Dynamics". This issue is an outgrowth of the international symposium "Deep Slab and Mantle Dynamics", which was held on February 25-27, 2009, in Kyoto, Japan. This symposium was organized by the "Stagnant Slab Project" (SSP) research group to present the results of the 5-year project and to facilitate intensive discussion with well-known international researchers in related fields. The SSP and the symposium were supported by a Grant-in-Aid for Scientific Research (16075101) from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government. In the symposium, key issues discussed by participants included: transportation of water into the deep mantle and its role in slab-related dynamics; observational and experimental constraints on deep slab properties and the slab environment; modeling of slab stagnation to constrain its mechanisms in comparison with observational and experimental data; observational, experimental and modeling constraints on the fate of stagnant slabs; eventual accumulation of stagnant slabs on the core-mantle boundary and its geodynamic implications. This special issue is a collection of papers presented in the symposium and other papers related to the subject of the symposium. The collected papers provide an overview of the wide range of multidisciplinary studies of mantle dynamics, particularly in the context of subduction, stagnation, and the fate of deep slabs.

The JPL roadmap for Deep Space navigation

NASA Technical Reports Server (NTRS)

Martin-Mur, Tomas J.; Abraham, Douglas S.; Berry, David; Bhaskaran, Shyam; Cesarone, Robert J.; Wood, Lincoln

2006-01-01

This paper reviews the tentative set of deep space missions that will be supported by NASA's Deep Space Mission System in the next twenty-five years, and extracts the driving set of navigation capabilities that these missions will require. There will be many challenges including the support of new mission navigation approaches such as formation flying and rendezvous in deep space, low-energy and low-thrust orbit transfers, precise landing and ascent vehicles, and autonomous navigation. Innovative strategies and approaches will be needed to develop and field advanced navigation capabilities.

Enhanced Experience Replay for Deep Reinforcement Learning

DTIC Science & Technology

2015-11-01

ARL-TR-7538 ● NOV 2015 US Army Research Laboratory Enhanced Experience Replay for Deep Reinforcement Learning by David Doria...Experience Replay for Deep Reinforcement Learning by David Doria, Bryan Dawson, and Manuel Vindiola Computational and Information Sciences Directorate...

Workshop to develop deep-life continental scientific drilling projects

DOE PAGES

Kieft, T. L.; Onstott, T. C.; Ahonen, L.; ...

2015-05-29

The International Continental Scientific Drilling Program (ICDP) has long espoused studies of deep subsurface life, and has targeted fundamental questions regarding subsurface life, including the following: "(1) What is the extent and diversity of deep microbial life and what are the factors limiting it? (2) What are the types of metabolism/carbon/energy sources and the rates of subsurface activity? (3) How is deep microbial life adapted to subsurface conditions? (4) How do subsurface microbial communities affect energy resources? And (5) how does the deep biosphere interact with the geosphere and atmosphere?" (Horsfield et al., 2014) Many ICDP-sponsored drilling projects have includedmore » a deep-life component; however, to date, not one project has been driven by deep-life goals, in part because geomicrobiologists have been slow to initiate deep biosphere-driven ICDP projects. Therefore, the Deep Carbon Observatory (DCO) recently partnered with the ICDP to sponsor a workshop with the specific aim of gathering potential proponents for deep-life-driven ICDP projects and ideas for candidate drilling sites. Twenty-two participants from nine countries proposed projects and sites that included compressional and extensional tectonic environments, evaporites, hydrocarbon-rich shales, flood basalts, Precambrian shield rocks, subglacial and subpermafrost environments, active volcano–tectonic systems, megafan deltas, and serpentinizing ultramafic environments. The criteria and requirements for successful ICDP applications were presented. Deep-life-specific technical requirements were discussed and it was concluded that, while these procedures require adequate planning, they are entirely compatible with the sampling needs of other disciplines. As a result of this workshop, one drilling workshop proposal on the Basin and Range Physiographic Province (BRPP) has been submitted to the ICDP, and several other drilling project proponents plan to submit proposals for ICDP

Characterization of tabanid flies (Diptera: Tabanidae) in South Africa and Zambia and detection of protozoan parasites they are harbouring.

PubMed

Taioe, Moeti O; Motloang, Makhosazana Y; Namangala, Boniface; Chota, Amos; Molefe, Nthatisi I; Musinguzi, Simon P; Suganuma, Keisuke; Hayes, Polly; Tsilo, Toi J; Chainey, John; Inoue, Noboru; Thekisoe, Oriel M M

2017-08-01

Tabanids are haematophagous flies feeding on livestock and wildlife. In the absence of information on the relationship of tabanid flies and protozoan parasites in South Africa and Zambia, the current study was aimed at characterizing tabanid flies collected in these two countries as well as detecting protozoan parasites they are harbouring. A total of 527 tabanid flies were collected whereby 70·2% were from South Africa and 29·8% were from Zambia. Morphological analysis revealed a total of five different genera collected from the sampled areas namely: Ancala, Atylotus, Haematopota, Philoliche and Tabanus. DNA extracted from South African Tabanus par and Tabanus taeniola tested positive for the presence of Trypanosoma congolense (Savannah) and Trypanosoma theileri whilst one member from T. par was positive for Trypanosoma brucei species. DNA extracted from Zambian tabanid flies tested positive for the presence of Besnoitia species at 1·27% (2/157), Babesia bigemina 5·73% (9/157), Theileria parva 30·11% (30/157) and 9·82% (14/157) for Trypanosoma evansi. This study is the first to report on relationship of Babesia and Theileria parasites with tabanid flies. Further investigations are required to determine the role of tabanids in transmission of the detected protozoan parasites in livestock and wildlife in South Africa and Zambia.

Presence of Streptococcus mutans strains harbouring the cnm gene correlates with dental caries status and IgA nephropathy conditions

PubMed Central

Misaki, Taro; Naka, Shuhei; Hatakeyama, Rina; Fukunaga, Akiko; Nomura, Ryota; Isozaki, Taisuke; Nakano, Kazuhiko

2016-01-01

Streptococcus mutans is a major pathogen of human dental caries. Strains harbouring the cnm gene, which encodes Cnm, a collagen-binding protein, contribute to the development of several systemic diseases. In this study, we analysed S. mutans strains isolated from the oral cavity of immunoglobulin (Ig)A nephropathy (IgAN) patients to determine potential relationships between cnm and caries status as well as IgAN conditions. Saliva specimens were collected from 109 IgAN patients and the cnm status of isolated S. mutans strains was determined using PCR. In addition, the dental caries status (decayed, missing or filled teeth [DMFT] index) in patients who agreed to dental consultation (n = 49) was evaluated. The DMFT index and urinary protein levels in the cnm-positive group were significantly higher than those in the cnm-negative group (p < 0.05). Moreover, the urinary protein levels in the high DMFT (≥15) group were significantly higher than those in the low DMFT (<15) group (p < 0.05). Our results show that isolation of cnm-positive S. mutans strains from the oral cavity may be associated with urinary protein levels in IgAN patients, especially those with a high dental caries status. PMID:27811984

SPRUCE Deep Peat Heating Manipulations: in situ Methods to Characterize the Response of Deep Peat to Warming

NASA Astrophysics Data System (ADS)

Hanson, P. J.; Riggs, J. S.; Barbier, C. N.; Nettles, W. R., IV; Phillips, J. R.; Hook, L.

2014-12-01

Deep soil heating infrastructure was completed in 2014 for a peatland whole-ecosystem warming study that will include air warming starting in 2015 (SPRUCE; http://mnspruce.ornl.gov). In June 2014, we initiated deep soil heating to test the responsiveness of deep peat carbon stocks, microbial communities and biogeochemical cycling processes to heating at 4 warming levels (+2.25, +4.5, +6.75 and +9 °C; 2 replicate plots) compared to fully-constructed control plots (+0 °C; 2 replicate plots). The warming treatments were deployed over eight 113 m2 areas using circular arrays of low-wattage (W) electrical resistance heaters. Perimeter heating was achieved by an exterior circle of 48 100W heaters that apply heat from the surface to a depth of 3 meters. Heating within the study area was accomplished utilizing three zones of 100W "deep only" heaters: an intermediate circle of 12 units, an interior circle of 6 units and one unit placed at the plot center. Heating elements inside the study area apply heat only from -2 to -3 m to keep active heater surfaces away from measured peat volumes. With an average peat depth of 2.5 meters this system was able to warm approximately 113 of the 282 m3 of peat within each target plot. In the absence of the air warming cap, in situ deep peat heating is only effective at sustaining warming in the deep peat layers. Warming levels at depth were achieved over a 25-day (+ 2.25 °C) to a 60-day (+9 °C) period depending on the target treatment temperatures in agreement with a priori energy balance model simulations. Homogeneous temperature distributions between heaters at a given depth interval continued to develop after these targets were reached. Biological and biogeochemical responses to these manipulations are being actively assessed. After one month of transient heating, data for ground-level surface flux of CO2 and CH4 had not shown changes from deep peat heating, but they continue to be tracked and will be summarized in this and related

HLA-G 14-bp Ins/Ins Genotype in Patients Harbouring Helicobacter pylori Infection: A Potential Risk Factor?

PubMed

Genre, J; Reginaldo, F P Santos; Andrade, J Marco de Leon; Lima, F P; da Camara, A V Coutinho; Donadi, E A; Crispim, J C

2016-01-01

H. pylori is a potent pathogen due to its capacity to successfully evade host defence mechanisms. Despite inducing immune responses in infected individuals, sometimes these responses fail to clear the infection and the bacterium establishes a persistent infection leading to chronic inflammation. In this context, we hypothesized that human leucocyte antigen G (HLA-G), a non-classical major histocompatibility complex molecule that has the ability to regulate immune responses both in physiological and in pathological conditions, may play an important role in promoting tolerance and helping H. pylori to subvert host defence and consequently establish a chronic infection. Therefore, we evaluated the expression of HLA-G 14-bp Ins/Del polymorphism in patients harbouring H. pylori infection, as well as their relationship with histological and demographic variables, to gain a better understanding of the actual role of HLA-G and its genetic polymorphisms in bacterial infection. Sixty-eight patients with clinical symptoms suggestive of H. pylori infection were enrolled to assess HLA-G 14-bp Ins/Del polymorphism allele and genotype frequencies. After adjustment for covariates (age and gender), the odds of having the genotype Ins/Ins, compared to Del/Del, were 3.77 times greater among HP+ cases than among controls. These findings suggest that the 14-bp Ins/Ins genotype, already associated with inflammatory and autoimmune diseases as well as some viral and parasitic infections, could confer a greater risk of developing H. pylori infection. © 2015 The Foundation for the Scandinavian Journal of Immunology.

The dynamics of biogeographic ranges in the deep sea

PubMed Central

McClain, Craig R.; Hardy, Sarah Mincks

2010-01-01

Anthropogenic disturbances such as fishing, mining, oil drilling, bioprospecting, warming, and acidification in the deep sea are increasing, yet generalities about deep-sea biogeography remain elusive. Owing to the lack of perceived environmental variability and geographical barriers, ranges of deep-sea species were traditionally assumed to be exceedingly large. In contrast, seamount and chemosynthetic habitats with reported high endemicity challenge the broad applicability of a single biogeographic paradigm for the deep sea. New research benefiting from higher resolution sampling, molecular methods and public databases can now more rigorously examine dispersal distances and species ranges on the vast ocean floor. Here, we explore the major outstanding questions in deep-sea biogeography. Based on current evidence, many taxa appear broadly distributed across the deep sea, a pattern replicated in both the abyssal plains and specialized environments such as hydrothermal vents. Cold waters may slow larval metabolism and development augmenting the great intrinsic ability for dispersal among many deep-sea species. Currents, environmental shifts, and topography can prove to be dispersal barriers but are often semipermeable. Evidence of historical events such as points of faunal origin and climatic fluctuations are also evident in contemporary biogeographic ranges. Continued synthetic analysis, database construction, theoretical advancement and field sampling will be required to further refine hypotheses regarding deep-sea biogeography. PMID:20667884

Progress to a Gallium-Arsenide Deep-Center Laser

PubMed Central

Pan, Janet L.

2009-01-01

Although photoluminescence from gallium-arsenide (GaAs) deep-centers was first observed in the 1960s, semiconductor lasers have always utilized conduction-to-valence-band transitions. Here we review recent materials studies leading to the first GaAs deep-center laser. First, we summarize well-known properties: nature of deep-center complexes, Franck-Condon effect, photoluminescence. Second, we describe our recent work: insensitivity of photoluminescence with heating, striking differences between electroluminescence and photoluminescence, correlation between transitions to deep-states and absence of bandgap-emission. Room-temperature stimulated-emission from GaAs deep-centers was observed at low electrical injection, and could be tuned from the bandgap to half-the-bandgap (900–1,600 nm) by changing the electrical injection. The first GaAs deep-center laser was demonstrated with electrical injection, and exhibited a threshold of less than 27 mA/cm2 in continuous-wave mode at room temperature at the important 1.54 μm fiber-optic wavelength. This small injection for laser action was explained by fast depopulation of the lower state of the optical transition (fast capture of free holes onto deep-centers), which maintains the population inversion. The evidence for laser action included: superlinear L-I curve, quasi-Fermi level separations satisfying Bernard-Duraffourg’s criterion, optical gains larger than known significant losses, clamping of the optical-emission from lossy modes unable to reach laser action, pinning of the population distribution during laser action.

[Isolated true aneurysm of the deep femoral artery].

PubMed

Salomon du Mont, L; Holzer, T; Kazandjian, C; Saucy, F; Corpataux, J M; Rinckenbach, S; Déglise, S

2016-07-01

Aneurysms of the deep femoral artery, accounting for 5% of all femoral aneurysms, are uncommon. There is a serious risk of rupture. We report the case of an 83-year-old patient with a painless pulsatile mass in the right groin due to an aneurysm of the deep femoral artery. History taking revealed no cardiovascular risk factors and no other aneurysms at other localizations. The etiology remained unclear because no recent history of local trauma or puncture was found. ACT angiography was performed, revealing a true isolated aneurysm of the deep femoral artery with a diameter of 90mm, beginning 1cm after its origin. There were no signs of rupture or distal emboli. Due to unsuitable anatomy for an endovascular approach, the patient underwent open surgery, with exclusion of the aneurysm and interposition of an 8-mm Dacron graft to preserve deep femoral artery flow. Due to their localization, the diagnosis and the management of aneurysms of the deep femoral artery can be difficult. Options are surgical exclusion or an endovascular approach in the absence of symptoms or as a bridging therapy. If possible, blood flow to the distal deep femoral artery should be maintained, the decision depending also on the patency of the superficial femoral artery. In case of large size, aneurysms of the deep femoral artery should be treated without any delay. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Deep learning with convolutional neural network in radiology.

PubMed

Yasaka, Koichiro; Akai, Hiroyuki; Kunimatsu, Akira; Kiryu, Shigeru; Abe, Osamu

2018-04-01

Deep learning with a convolutional neural network (CNN) is gaining attention recently for its high performance in image recognition. Images themselves can be utilized in a learning process with this technique, and feature extraction in advance of the learning process is not required. Important features can be automatically learned. Thanks to the development of hardware and software in addition to techniques regarding deep learning, application of this technique to radiological images for predicting clinically useful information, such as the detection and the evaluation of lesions, etc., are beginning to be investigated. This article illustrates basic technical knowledge regarding deep learning with CNNs along the actual course (collecting data, implementing CNNs, and training and testing phases). Pitfalls regarding this technique and how to manage them are also illustrated. We also described some advanced topics of deep learning, results of recent clinical studies, and the future directions of clinical application of deep learning techniques.

The biodiversity of the deep Southern Ocean benthos.

PubMed

Brandt, A; De Broyer, C; De Mesel, I; Ellingsen, K E; Gooday, A J; Hilbig, B; Linse, K; Thomson, M R A; Tyler, P A

2007-01-29

Our knowledge of the biodiversity of the Southern Ocean (SO) deep benthos is scarce. In this review, we describe the general biodiversity patterns of meio-, macro- and megafaunal taxa, based on historical and recent expeditions, and against the background of the geological events and phylogenetic relationships that have influenced the biodiversity and evolution of the investigated taxa. The relationship of the fauna to environmental parameters, such as water depth, sediment type, food availability and carbonate solubility, as well as species interrelationships, probably have shaped present-day biodiversity patterns as much as evolution. However, different taxa exhibit different large-scale biodiversity and biogeographic patterns. Moreover, there is rarely any clear relationship of biodiversity pattern with depth, latitude or environmental parameters, such as sediment composition or grain size. Similarities and differences between the SO biodiversity and biodiversity of global oceans are outlined. The high percentage (often more than 90%) of new species in almost all taxa, as well as the high degree of endemism of many groups, may reflect undersampling of the area, and it is likely to decrease as more information is gathered about SO deep-sea biodiversity by future expeditions. Indeed, among certain taxa such as the Foraminifera, close links at the species level are already apparent between deep Weddell Sea faunas and those from similar depths in the North Atlantic and Arctic. With regard to the vertical zonation from the shelf edge into deep water, biodiversity patterns among some taxa in the SO might differ from those in other deep-sea areas, due to the deep Antarctic shelf and the evolution of eurybathy in many species, as well as to deep-water production that can fuel the SO deep sea with freshly produced organic matter derived not only from phytoplankton, but also from ice algae.

The biodiversity of the deep Southern Ocean benthos

PubMed Central

Brandt, A; De Broyer, C; De Mesel, I; Ellingsen, K.E; Gooday, A.J; Hilbig, B; Linse, K; Thomson, M.R.A; Tyler, P.A

2006-01-01

Our knowledge of the biodiversity of the Southern Ocean (SO) deep benthos is scarce. In this review, we describe the general biodiversity patterns of meio-, macro- and megafaunal taxa, based on historical and recent expeditions, and against the background of the geological events and phylogenetic relationships that have influenced the biodiversity and evolution of the investigated taxa. The relationship of the fauna to environmental parameters, such as water depth, sediment type, food availability and carbonate solubility, as well as species interrelationships, probably have shaped present-day biodiversity patterns as much as evolution. However, different taxa exhibit different large-scale biodiversity and biogeographic patterns. Moreover, there is rarely any clear relationship of biodiversity pattern with depth, latitude or environmental parameters, such as sediment composition or grain size. Similarities and differences between the SO biodiversity and biodiversity of global oceans are outlined. The high percentage (often more than 90%) of new species in almost all taxa, as well as the high degree of endemism of many groups, may reflect undersampling of the area, and it is likely to decrease as more information is gathered about SO deep-sea biodiversity by future expeditions. Indeed, among certain taxa such as the Foraminifera, close links at the species level are already apparent between deep Weddell Sea faunas and those from similar depths in the North Atlantic and Arctic. With regard to the vertical zonation from the shelf edge into deep water, biodiversity patterns among some taxa in the SO might differ from those in other deep-sea areas, due to the deep Antarctic shelf and the evolution of eurybathy in many species, as well as to deep-water production that can fuel the SO deep sea with freshly produced organic matter derived not only from phytoplankton, but also from ice algae. PMID:17405207

Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump

PubMed Central

Agusti, S.; González-Gordillo, J. I.; Vaqué, D.; Estrada, M.; Cerezo, M. I.; Salazar, G.; Gasol, J. M.; Duarte, C. M.

2015-01-01

The role of the ocean as a sink for CO2 is partially dependent on the downward transport of phytoplankton cells packaged within fast-sinking particles. However, whether such fast-sinking mechanisms deliver fresh organic carbon down to the deep bathypelagic sea and whether this mechanism is prevalent across the ocean requires confirmation. Here we report the ubiquitous presence of healthy photosynthetic cells, dominated by diatoms, down to 4,000 m in the deep dark ocean. Decay experiments with surface phytoplankton suggested that the large proportion (18%) of healthy photosynthetic cells observed, on average, in the dark ocean, requires transport times from a few days to a few weeks, corresponding to sinking rates (124–732 m d−1) comparable to those of fast-sinking aggregates and faecal pellets. These results confirm the expectation that fast-sinking mechanisms inject fresh organic carbon into the deep sea and that this is a prevalent process operating across the global oligotrophic ocean. PMID:26158221

Interpreting the strongest deep earthquake ever observed

NASA Astrophysics Data System (ADS)

Schultz, Colin

2013-12-01

Massive earthquakes that strike deep within the Earth may be more efficient at dissipating pent-up energy than similar quakes near the surface, according to new research by Wei et al. The authors analyzed the rupture of the most powerful deep earthquake ever recorded.

DRREP: deep ridge regressed epitope predictor.

PubMed

Sher, Gene; Zhi, Degui; Zhang, Shaojie

2017-10-03

The ability to predict epitopes plays an enormous role in vaccine development in terms of our ability to zero in on where to do a more thorough in-vivo analysis of the protein in question. Though for the past decade there have been numerous advancements and improvements in epitope prediction, on average the best benchmark prediction accuracies are still only around 60%. New machine learning algorithms have arisen within the domain of deep learning, text mining, and convolutional networks. This paper presents a novel analytically trained and string kernel using deep neural network, which is tailored for continuous epitope prediction, called: Deep Ridge Regressed Epitope Predictor (DRREP). DRREP was tested on long protein sequences from the following datasets: SARS, Pellequer, HIV, AntiJen, and SEQ194. DRREP was compared to numerous state of the art epitope predictors, including the most recently published predictors called LBtope and DMNLBE. Using area under ROC curve (AUC), DRREP achieved a performance improvement over the best performing predictors on SARS (13.7%), HIV (8.9%), Pellequer (1.5%), and SEQ194 (3.1%), with its performance being matched only on the AntiJen dataset, by the LBtope predictor, where both DRREP and LBtope achieved an AUC of 0.702. DRREP is an analytically trained deep neural network, thus capable of learning in a single step through regression. By combining the features of deep learning, string kernels, and convolutional networks, the system is able to perform residue-by-residue prediction of continues epitopes with higher accuracy than the current state of the art predictors.

Deep-levels in gallium arsenide for device applications

NASA Astrophysics Data System (ADS)

McManis, Joseph Edward

Defects in semiconductors have been studied for over 40 years as a diagnostic of the quality of crystal growth. In this thesis, we investigate GaAs deep-levels specifically intended for devices. This thesis summarizes our efforts to characterize the near-infrared photoluminescence from deep-levels, study optical transitions via absorption, and fabricate and characterize deep-level light-emitting diodes (LEDs). This thesis also describes the first tunnel diodes which explicitly make use of GaAs deep-levels. Photoluminescence measurements of GaAs deep-levels showed a broad peak around a wavelength extending from 1.0--1.7 mum, which includes important wavelengths for fiber-optic communications (1.3--1.55 mum). Transmission measurements show the new result that very little of the radiative emission is self-absorbed. We measured the deep-level photoluminescence at several temperatures. We are also the first to report the internal quantum efficiency associated with the deep-level transitions. We have fabricated LEDs that, utilize the optical transitions of GaAs deep-levels. The electroluminescence spectra showed a broad peak from 1.0--1.7 mum at low currents, but the spectrum exhibited a blue-shift as the current was increased. To improve device performance, we designed an AlGaAs layer into the structure of the LEDs. The AlGaAs barrier layer acts as a resistive barrier so that the holes in the p-GaAs layer are swept away from underneath the gold p-contact. The AlGaAs layer also reduces the blue-shift by acting as a potential barrier so that only higher-energy holes are injected. We found that the LEDs with AlGaAs were brighter at long wavelengths, which was a significant improvement. Photoluminescence measurements show that the spectral blue-shift is not due to sample heating. We have developed a new physical model to explain the blue-shift: it is caused by Coloumb charging of the deep-centers. We have achieved the first tunnel diodes with which specifically utilize deep

DEEP MOTIF DASHBOARD: VISUALIZING AND UNDERSTANDING GENOMIC SEQUENCES USING DEEP NEURAL NETWORKS.

PubMed

Lanchantin, Jack; Singh, Ritambhara; Wang, Beilun; Qi, Yanjun

2017-01-01

Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA sequence signals and give insights as to why TFs bind to certain locations. In this paper, we propose a toolkit called the Deep Motif Dashboard (DeMo Dashboard) which provides a suite of visualization strategies to extract motifs, or sequence patterns from deep neural network models for TFBS classification. We demonstrate how to visualize and understand three important DNN models: convolutional, recurrent, and convolutional-recurrent networks. Our first visualization method is finding a test sequence's saliency map which uses first-order derivatives to describe the importance of each nucleotide in making the final prediction. Second, considering recurrent models make predictions in a temporal manner (from one end of a TFBS sequence to the other), we introduce temporal output scores, indicating the prediction score of a model over time for a sequential input. Lastly, a class-specific visualization strategy finds the optimal input sequence for a given TFBS positive class via stochastic gradient optimization. Our experimental results indicate that a convolutional-recurrent architecture performs the best among the three architectures. The visualization techniques indicate that CNN-RNN makes predictions by modeling both motifs as well as dependencies among them.

Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks

PubMed Central

Lanchantin, Jack; Singh, Ritambhara; Wang, Beilun; Qi, Yanjun

2018-01-01

Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA sequence signals and give insights as to why TFs bind to certain locations. In this paper, we propose a toolkit called the Deep Motif Dashboard (DeMo Dashboard) which provides a suite of visualization strategies to extract motifs, or sequence patterns from deep neural network models for TFBS classification. We demonstrate how to visualize and understand three important DNN models: convolutional, recurrent, and convolutional-recurrent networks. Our first visualization method is finding a test sequence’s saliency map which uses first-order derivatives to describe the importance of each nucleotide in making the final prediction. Second, considering recurrent models make predictions in a temporal manner (from one end of a TFBS sequence to the other), we introduce temporal output scores, indicating the prediction score of a model over time for a sequential input. Lastly, a class-specific visualization strategy finds the optimal input sequence for a given TFBS positive class via stochastic gradient optimization. Our experimental results indicate that a convolutional-recurrent architecture performs the best among the three architectures. The visualization techniques indicate that CNN-RNN makes predictions by modeling both motifs as well as dependencies among them. PMID:27896980

Parallel Distributed Processing Theory in the Age of Deep Networks.

PubMed

Bowers, Jeffrey S

2017-12-01

Parallel distributed processing (PDP) models in psychology are the precursors of deep networks used in computer science. However, only PDP models are associated with two core psychological claims, namely that all knowledge is coded in a distributed format and cognition is mediated by non-symbolic computations. These claims have long been debated in cognitive science, and recent work with deep networks speaks to this debate. Specifically, single-unit recordings show that deep networks learn units that respond selectively to meaningful categories, and researchers are finding that deep networks need to be supplemented with symbolic systems to perform some tasks. Given the close links between PDP and deep networks, it is surprising that research with deep networks is challenging PDP theory. Copyright © 2017. Published by Elsevier Ltd.

The deep space network

NASA Technical Reports Server (NTRS)

1977-01-01

Presented is Deep Space Network (DSN) progress in flight project support, tracking and data acquisition (TDA) research and technology, network engineering, hardware and software implementation, and operations.

The deep space network

NASA Technical Reports Server (NTRS)

1975-01-01

Summaries are given of Deep Space Network progress in flight project support, tracking and data acquisition research and technology, network engineering, hardware and software implementation, and operations.

Deep Visual Attention Prediction

NASA Astrophysics Data System (ADS)

Wang, Wenguan; Shen, Jianbing

2018-05-01

In this work, we aim to predict human eye fixation with view-free scenes based on an end-to-end deep learning architecture. Although Convolutional Neural Networks (CNNs) have made substantial improvement on human attention prediction, it is still needed to improve CNN based attention models by efficiently leveraging multi-scale features. Our visual attention network is proposed to capture hierarchical saliency information from deep, coarse layers with global saliency information to shallow, fine layers with local saliency response. Our model is based on a skip-layer network structure, which predicts human attention from multiple convolutional layers with various reception fields. Final saliency prediction is achieved via the cooperation of those global and local predictions. Our model is learned in a deep supervision manner, where supervision is directly fed into multi-level layers, instead of previous approaches of providing supervision only at the output layer and propagating this supervision back to earlier layers. Our model thus incorporates multi-level saliency predictions within a single network, which significantly decreases the redundancy of previous approaches of learning multiple network streams with different input scales. Extensive experimental analysis on various challenging benchmark datasets demonstrate our method yields state-of-the-art performance with competitive inference time.

Deep space optical communications experiment

NASA Technical Reports Server (NTRS)

Kinman, P.; Katz, J.; Gagliardi, R.

1983-01-01

An optical communications experiment between a deep space vehicle and an earth terminal is under consideration for later in this decade. The experimental link would be incoherent (direct detection) and would employ two-way cooperative pointing. The deep space optical transceiver would ride piggyback on a spacecraft with an independent scientific objective. Thus, this optical transceiver is being designed for minimum spacecraft impact - specifically, low mass and low power. The choices of laser transmitter, coding/modulation scheme, and pointing mechanization are discussed. A representative telemetry link budget is presented.

Coral Colonisation of an Artificial Reef in a Turbid Nearshore Environment, Dampier Harbour, Western Australia

PubMed Central

Blakeway, David; Byers, Michael; Stoddart, James; Rossendell, Jason

2013-01-01

A 0.6 hectare artificial reef of local rock and recycled concrete sleepers was constructed in December 2006 at Parker Point in the industrial port of Dampier, western Australia, with the aim of providing an environmental offset for a nearshore coral community lost to land reclamation. Corals successfully colonised the artificial reef, despite the relatively harsh environmental conditions at the site (annual water temperature range 18-32°C, intermittent high turbidity, frequent cyclones, frequent nearby ship movements). Coral settlement to the artificial reef was examined by terracotta tile deployments, and later stages of coral community development were examined by in-situ visual surveys within fixed 25 x 25 cm quadrats on the rock and concrete substrates. Mean coral density on the tiles varied from 113 ± 17 SE to 909 ± 85 SE per m2 over five deployments, whereas mean coral density in the quadrats was only 6.0 ± 1.0 SE per m2 at eight months post construction, increasing to 24.0 ± 2.1 SE per m2 at 62 months post construction. Coral taxa colonising the artificial reef were a subset of those on the surrounding natural reef, but occurred in different proportions— Pseudosiderastreatayami , Mycediumelephantotus and Leptastrea purpurea being disproportionately abundant on the artificial reef. Coral cover increased rapidly in the later stages of the study, reaching 2.3 ± 0.7 SE % at 62 months post construction. This study indicates that simple materials of opportunity can provide a suitable substrate for coral recruitment in Dampier Harbour, and that natural colonisation at the study site remains sufficient to initiate a coral community on artificial substrate despite ongoing natural and anthropogenic perturbations. PMID:24040405

Coral colonisation of an artificial reef in a turbid nearshore environment, Dampier Harbour, western Australia.

PubMed

Blakeway, David; Byers, Michael; Stoddart, James; Rossendell, Jason

2013-01-01

A 0.6 hectare artificial reef of local rock and recycled concrete sleepers was constructed in December 2006 at Parker Point in the industrial port of Dampier, western Australia, with the aim of providing an environmental offset for a nearshore coral community lost to land reclamation. Corals successfully colonised the artificial reef, despite the relatively harsh environmental conditions at the site (annual water temperature range 18-32°C, intermittent high turbidity, frequent cyclones, frequent nearby ship movements). Coral settlement to the artificial reef was examined by terracotta tile deployments, and later stages of coral community development were examined by in-situ visual surveys within fixed 25 x 25 cm quadrats on the rock and concrete substrates. Mean coral density on the tiles varied from 113 ± 17 SE to 909 ± 85 SE per m(2) over five deployments, whereas mean coral density in the quadrats was only 6.0 ± 1.0 SE per m(2) at eight months post construction, increasing to 24.0 ± 2.1 SE per m(2) at 62 months post construction. Coral taxa colonising the artificial reef were a subset of those on the surrounding natural reef, but occurred in different proportions--Pseudosiderastrea tayami, Mycedium elephantotus and Leptastrea purpurea being disproportionately abundant on the artificial reef. Coral cover increased rapidly in the later stages of the study, reaching 2.3 ± 0.7 SE % at 62 months post construction. This study indicates that simple materials of opportunity can provide a suitable substrate for coral recruitment in Dampier Harbour, and that natural colonisation at the study site remains sufficient to initiate a coral community on artificial substrate despite ongoing natural and anthropogenic perturbations.

Deep Learning in Medical Image Analysis.

PubMed

Shen, Dinggang; Wu, Guorong; Suk, Heung-Il

2017-06-21

This review covers computer-assisted analysis of images in the field of medical imaging. Recent advances in machine learning, especially with regard to deep learning, are helping to identify, classify, and quantify patterns in medical images. At the core of these advances is the ability to exploit hierarchical feature representations learned solely from data, instead of features designed by hand according to domain-specific knowledge. Deep learning is rapidly becoming the state of the art, leading to enhanced performance in various medical applications. We introduce the fundamentals of deep learning methods and review their successes in image registration, detection of anatomical and cellular structures, tissue segmentation, computer-aided disease diagnosis and prognosis, and so on. We conclude by discussing research issues and suggesting future directions for further improvement.

Compact Deep-Space Optical Communications Transceiver

NASA Technical Reports Server (NTRS)

Roberts, W. Thomas; Charles, Jeffrey R.

2009-01-01

Deep space optical communication transceivers must be very efficient receivers and transmitters of optical communication signals. For deep space missions, communication systems require high performance well beyond the scope of mere power efficiency, demanding maximum performance in relation to the precious and limited mass, volume, and power allocated. This paper describes the opto-mechanical design of a compact, efficient, functional brassboard deep space transceiver that is capable of achieving megabyte-per-second rates at Mars ranges. The special features embodied to enhance the system operability and functionality, and to reduce the mass and volume of the system are detailed. System tests and performance characteristics are described in detail. Finally, lessons learned in the implementation of the brassboard design and suggestions for improvements appropriate for a flight prototype are covered.

Detecting deep crustal magma movement: Exploring linkages between increased gas emission, deep seismicity, and deformation (Invited)

NASA Astrophysics Data System (ADS)

Werner, C. A.; Poland, M. P.; Power, J. A.; Sutton, A. J.; Elias, T.; Grapenthin, R.; Thelen, W. A.

2013-12-01

Typically in the weeks to days before a volcanic eruption there are indisputable signals of unrest that can be identified in geophysical and geochemical data. Detection of signals of volcanic unrest months to years prior to an eruption, however, relies on our ability to recognize and link more subtle changes. Deep long-period earthquakes, typically 10-45 km beneath volcanoes, are thought to represent magma movement and may indicate near future unrest. Carbon dioxide (CO2 ) exsolves from most magmas at similar depths and increases in CO2 discharge may also provide a months-to-years precursor as it emits at the surface in advance of the magma from which it exsolved. Without the use of sensitive monitoring equipment and routine measurements, changes in CO2 can easily go undetected. Finally, inflation of the surface, through use of InSAR or GPS stations (especially at sites tens of km from the volcano) can also indicate accumulation of magma in the deep crust. Here we present three recent examples, from Redoubt, Kilauea, and Mammoth Mountain volcanoes, where increases in CO2 emission, deep long-period earthquakes, and surface deformation data indicate either the intrusion of magma into the deep crust in the months to years preceding volcanic eruptions or a change in ongoing volcanic unrest. At Redoubt volcano, Alaska, elevated CO2 emission (~ 1200 t/d, or roughly 20 times the background emission) was measured in October, 2008, over 5 months prior to the first magmatic eruption in March, 2009. In addition to CO2 release, deep long-period earthquakes were first recorded in December, 2008, and a deep deformation signal was detected starting in May 2008, albeit retrospectively. At Kilauea, Hawaii, increases in CO2 emissions from the summit (up to nearly 25 kt/d, over three times the background emission) were measured mid-2004, roughly coincident with a change in deformation behavior from deflation to inflation. Nearly 3 years later, a change in eruptive activity occurred

Deep water recycling through time

PubMed Central

Magni, Valentina; Bouilhol, Pierre; van Hunen, Jeroen

2014-01-01

We investigate the dehydration processes in subduction zones and their implications for the water cycle throughout Earth's history. We use a numerical tool that combines thermo-mechanical models with a thermodynamic database to examine slab dehydration for present-day and early Earth settings and its consequences for the deep water recycling. We investigate the reactions responsible for releasing water from the crust and the hydrated lithospheric mantle and how they change with subduction velocity (vs), slab age (a) and mantle temperature (Tm). Our results show that faster slabs dehydrate over a wide area: they start dehydrating shallower and they carry water deeper into the mantle. We parameterize the amount of water that can be carried deep into the mantle, W (×105 kg/m2), as a function of vs (cm/yr), a (Myrs), and Tm (°C):. We generally observe that a 1) 100°C increase in the mantle temperature, or 2) ∼15 Myr decrease of plate age, or 3) decrease in subduction velocity of ∼2 cm/yr all have the same effect on the amount of water retained in the slab at depth, corresponding to a decrease of ∼2.2×105 kg/m2 of H2O. We estimate that for present-day conditions ∼26% of the global influx water, or 7×108 Tg/Myr of H2O, is recycled into the mantle. Using a realistic distribution of subduction parameters, we illustrate that deep water recycling might still be possible in early Earth conditions, although its efficiency would generally decrease. Indeed, 0.5–3.7 × 108 Tg/Myr of H2O could still be recycled in the mantle at 2.8 Ga. Key Points Deep water recycling might be possible even in early Earth conditions We provide a scaling law to estimate the amount of H2O flux deep into the mantle Subduction velocity has a a major control on the crustal dehydration pattern PMID:26321881

Deep water recycling through time.

PubMed

Magni, Valentina; Bouilhol, Pierre; van Hunen, Jeroen

2014-11-01

We investigate the dehydration processes in subduction zones and their implications for the water cycle throughout Earth's history. We use a numerical tool that combines thermo-mechanical models with a thermodynamic database to examine slab dehydration for present-day and early Earth settings and its consequences for the deep water recycling. We investigate the reactions responsible for releasing water from the crust and the hydrated lithospheric mantle and how they change with subduction velocity ( v s ), slab age ( a ) and mantle temperature (T m ). Our results show that faster slabs dehydrate over a wide area: they start dehydrating shallower and they carry water deeper into the mantle. We parameterize the amount of water that can be carried deep into the mantle, W (×10 5 kg/m 2 ), as a function of v s (cm/yr), a (Myrs), and T m (°C):[Formula: see text]. We generally observe that a 1) 100°C increase in the mantle temperature, or 2) ∼15 Myr decrease of plate age, or 3) decrease in subduction velocity of ∼2 cm/yr all have the same effect on the amount of water retained in the slab at depth, corresponding to a decrease of ∼2.2×10 5 kg/m 2 of H 2 O. We estimate that for present-day conditions ∼26% of the global influx water, or 7×10 8 Tg/Myr of H 2 O, is recycled into the mantle. Using a realistic distribution of subduction parameters, we illustrate that deep water recycling might still be possible in early Earth conditions, although its efficiency would generally decrease. Indeed, 0.5-3.7 × 10 8 Tg/Myr of H 2 O could still be recycled in the mantle at 2.8 Ga. Deep water recycling might be possible even in early Earth conditions We provide a scaling law to estimate the amount of H 2 O flux deep into the mantle Subduction velocity has a a major control on the crustal dehydration pattern.

Ka-band (32 GHz) allocations for deep space

NASA Technical Reports Server (NTRS)

Degroot, N. F.

1987-01-01

At the 1979 World Administrative Conference, two new bands were allocated for deep space telecommunications: 31.8 to 32.3 GHz, space-to-Earth, and 34.2 to 34.7 GHz, Earth-to-space. These bands provide opportunity for further development of the Deep Space Network and its support of deep space research. The history of the process by which JPL/NASA developed the rationale, technical background, and statement of requirement for the bands are discussed. Based on this work, United States proposals to the conference included the bands, and subsequent U.S. and NASA participation in the conference led to successful allocations for deep space telecommunications in the 30 GHz region of the spectrum. A detailed description of the allocations is included.

Deep earthquakes beneath the Fiji Basin, SW Pacific: Earth's most intense deep seismicity in stagnant slabs

USGS Publications Warehouse

Okal, E.A.; Kirby, S.H.

1998-01-01

Previous work has suggested that many of the deep earthquakes beneath the Fiji Basin occur in slab material that has been detached and foundered to the bottom of the transition zone or has been laid down by trench migration in a similar recumbent position. Since nowhere else in the Earth do so many earthquakes occur in slabs stagnated in the transition zone, these earthquakes merit closer study. Accordingly, we have assembled from historical and modern data a comprehensive catalogue of the relocated hypocenters and focal mechanisms of well-located deep events in the geographic area between the bottoms of the main Vanuatu and Tonga Wadati-Benioff zones. Two regions of deep seismogenesis are recognized there: (i) 163 deep shocks have occurred north of 15??S in the Vityaz Group from 1949 to 1996. These seismological observations and the absence of other features characteristic of active subduction suggest that the Vityaz group represents deep failure in a detached slab that has foundered to a horizontal orientation near the bottom of the transition zone. (ii) Another group of nearly 50 'outboard' deep shocks occur between about 450 and 660 km depth, west of the complexly buckled and offset western edge of the Tonga Wadati-Benioff zone. Their geometry is in the form of two or possibly three small-circle arcs that roughly parallel the inferred motion of Tonga trench migration. Earthquakes in the southernmost of these arcs occur in a recumbent high-seismic-wavespeed slab anomaly that connects both to the main inclined Tonga anomaly to the east and a lower mantle anomaly to the west [Van der Hilst, R., 1995. Complex morphology of subducted lithosphere in the mantle beneath the Tonga trench. Nature, Vol. 374, pp. 154-157.]. Both groups show complexity in their focal mechanisms. The major question raised by these observations is the cause of this apparent temporary arrest in the descent of the Tonga slab into the lower mantle. We approach these questions by considering the

The deep space network

NASA Technical Reports Server (NTRS)

1977-01-01

A Deep Space Network progress report is presented dealing with in flight project support, tracking and data acquisition research and technology, network engineering, hardware and software implementation, and operations.

Deep neural networks to enable real-time multimessenger astrophysics

NASA Astrophysics Data System (ADS)

George, Daniel; Huerta, E. A.

2018-02-01

Gravitational wave astronomy has set in motion a scientific revolution. To further enhance the science reach of this emergent field of research, there is a pressing need to increase the depth and speed of the algorithms used to enable these ground-breaking discoveries. We introduce Deep Filtering—a new scalable machine learning method for end-to-end time-series signal processing. Deep Filtering is based on deep learning with two deep convolutional neural networks, which are designed for classification and regression, to detect gravitational wave signals in highly noisy time-series data streams and also estimate the parameters of their sources in real time. Acknowledging that some of the most sensitive algorithms for the detection of gravitational waves are based on implementations of matched filtering, and that a matched filter is the optimal linear filter in Gaussian noise, the application of Deep Filtering using whitened signals in Gaussian noise is investigated in this foundational article. The results indicate that Deep Filtering outperforms conventional machine learning techniques, achieves similar performance compared to matched filtering, while being several orders of magnitude faster, allowing real-time signal processing with minimal resources. Furthermore, we demonstrate that Deep Filtering can detect and characterize waveform signals emitted from new classes of eccentric or spin-precessing binary black holes, even when trained with data sets of only quasicircular binary black hole waveforms. The results presented in this article, and the recent use of deep neural networks for the identification of optical transients in telescope data, suggests that deep learning can facilitate real-time searches of gravitational wave sources and their electromagnetic and astroparticle counterparts. In the subsequent article, the framework introduced herein is directly applied to identify and characterize gravitational wave events in real LIGO data.

Deep-Sea coral evidence for rapid change in ventilation of the deep north atlantic 15,400 years Ago

PubMed

Adkins; Cheng; Boyle; Druffel; Edwards

1998-05-01

Coupled radiocarbon and thorium-230 dates from benthic coral species reveal that the ventilation rate of the North Atlantic upper deep water varied greatly during the last deglaciation. Radiocarbon ages in several corals of the same age, 15.41 +/- 0.17 thousand years, and nearly the same depth, 1800 meters, in the western North Atlantic Ocean increased by as much as 670 years during the 30- to 160-year life spans of the samples. Cadmium/calcium ratios in one coral imply that the nutrient content of these deep waters also increased. Our data show that the deep ocean changed on decadal-centennial time scales during rapid changes in the surface ocean and the atmosphere.

[Multiple cephalic deep granuloma annulare of children].

PubMed

Bulinckx, A; Cambier, N; Wayllace Gaspar, L; Théate, I; Roquet-Gravy, P P; Bessis, D

2017-10-01

Deep granuloma annulare is a fairly rare variety of granuloma annulare. It is seen predominantly in children and mainly affects the anterior aspect of the legs and the top of the feet; cephalic presentation is rare. Below, we report three cases of deep granuloma annulare in children presenting solely at the cephalic extremity. Case 1: a six-year-old boy presented 7 cutaneous nodules measuring 1 to 2cm that were flesh-coloured, insensitive to palpation, of hard consistency and deeply attached. The lesions were grouped together on the anterior half of the left temporal fossa. While spontaneous regression of the three nodules was noted in the month following cutaneous biopsy, these nodules recurred a few months later. Case 2: a four-year-old girl with five deep cephalic nodules measuring around one centimetre and the colour of normal skin were seen on her right temporal fossa. The child was lost to follow-up after biopsy. Case 3: a four-month-old infant was presenting some 15 deep cutaneous nodules arranged in linear fashion on the forehead next to the left temporal fossa. These nodules regressed spontaneously one month after biopsy. In all three cases, histological examination confirmed the diagnosis of deep granuloma annulare. There have been few published cases of multiple, cephalic, deep granuloma annulare at a single site in children. The condition has an extensive differential diagnosis that includes malignant tumours; in addition, histological confirmation is normally essential. Treatment is not qualified and therapeutic extension with clinical monitoring alone may frequently be recommended. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Deep-sea Hexactinellida (Porifera) of the Weddell Sea

NASA Astrophysics Data System (ADS)

Janussen, Dorte; Tabachnick, Konstantin R.; Tendal, Ole S.

2004-07-01

New Hexactinellida from the deep Weddel Sea are described. This moderately diverse hexactinellid fauna includes 14 species belonging to 12 genera, of which five species and one subgenus are new to science: Periphragella antarctica n. sp., Holascus pseudostellatus n. sp., Caulophacus (Caulophacus) discohexactinus n. sp., C. ( Caulodiscus) brandti n. sp., C. ( Oxydiscus) weddelli n. sp., and C. ( Oxydiscus) n. subgen. So far, 20 hexactinellid species have been reported from the deep Weddell Sea, 15 are known from the northern part and 10 only from here, while 10 came from the southern area, and five of these only from there. However, this apparent high "endemism" of Antarctic hexactinellid sponges is most likely the result of severe undersampling of the deep-sea fauna. We find no reason to believe that a division between an oceanic and a more continental group of species exists. The current poor database indicates that a substantial part of the deep hexactinellid fauna of the Weddell Sea is shared with other deep-sea regions, but it does not indicate a special biogeographic relationship with any other ocean.

Deepwater Program: Lophelia II, continuing ecological research on deep-sea corals and deep-reef habitats in the Gulf of Mexico

USGS Publications Warehouse

Demopoulos, Amanda W.J.; Ross, Steve W.; Kellogg, Christina A.; Morrison, Cheryl L.; Nizinski, Martha S.; Prouty, Nancy G.; Bourque, Jill R.; Galkiewicz, Julie P.; Gray, Michael A.; Springmann, Marcus J.; Coykendall, D. Katharine; Miller, Andrew; Rhode, Mike; Quattrini, Andrea; Ames, Cheryl L.; Brooke, Sandra D.; McClain Counts, Jennifer; Roark, E. Brendan; Buster, Noreen A.; Phillips, Ryan M.; Frometa, Janessy

2017-12-11

The deep sea is a rich environment composed of diverse habitat types. While deep-sea coral habitats have been discovered within each ocean basin, knowledge about the ecology of these habitats and associated inhabitants continues to grow. This report presents information and results from the Lophelia II project that examined deep-sea coral habitats in the Gulf of Mexico. The Lophelia II project focused on Lophelia pertusa habitats along the continental slope, at depths ranging from 300 to 1,000 meters. The chapters are authored by several scientists from the U.S. Geological Survey, National Oceanic and Atmospheric Administration, University of North Carolina Wilmington, and Florida State University who examined the community ecology (from microbes to fishes), deep-sea coral age, growth, and reproduction, and population connectivity of deep-sea corals and inhabitants. Data from these studies are presented in the chapters and appendixes of the report as well as in journal publications. This study was conducted by the Ecosystems Mission Area of the U.S. Geological Survey to meet information needs identified by the Bureau of Ocean Energy Management.

Wishart Deep Stacking Network for Fast POLSAR Image Classification.

PubMed

Jiao, Licheng; Liu, Fang

2016-05-11

Inspired by the popular deep learning architecture - Deep Stacking Network (DSN), a specific deep model for polarimetric synthetic aperture radar (POLSAR) image classification is proposed in this paper, which is named as Wishart Deep Stacking Network (W-DSN). First of all, a fast implementation of Wishart distance is achieved by a special linear transformation, which speeds up the classification of POLSAR image and makes it possible to use this polarimetric information in the following Neural Network (NN). Then a single-hidden-layer neural network based on the fast Wishart distance is defined for POLSAR image classification, which is named as Wishart Network (WN) and improves the classification accuracy. Finally, a multi-layer neural network is formed by stacking WNs, which is in fact the proposed deep learning architecture W-DSN for POLSAR image classification and improves the classification accuracy further. In addition, the structure of WN can be expanded in a straightforward way by adding hidden units if necessary, as well as the structure of the W-DSN. As a preliminary exploration on formulating specific deep learning architecture for POLSAR image classification, the proposed methods may establish a simple but clever connection between POLSAR image interpretation and deep learning. The experiment results tested on real POLSAR image show that the fast implementation of Wishart distance is very efficient (a POLSAR image with 768000 pixels can be classified in 0.53s), and both the single-hidden-layer architecture WN and the deep learning architecture W-DSN for POLSAR image classification perform well and work efficiently.

The DEEP-South: Scheduling and Data Reduction Software System

NASA Astrophysics Data System (ADS)

Yim, Hong-Suh; Kim, Myung-Jin; Bae, Youngho; Moon, Hong-Kyu; Choi, Young-Jun; Roh, Dong-Goo; the DEEP-South Team

2015-08-01

The DEep Ecliptic Patrol of the Southern sky (DEEP-South), started in October 2012, is currently in test runs with the first Korea Microlensing Telescope Network (KMTNet) 1.6 m wide-field telescope located at CTIO in Chile. While the primary objective for the DEEP-South is physical characterization of small bodies in the Solar System, it is expected to discover a large number of such bodies, many of them previously unknown.An automatic observation planning and data reduction software subsystem called "The DEEP-South Scheduling and Data reduction System" (the DEEP-South SDS) is currently being designed and implemented for observation planning, data reduction and analysis of huge amount of data with minimum human interaction. The DEEP-South SDS consists of three software subsystems: the DEEP-South Scheduling System (DSS), the Local Data Reduction System (LDR), and the Main Data Reduction System (MDR). The DSS manages observation targets, makes decision on target priority and observation methods, schedules nightly observations, and archive data using the Database Management System (DBMS). The LDR is designed to detect moving objects from CCD images, while the MDR conducts photometry and reconstructs lightcurves. Based on analysis made at the LDR and the MDR, the DSS schedules follow-up observation to be conducted at other KMTNet stations. In the end of 2015, we expect the DEEP-South SDS to achieve a stable operation. We also have a plan to improve the SDS to accomplish finely tuned observation strategy and more efficient data reduction in 2016.

A Modeling Study of Deep Water Renewal in the Red Sea

NASA Astrophysics Data System (ADS)

Yao, F.; Hoteit, I.

2016-02-01

Deep water renewal processes in the Red Sea are examined in this study using a 50-year numerical simulation from 1952-2001. The deep water in the Red Sea below the thermocline ( 200 m) exhibits a near-uniform vertical structure in temperature and salinity, but geochemical tracer distributions, such as 14C and 3He, and dissolved oxygen concentrations indicate that the deep water is renewed on time scales as short as 36 years. The renewal process is accomplished through a deep overturning cell that consists of a southward bottom current and a northward returning current at depths of 400-600 m. Three sources regions are proposed for the formation of the deep water, including two deep outflows from the Gulfs of Aqaba and Suez and winter deep convections in the northern Red Sea. The MITgcm (MIT general circulation model), which has been used to simulate the shallow overturning circulations in the Red Sea, is configured in this study with increased resolutions in the deep water. During the 50 years of simulation, artificial passive tracers added in the model indicate that the deep water in the Red Sea was only episodically renewed during some anomalously cold years; two significant episodes of deep water renewal are reproduced in the winters of 1983 and 1992, in accordance with reported historical hydrographic observations. During these renewal events, deep convections reaching the bottom of the basin occurred, which further facilitated deep sinking of the outflows from the Gulfs of Aqaba and Suez. Ensuing spreading of the newly formed deep water along the bottom caused upward displacements of thermocline, which may have profound effects on the water exchanges in the Strait of Bab el Mandeb between the Red Sea and the Gulf of Aden and the functioning of the ecosystem in the Red Sea by changing the vertical distributions of nutrients.

The biomass of the deep-sea benthopelagic plankton

NASA Astrophysics Data System (ADS)

Wishner, K. F.

1980-04-01

Deep-sea benthopelagic plankton samples were collected with a specially designed opening-closing net system 10 to 100 m above the bottom in five different oceanic regions at depths from 1000 to 4700 m. Benthopelagic plankton biomasses decrease exponentially with depth. At 1000 m the biomass is about 1% that of the surface zooplankton, at 5000 m about 0.1%. Effects of differences in surface primary productivity on deep-sea plankton biomass are much less than the effect of depth and are detectable only in a few comparisons of extreme oceanic regions. The biomass at 10 m above the bottom is greater than that at 100 m above the bottom (in a three-sample comparison), which could be a consequence of an enriched near-bottom environment. The deep-sea plankton biomass in the Red Sea is anomalously low. This may be due to increased decomposition rates in the warm (22°C) deep Red Sea water, which prevent much detritus from reaching the deep sea. A model of organic carbon utilization in the benthic boundary layer (bottom 100 m), incorporating results from deep-sea sediment trap and respiration studies, indicates that the benthopelagic plankton use only a small amount of the organic carbon flux. A large fraction of the flux is unaccounted for by present estimates of benthic and benthopelagic respiration.

Evolving Deep Networks Using HPC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, Steven R.; Rose, Derek C.; Johnston, Travis

While a large number of deep learning networks have been studied and published that produce outstanding results on natural image datasets, these datasets only make up a fraction of those to which deep learning can be applied. These datasets include text data, audio data, and arrays of sensors that have very different characteristics than natural images. As these “best” networks for natural images have been largely discovered through experimentation and cannot be proven optimal on some theoretical basis, there is no reason to believe that they are the optimal network for these drastically different datasets. Hyperparameter search is thus oftenmore » a very important process when applying deep learning to a new problem. In this work we present an evolutionary approach to searching the possible space of network hyperparameters and construction that can scale to 18, 000 nodes. This approach is applied to datasets of varying types and characteristics where we demonstrate the ability to rapidly find best hyperparameters in order to enable practitioners to quickly iterate between idea and result.« less

Deep Space Gateway - Enabling Missions to Mars

NASA Technical Reports Server (NTRS)

Rucker, Michelle; Connolly, John

2017-01-01

There are many opportunities for commonality between Lunar vicinity and Mars mission hardware and operations. Best approach: Identify Mars mission risks that can be bought down with testing in the Lunar vicinity, then explore hardware and operational concepts that work for both missions with minimal compromise. Deep Space Transport will validate the systems and capabilities required to send humans to Mars orbit and return to Earth. Deep Space Gateway provides a convenient assembly, checkout, and refurbishment location to enable Mars missions Current deep space transport concept is to fly missions of increasing complexity: Shakedown cruise, Mars orbital mission, Mars surface mission; Mars surface mission would require additional elements.

Development of deep-ultraviolet metal vapor lasers

NASA Astrophysics Data System (ADS)

Sabotinov, Nikola V.

2004-06-01

Deep ultraviolet laser generation is of great interest in connection with both the development of new industrial technologies and applications in medicine, biology, chemistry, etc. The development of metal vapor UV lasers oscillating in the pulsed mode with high pulse repetition frequencies and producing high average output powers is of particular interest for microprocessing of polymers, photolithography and fluorescence applications. At present, metal vapor lasers generate deep-UV radiation on the base of two methods. The first method is non-linear conversion of powerful laser generation from the visible region into the deep ultraviolet region. The second method is direct UV laser action on ion and atomic transitions of different metals.

30 CFR 203.41 - If I have a qualified deep well or a qualified phase 1 ultra-deep well, what royalty relief would...

Code of Federal Regulations, 2011 CFR

2011-07-01

... MINERALS REVENUE MANAGEMENT RELIEF OR REDUCTION IN ROYALTY RATES OCS Oil, Gas, and Sulfur General Royalty Relief for Drilling Deep Gas Wells on Leases Not Subject to Deep Water Royalty Relief § 203.41 If I have... not . . . And if it later . . . Then your lease . . . (1) produced gas or oil from any deep well or...

The Deep Space Network

NASA Technical Reports Server (NTRS)

1977-01-01

The various systems and subsystems are discussed for the Deep Space Network (DSN). A description of the DSN is presented along with mission support, program planning, facility engineering, implementation and operations.

Spaceport operations for deep space missions

NASA Technical Reports Server (NTRS)