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    In:  EPIC3The Cryosphere, Copernicus, 10(5), pp. 2517-2532, ISSN: 1994-0424
    Publikationsdatum: 2020-09-06
    Beschreibung: Permafrost temperatures are increasing in Alaska due to climate change and in some cases permafrost is thawing and degrading. In areas where degradation has already occurred the effects can be dramatic, resulting in changing ecosystems, carbon release, and damage to infrastructure. However, in many areas we lack baseline data, such as subsurface temperatures, needed to assess future changes and potential risk areas. Besides climate, the physical properties of the vegetation cover and subsurface material have a major influence on the thermal state of permafrost. These properties are often directly related to the type of ecosystem overlaying permafrost. In this paper we demonstrate that classifying the landscape into general ecotypes is an effective way to scale up permafrost thermal data collected from field monitoring sites. Additionally, we find that within some ecotypes the absence of a moss layer is indicative of the absence of near-surface permafrost. As a proof of concept, we used the ground temperature data collected from the field sites to recode an ecotype land cover map into a map of mean annual ground temperature ranges at 1 m depth based on analysis and clustering of observed thermal regimes. The map should be useful for decision making with respect to land use and understanding how the landscape might change under future climate scenarios.
    Repository-Name: EPIC Alfred Wegener Institut
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  • 2
    Publikationsdatum: 2016-11-16
    Beschreibung: Permafrost presence is determined by a complex interaction of climatic, topographic, and ecological conditions operating over long time scales. In particular, vegetation and organic layer characteristics may act to protect permafrost in regions with a mean annual air temperature (MAAT) above 0°C. In this study, we document the presence of residual permafrost plateaus in the western Kenai Peninsula lowlands of south-central Alaska, a region with a MAAT of 1.5+/-1 °C (1981–2010). Continuous ground temperature measurements between 16 September 2012 and 15 September 2015, using calibrated thermistor strings, documented the presence of warm permafrost (-0.04 to -0.08 °C). Field measurements (probing) on several plateau features during the fall of 2015 showed that the depth to the permafrost table averaged 1.48m but at some locations was as shallow as 0.53 m. Late winter surveys (augering, coring, and GPR) in 2016 showed that the average seasonally frozen ground thickness was 0.45 m, overlying a talik above the permafrost table. Measured permafrost thickness ranged from 0.33 to 〉6.90 m. Manual interpretation of historic aerial photography acquired in 1950 indicates that residual permafrost plateaus covered 920 ha as mapped across portions of four wetland complexes encompassing 4810 ha. However, between 1950 and ca. 2010, permafrost plateau extent decreased by 60.0 %, with lateral feature degradation accounting for 85.0% of the reduction in area. Permafrost loss on the Kenai Peninsula is likely associated with a warming climate, wildfires that remove the protective forest and organic layer cover, groundwater flow at depth, and lateral heat transfer from wetland surface waters in the summer. Better understanding the resilience and vulnerability of ecosystem-protected permafrost is critical for mapping and predicting future permafrost extent and degradation across all permafrost regions that are currently warming. Further work should focus on reconstructing permafrost history in south-central Alaska as well as additional contemporary observations of these ecosystem-protected permafrost sites south of the regions with relatively stable permafrost.
    Repository-Name: EPIC Alfred Wegener Institut
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  • 3
    Publikationsdatum: 2017-04-04
    Beschreibung: In recent years, an increasing number of surveys have definitively confirmed the seasonal presence of fin whales (Balaenoptera physalus) in highly productive regions of the Mediterranean Sea. Despite this, very little is yet known about the routes that the species seasonally follows within the Mediterranean basin and, particularly, in the Ionian area. The present study assesses for the first time fin whale acoustic presence offshore Eastern Sicily (Ionian Sea), throughout the processing of about 10 months of continuous acoustic monitoring. The recording of fin whale vocalizations was made possible by the cabled deep-sea multidisciplinary observatory, “NEMO-SN1”, deployed 25 km off the Catania harbor at a depth of about 2,100 meters. NEMO-SN1 is an operational node of the European Multidisciplinary Seafloor and water-column Observatory (EMSO) Research Infrastructure. The observatory was equipped with a low-frequency hydrophone (bandwidth: 0.05 Hz–1 kHz, sampling rate: 2 kHz) which continuously acquired data from July 2012 to May 2013. About 7,200 hours of acoustic data were analyzed by means of spectrogram display. Calls with the typical structure and patterns associated to the Mediterranean fin whale population were identified and monitored in the area for the first time. Furthermore, a background noise analysis within the fin whale communication frequency band (17.9–22.5 Hz) was conducted to investigate possible detection-masking effects. The study confirms the hypothesis that fin whales are present in the Ionian Sea throughout all seasons, with peaks in call detection rate during spring and summer months. The analysis also demonstrates that calls were more frequently detected in low background noise conditions. Further analysis will be performed to understand whether observed levels of noise limit the acoustic detection of the fin whales vocalizations, or whether the animals vocalize less in the presence of high background noise.
    Beschreibung: Published
    Beschreibung: e0141838
    Beschreibung: 3A. Ambiente Marino
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): Whales ; Bioacoustics ; Background noise (acoustics) ; Acoustic signals ; Sperm whales ; Vocalization ; Acoustics ; Data acquisition ; 03. Hydrosphere::03.01. General::03.01.08. Instruments and techniques ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 03. Hydrosphere::03.02. Hydrology::03.02.07. Instruments and techniques ; 03. Hydrosphere::03.04. Chemical and biological::03.04.99. General or miscellaneous
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 4
    Publikationsdatum: 2016-05-26
    Beschreibung: Permafrost presence is determined by a complex interaction of climatic, topographic, and ecological conditions operating over long time scales. In particular, vegetation and organic layer characteristics may act to protect permafrost in regions with a mean annual air temperature (MAAT) above 0 °C. In this study, we document the presence of residual permafrost plateaus on the western Kenai Peninsula lowlands of southcentral Alaska, a region with a MAAT of 1.5 ± 1 °C (1981 to 2010). Continuous ground temperature measurements between 16 September 2012 and 15 September 2015, using calibrated thermistor strings, documented the presence of warm permafrost (−0.04 to −0.08 °C). Field measurements (probing) on several plateau features during the fall of 2015 showed that the depth to the permafrost table averaged 1.48 m but was as shallow as 0.53 m. Late winter surveys (drilling, coring, and GPR) in 2016 showed that the average seasonally frozen ground thickness was 0.45 m, overlying a talik above the permafrost table. Measured permafrost thickness ranged from 0.33 to 〉 6.90 m. Manual interpretation of historic aerial photography acquired in 1950 indicates that residual permafrost plateaus covered 920 ha as mapped across portions of four wetland complexes encompassing 4810 ha. However, between 1950 and ca. 2010, permafrost plateau extent decreased by 60 %, with lateral feature degradation accounting for 85 % of the reduction in area. Permafrost loss on the Kenai Peninsula is likely associated with a warming climate, wildfires that remove the protective forest and organic layer cover, groundwater flow at depth, and lateral heat transfer from wetland surface waters in the summer. Better understanding the resilience and vulnerability of ecosystem-protected permafrost is critical for mapping and predicting future permafrost extent and degradation across all permafrost regions that are currently warming. Further work should focus on reconstructing permafrost history in southcentral Alaska as well as additional contemporary observations of these ecosystem-protected permafrost sites lying south of the regions with relatively stable permafrost.
    Repository-Name: EPIC Alfred Wegener Institut
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  • 5
    Publikationsdatum: 2016-02-05
    Beschreibung: Background: Reactive oxygen (ROS) and nitrogen (RNS) species are produced during normal unstressed metabolic activity in aerobic tissues. Most analytical work uses tissue homogenates, and lacks spatial information on the tissue specific sites of actual ROS formation. Live-imaging techniques (LIT) utilize target-specific fluorescent dyes to visualize biochemical processes at cellular level. Results: Together with oxidative stress measurements, here we report application of LIT to bivalve gills for ex-vivo analysis of gill physiology and mapping of ROS and RNS formation in the living tissue. Our results indicate that a) mitochondria located in the basal parts of the epithelial cells close to the blood vessels are hyperpolarized with high Δψm, whereas b) the peripheral mitochondria close to the cilia have low (depolarized) Δψm. These mitochondria are densely packed (mitotracker Deep Red 633 staining), have acidic pH (Ageladine-A) and collocate with high formation of nitric oxide (DAF-2DA staining). NO formation is also observed in the endothelial cells surrounding the filament blood sinus. ROS (namely H2O2, HOO• and ONOO− radicals, assessed through C-H2DFFDA staining) are mainly formed within the blood sinus of the filaments and are likely to be produced by hemocytes as defense against invading pathogens. On the ventral bend of the gills, subepithelial mucus glands contain large mucous vacuoles showing higher fluorescence intensities for O2 •- than the rest of the tissue. Whether this O2 •- production is instrumental to mucus formation or serves antimicrobial protection of the gill surface is unknown. Cells of the ventral bends contain the superoxide forming mucocytes and show significantly higher protein carbonyl formation than the rest of the gill tissue. Conclusions: In summary, ROS and RNS formation is highly compartmentalized in bivalve gills under unstressed conditions. The main mechanisms are the differentiation of mitochondria membrane potential and basal ROS formation in inner and outer filament layers, as well as potentially antimicrobial ROS formation in the central blood vessel. Our results provide new insight into this subject and highlight the fact that studying ROS formation in tissue homogenates may not be adequate to understand the underlying mechanism in complex tissues. Keywords: Bivalve, Gill, Live-imaging, Fluorescence, Mitochondria, ROS, RNS * Correspondence:
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  • 6
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Biology 13 (2015): 105, doi:10.1186/s12915-015-0213-6
    Beschreibung: The deep-sea hypersaline anoxic basins (DHABs) of the Mediterranean (water depth ~3500 m) are some of the most extreme oceanic habitats known. Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB haloclines and brines, loriciferans are the only metazoan reported to inhabit the anoxic DHAB brines. Our goal was to further investigate metazoan communities in DHAB haloclines and brines. We report observations from sediments of three DHAB (Urania, Discovery, L’Atalante) haloclines, comparing these to observations from sediments underlying normoxic waters of typical Mediterranean salinity. Due to technical difficulties, sampling of the brines was not possible. Morphotype analysis indicates nematodes are the most abundant taxon; crustaceans, loriciferans and bryozoans were also noted. Among nematodes, Daptonema was the most abundant genus; three morphotypes were noted with a degree of endemicity. The majority of rRNA sequences were from planktonic taxa, suggesting that at least some individual metazoans were preserved and inactive. Nematode abundance data, in some cases determined from direct counts of sediments incubated in situ with CellTrackerTM Green, was patchy but generally indicates the highest abundances in either normoxic control samples or in upper halocline samples; nematodes were absent or very rare in lower halocline samples. Ultrastructural analysis indicates the nematodes in L’Atalante normoxic control sediments were fit, while specimens from L’Atalante upper halocline were healthy or had only recently died and those from the lower halocline had no identifiable organelles. Loriciferans, which were only rarely encountered, were found in both normoxic control samples as well as in Discovery and L’Atalante haloclines. It is not clear how a metazoan taxon could remain viable under this wide range of conditions. We document a community of living nematodes in normoxic, normal saline deep-sea Mediterranean sediments and in the upper halocline portions of the DHABs. Occurrences of nematodes in mid-halocline and lower halocline samples did not provide compelling evidence of a living community in those zones. The possibility of a viable metazoan community in brines of DHABs is not supported by our data at this time.
    Beschreibung: Supported by NSF grants OCE-0849578 to VPE and JMB, OCE-1061391 to JMB and VPE, and The Investment in Science Fund at WHOI.
    Schlagwort(e): Athalassohaline ; Bryozoa ; CellTrackerTM Green ; Discovery ; L’Atalante ; Loricifera ; Meiofauna ; Nematoda ; Ultrastructure ; Urania
    Repository-Name: Woods Hole Open Access Server
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  • 7
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0147808, doi:10.1371/journal.pone.0147808.
    Beschreibung: The amyloid precursor protein (APP) is a causal agent in the pathogenesis of Alzheimer’s disease and is a transmembrane protein that associates with membrane-limited organelles. APP has been shown to co-purify through immunoprecipitation with a kinesin light chain suggesting that APP may act as a trailer hitch linking kinesin to its intercellular cargo, however this hypothesis has been challenged. Previously, we identified an mRNA transcript that encodes a squid homolog of human APP770. The human and squid isoforms share 60% sequence identity and 76% sequence similarity within the cytoplasmic domain and share 15 of the final 19 amino acids at the C-terminus establishing this highly conserved domain as a functionally import segment of the APP molecule. Here, we study the distribution of squid APP in extruded axoplasm as well as in a well-characterized reconstituted organelle/microtubule preparation from the squid giant axon in which organelles bind microtubules and move towards the microtubule plus-ends. We find that APP associates with microtubules by confocal microscopy and co-purifies with KI-washed axoplasmic organelles by sucrose density gradient fractionation. By electron microscopy, APP clusters at a single focal point on the surfaces of organelles and localizes to the organelle/microtubule interface. In addition, the association of APP-organelles with microtubules is an ATP dependent process suggesting that the APP-organelles contain a microtubule-based motor protein. Although a direct kinesin/APP association remains controversial, the distribution of APP at the organelle/microtubule interface strongly suggests that APP-organelles have an orientation and that APP like the Alzheimer’s protein tau has a microtubule-based function.
    Beschreibung: Research reported in this publication was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103430.
    Repository-Name: Woods Hole Open Access Server
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  • 8
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0153197, doi:10.1371/journal.pone.0153197.
    Beschreibung: Benthic dinoflagellates in the genus Gambierdiscus produce the ciguatoxin precursors responsible for the occurrence of ciguatera toxicity. The prevalence of ciguatera toxins in fish has been linked to the presence and distribution of toxin-producing species in coral reef ecosystems, which is largely determined by the presence of suitable benthic habitat and environmental conditions favorable for growth. Here using single factor experiments, we examined the effects of salinity, irradiance, and temperature on growth of 17 strains of Gambierdiscus representing eight species/phylotypes (G. belizeanus, G. caribaeus, G. carolinianus, G. carpenteri, G. pacificus, G. silvae, Gambierdiscus sp. type 4–5), most of which were established from either Marakei Island, Republic of Kiribati, or St. Thomas, United States Virgin Island (USVI). Comparable to prior studies, growth rates fell within the range of 0–0.48 divisions day-1. In the salinity and temperature studies, Gambierdiscus responded in a near Gaussian, non-linear manner typical for such studies, with optimal and suboptimal growth occurring in the range of salinities of 25 and 45 and 21.0 and 32.5°C. In the irradiance experiment, no mortality was observed; however, growth rates at 55μmol photons · m-2 · s-1 were lower than those at 110–400μmol photons · m-2 · s-1. At the extremes of the environmental conditions tested, growth rates were highly variable, evidenced by large coefficients of variability. However, significant differences in intraspecific growth rates were typically found only at optimal or near-optimal growth conditions. Polynomial regression analyses showed that maximum growth occurred at salinity and temperature levels of 30.1–38.5 and 23.8–29.2°C, respectively. Gambierdiscus growth patterns varied among species, and within individual species: G. belizeanus, G. caribaeus, G. carpenteri, and G. pacificus generally exhibited a wider range of tolerance to environmental conditions, which may explain their broad geographic distribution. In contrast, G. silvae and Gambierdiscus sp. types 4–5 all displayed a comparatively narrow range of tolerance to temperature, salinity, and irradiance.
    Beschreibung: This study was funded by the National Natural Science Foundation of China (41506137); Guangxi Natural Science Foundation (2015GXNSFCA139003), Centers for Disease Control and Prevention (U01 EH000421); USFDA (F223201000060C); NOAA NOS through the CiguaHAB program (Cooperative Agreement NA11NOS4780060, NA11NOS4780028); the Lana Vento Trust and VI-EPSCoR Program (NSF award # 346483 & 081441); and a System Fund from Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (2014BGERLXT01). Support was also provided by the Woods Hole Center for Oceans and Human Health through National Science Foundation (NSF) Grant OCE-1314642, National Institute of Environmental Health Sciences (NIEHS) Grant 1-P01-ES021923-014, as well as the China Scholarship Council.
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  • 9
    Publikationsdatum: 2022-05-25
    Beschreibung: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
    Beschreibung: Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.
    Beschreibung: This work was supported by the National Science Foundation (www.nsf.gov), grant numbers EAR-1249489 and CBET-1336496, both awarded to CMH. Personal support for CAZ was also provided by Harvard University (www.harvard.edu) and by a Ford Foundation (www.fordfoundation.org) Predoctoral Fellowship administered by the National Academies.
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  • 10
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0160830, doi:10.1371/journal.pone.0160830 .
    Beschreibung: Advances in offshore wind farm (OWF) technology have recently led to their construction in coastal waters that are deep enough to be seasonally stratified. As tidal currents move past the OWF foundation structures they generate a turbulent wake that will contribute to a mixing of the stratified water column. In this study we show that the mixing generated in this way may have a significant impact on the large-scale stratification of the German Bight region of the North Sea. This region is chosen as the focus of this study since the planning of OWFs is particularly widespread. Using a combination of idealised modelling and in situ measurements, we provide order-of-magnitude estimates of two important time scales that are key to understanding the impacts of OWFs: (i) a mixing time scale, describing how long a complete mixing of the stratification takes, and (ii) an advective time scale, quantifying for how long a water parcel is expected to undergo enhanced wind farm mixing. The results are especially sensitive to both the drag coefficient and type of foundation structure, as well as the evolution of the pycnocline under enhanced mixing conditions—both of which are not well known. With these limitations in mind, the results show that OWFs could impact the large-scale stratification, but only when they occupy extensive shelf regions. They are expected to have very little impact on large-scale stratification at the current capacity in the North Sea, but the impact could be significant in future large-scale development scenarios.
    Beschreibung: Funding was provided by the Helmholtz Foundation through the Polar Regions and Coasts in the Changing Earth System II (PACES II) program.
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  • 11
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 11 (2016): e0164107, doi:10.1371/journal.pone.0164107.
    Beschreibung: Common dolphins (Delphinus delphis) are responsible for the large majority of interactions with the pole-and-line tuna fishery in the Azores but the underlying drivers remain poorly understood. In this study we investigate the influence of various environmental and fisheries-related factors in promoting the interaction of common dolphins with this fishery and estimate the resultant catch losses. We analysed 15 years of fishery and cetacean interaction data (1998–2012) collected by observers placed aboard tuna fishing vessels. Dolphins interacted in less than 3% of the fishing events observed during the study period. The probability of dolphin interaction varied significantly between years with no evident trend over time. Generalized additive modeling results suggest that fishing duration, sea surface temperature and prey abundance in the region were the most important factors explaining common dolphin interaction. Dolphin interaction had no impact on the catches of albacore, skipjack and yellowfin tuna but resulted in significantly lower catches of bigeye tuna, with a predicted median annual loss of 13.5% in the number of fish captured. However, impact on bigeye catches varied considerably both by year and fishing area. Our work shows that rates of common dolphin interaction with the pole-and-line tuna fishery in the Azores are low and showed no signs of increase over the study period. Although overall economic impact was low, the interaction may lead to significant losses in some years. These findings emphasize the need for continued monitoring and for further research into the consequences and economic viability of potential mitigation measures.
    Beschreibung: This work was funded by Fundação para a Ciência e a Tecnologia (FCT) and DRCT/SRCTE, though FEDER, the Competitiveness Factors Operational (COMPETE), QREN European Social Fund, the Portuguese Ministry for Science and Education, under research projects TRACE (PTDC/MAR/74071/2006), FCT Exploratory Project (IF/00943/2013/CP1199/CT0001), and MAPCET (M2.1.2/F/012/2011). We acknowledge the support of Fundação para a Ciência e Tecnologia (FCT), through the strategic project UID/MAR/04292/2013 granted to MARE. We thank the Azorean Regional Government for funding POPA, the Ship-owners Association and the Association of the Tuna Canning Industries for their support to the program. MJC was supported by a DRCT doctoral grant (M3.1.2/F/008/2009). MAS was supported by POPH, QREN, European Social Fund and Portuguese Ministry for Science and Education, through an FCT Investigator grant (IF/00943/2013).
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  • 12
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 79, doi:10.1186/s40168-015-0141-2.
    Beschreibung: A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we evaluate the use of a novel device, which has no technical complexity and is easily deployable. An air-cleaning device powered by electrokinetic propulsion has been adapted to provide a universal method for collecting samples of the aerobiome. Plasma-induced charge in aerosol particles causes propulsion to and capture on a counter-electrode. The flow of ions creates net bulk airflow, with no moving parts. A device and electrode assembly have been re-designed from air-cleaning technology to provide an average air flow of 120 lpm. This compares favorably with current air sampling devices based on physical air pumping. Capture efficiency was determined by comparison with a 0.4 μm polycarbonate reference filter, using fluorescent latex particles in a controlled environment chamber. Performance was compared with the same reference filter method in field studies in three different environments. For 23 common fungal species by quantitative polymerase chain reaction (qPCR), there was 100 % sensitivity and apparent specificity of 87 %, with the reference filter taken as “gold standard.” Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. Unlike other current air sampling methods, capture of particles is determined by charge and so is not controlled by particle mass. We analyzed particle sizes captured from air, without regard to specific analyte by atomic force microscopy: particles at least as low as 100 nM could be captured from ambient air. This work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing.
    Beschreibung: This work was partly supported by Breakout Labs, a program of the Thiel Foundation, and partly from personal funds from Julian Gordon and Prasanthi Gandhi. This work was supported in part by the US Dept. of Energy under Contract DE-AC02-06CH11357.
    Schlagwort(e): Atomic force microscopy ; Reverse transcriptase PCR ; Air sampling ; Field study ; Aerosol ; Nanoparticles ; Aerobiome ; Amplicon sequencing ; Bacteria ; Molds
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  • 13
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Emerging Themes in Epidemiology 13 (2016): 2, doi:10.1186/s12982-015-0044-5.
    Beschreibung: The obesity epidemic has emerged over the past few decades and is thought to be a result of both genetic and environmental factors. A newly identified factor, the gut microbiota, which is a bacterial ecosystem residing within the gastrointestinal tract of humans, has now been implicated in the obesity epidemic. Importantly, this bacterial community is impacted by external environmental factors through a variety of undefined mechanisms. We focus this review on how the external environment may impact the gut microbiota by considering, the host’s geographic location ‘human geography’, and behavioral factors (diet and physical activity). Moreover, we explore the relationship between the gut microbiota and obesity with these external factors. And finally, we highlight here how an epidemiologic model can be utilized to elucidate causal relationships between the gut microbiota and external environment independently and collectively, and how this will help further define this important new factor in the obesity epidemic.
    Beschreibung: BTL is supported by the Department of Veterans Affairs, Veterans Health Administration, Office of Research and Development, Career Development (Grant no. 1IK2BX001587-01).
    Schlagwort(e): Obesity ; Gut microbiome ; Geographical differences
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  • 14
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 16 (2016): 108, doi:10.1186/s12862-016-0654-8.
    Beschreibung: In recent years, several types of molecular markers and new microscale skeletal characters have shown potential as powerful tools for phylogenetic reconstructions and higher-level taxonomy of scleractinian corals. Nonetheless, discrimination of closely related taxa is still highly controversial in scleractinian coral research. Here we used newly sequenced complete mitochondrial genomes and 30 microsatellites to define the genetic divergence between two closely related azooxanthellate taxa of the family Caryophylliidae: solitary Desmophyllum dianthus and colonial Lophelia pertusa. In the mitochondrial control region, an astonishing 99.8 % of nucleotides between L. pertusa and D. dianthus were identical. Variability of the mitochondrial genomes of the two species is represented by only 12 non-synonymous out of 19 total nucleotide substitutions. Microsatellite sequence (37 loci) analysis of L. pertusa and D. dianthus showed genetic similarity is about 97 %. Our results also indicated that L. pertusa and D. dianthus show high skeletal plasticity in corallum shape and similarity in skeletal ontogeny, micromorphological (septal and wall granulations) and microstructural characters (arrangement of rapid accretion deposits, thickening deposits). Molecularly and morphologically, the solitary Desmophyllum and the dendroid Lophelia appear to be significantly more similar to each other than other unambiguous coral genera analysed to date. This consequently leads to ascribe both taxa under the generic name Desmophyllum (priority by date of publication). Findings of this study demonstrate that coloniality may not be a robust taxonomic character in scleractinian corals.
    Beschreibung: This research was supported by the Spanish Ministry of Science and Innovation (CGL2011-23306 and CTM2014-57949R) and EU CoCoNET—“Towards COast to COast NETworks of marine protected areas (from the shore to the high and deep sea), coupled with sea-based wind energy potential”—from the VII FP of the European Commission under grant agreement n° 287844. This paper also benefited from the ESF COCARDE network activities and commits to the Italian Flag Project ‘Ritmare’. Fund within the Innovation Economy Operational Programme POIG.02.02.00-00-025/09
    Schlagwort(e): Mitochondrial genome ; Microsatellites ; Genetic divergence ; Skeletal plasticity ; Desmophyllum dianthus ; Lophelia pertusa
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  • 15
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 11 (2016): 46, doi:10.1186/s40793-016-0168-4.
    Beschreibung: Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.
    Beschreibung: The work was supported by the U.S. Department of Energy, Office of Science JGI under Contract No. DE-AC02-05CH11231 for CSP 2010 project 1012224; USDA NIFA Award 2011-67019-30178, and the Utah Agricultural Experiment Station, Utah State University project UTA00371.
    Schlagwort(e): Nitrosospira ; Ammonia-oxidizing bacteria ; Nitrification ; Agricultural soil ; Ammonia monooxygenase ; Nitrous oxide ; Chemolithotroph
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  • 16
    Publikationsdatum: 2022-05-25
    Beschreibung: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The definitive version was published in PLoS One 11 (2016): e0162401, doi:10.1371/journal.pone.0162401.
    Beschreibung: Heavy metals such as mercury (Hg) pose a significant health hazard through bioaccumulation and biomagnification. By penetrating cell membranes, heavy metal ions may lead to pathological conditions. Here we examined the responses of Ammonia parkinsoniana, a benthic foraminiferan, to different concentrations of Hg in the artificial sea water. Confocal images of untreated and treated specimens using fluorescent probes (Nile Red and Acridine Orange) provided an opportunity for visualizing the intracellular lipid accumulation and acidic compartment regulation. With increased Hg over time, we observed an increased number of lipid droplets, which may have acted as a detoxifying organelle where Hg is sequestered and biologically inactivated. Further, Hg seems to promote the proliferation of lysosomes both in terms of number and dimension that, at the highest level of Hg, resulted in cell death. We report, for the first time, the presence of Hg within the foraminiferal cell: at the basal part of pores, in the organic linings of the foramen/septa, and as cytoplasmic accumulations.
    Beschreibung: The research for this paper was partially made possible by the financial support from the PRIN 2010-2011 Ministero dell’Istruzione, dell’Università e della Ricerca (MIUR) (protocollo 2010RMTLYR) to RC. JMB acknowledges support from The Investment in Science Fund at WHOI. BG, JRE, AJ, LZ, and EMP were supported in part by the Office of Biological and Environmental Research, US Department of Energy (DOE) as part of the Mercury Science Focus Area at Oak Ridge National Laboratory, which is managed by UT-Battelle LLC for the DOE under contract DE-AC05-00OR22725.
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  • 17
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chemistry Central Journal 10 (2016): 75, doi:10.1186/s13065-016-0211-y.
    Beschreibung: Comprehensive two-dimensional gas chromatography (GC×GC) provides high-resolution separations across hundreds of compounds in a complex mixture, thus unlocking unprecedented information for intricate quantitative interpretation. We exploit this compound diversity across the (GC×GC) topography to provide quantitative compound-cognizant interpretation beyond target compound analysis with petroleum forensics as a practical application. We focus on the (GC×GC) topography of biomarker hydrocarbons, hopanes and steranes, as they are generally recalcitrant to weathering. We introduce peak topography maps (PTM) and topography partitioning techniques that consider a notably broader and more diverse range of target and non-target biomarker compounds compared to traditional approaches that consider approximately 20 biomarker ratios. Specifically, we consider a range of 33–154 target and non-target biomarkers with highest-to-lowest peak ratio within an injection ranging from 4.86 to 19.6 (precise numbers depend on biomarker diversity of individual injections). We also provide a robust quantitative measure for directly determining “match” between samples, without necessitating training data sets. We validate our methods across 34 (GC×GC) injections from a diverse portfolio of petroleum sources, and provide quantitative comparison of performance against established statistical methods such as principal components analysis (PCA). Our data set includes a wide range of samples collected following the 2010 Deepwater Horizon disaster that released approximately 160 million gallons of crude oil from the Macondo well (MW). Samples that were clearly collected following this disaster exhibit statistically significant match (99.23±1.66)% using PTM-based interpretation against other closely related sources. PTM-based interpretation also provides higher differentiation between closely correlated but distinct sources than obtained using PCA-based statistical comparisons. In addition to results based on this experimental field data, we also provide extentive perturbation analysis of the PTM method over numerical simulations that introduce random variability of peak locations over the (GC×GC) biomarker ROI image of the MW pre-spill sample (sample #1 in Additional file 4: Table S1). We compare the robustness of the cross-PTM score against peak location variability in both dimensions and compare the results against PCA analysis over the same set of simulated images. Detailed description of the simulation experiment and discussion of results are provided in Additional file 1: Section S8. We provide a peak-cognizant informational framework for quantitative interpretation of (GC×GC) topography. Proposed topographic analysis enables (GC×GC) forensic interpretation across target petroleum biomarkers, while including the nuances of lesser-known non-target biomarkers clustered around the target peaks. This allows potential discovery of hitherto unknown connections between target and non-target biomarkers.
    Beschreibung: This research was made possible in part by a grant from the Gulf of Mexico Research Initiative (GoMRI-015), and the DEEP-C consortium, and in part by NSF Grants OCE-0969841 and RAPID OCE-1043976 as well as a WHOI interdisciplinary study award.
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  • 18
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0143299, doi:10.1371/journal.pone.0143299.
    Beschreibung: For phytoplankton and other microbes, nutrient receptors are often the passages through which viruses invade. This presents a bottom-up vs. top-down, co-limitation scenario; how do these would-be-hosts balance minimizing viral susceptibility with maximizing uptake of limiting nutrient(s)? This question has been addressed in the biological literature on evolutionary timescales for populations, but a shorter timescale, mechanistic perspective is lacking, and marine viral literature suggests the strong influence of additional factors, e.g. host size; while the literature on both nutrient uptake and host-virus interactions is expansive, their intersection, of ubiquitous relevance to marine environments, is understudied. I present a simple, mechanistic model from first principles to analyze the effect of this co-limitation scenario on individual growth, which suggests that in environments with high risk of viral invasion or spatial/temporal heterogeneity, an individual host’s growth rate may be optimized with respect to receptor coverage, producing top-down selective pressure on short timescales. The model has general applicability, is suggestive of hypotheses for empirical exploration, and can be extended to theoretical studies of more complex behaviors and systems.
    Beschreibung: This work was supported by the Massachusetts Institute of Technology Charles Vest Presidential Fellowship.
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  • 19
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Animal Biotelemetry 3 (2015): 31, doi:10.1186/s40317-015-0076-1.
    Beschreibung: Soft-bodied marine invertebrates comprise a keystone component of ocean ecosystems; however, we know little of their behaviors and physiological responses within their natural habitat. Quantifying ocean conditions and measuring organismal responses to the physical environment is vital to understanding the species or ecosystem-level influences of a changing ocean. Here we describe a novel, soft-bodied invertebrate eco-sensor tag (the ITAG), its trial attachments to squid and jellyfish, and the fine-scale behavioral measurements recorded on captive animals. Tags were deployed on five jellyfish (Aurelia aurita) and eight squid (Loligo forbesi) in laboratory conditions for up to 24 h. Using concurrent video and tag data, movement signatures for specific behaviors were identified. These behaviors included straight swimming (for jellyfish), and finning, jetting, direction reversal and turning (for squid). Overall activity levels were quantified using the root-mean-squared magnitude of acceleration, and finning was found to be the dominant squid swimming gait during captive squid experiments. External light sensors on the ITAG were used to compare squid swimming activity relative to ambient light across a ca. 20-h trial. The deployments revealed that while swimming was continuous for captive squid, energetically costly swimming behaviors (i.e., jetting and rapid direction reversals) occurred infrequently. These data reflect the usefulness of the ITAG to study trade-offs between behavior and energy expenditure in captive and wild animals. These data demonstrate that eco-sensors with sufficiently high sampling rates can be applied to quantify behavior of soft-bodied taxa and changes in behavior due to interactions with the surrounding environment. The methods and tool described here open the door for substantial lab and field-based measurements of fine-scale behavior, physiology, and concurrent environmental parameters that will inform fisheries management, and elucidate the ecology of these important keystone taxa.
    Beschreibung: This work was supported by WHOI’s Ocean Life Institute and the Innovative Technology Program, Hopkins Marine Station’s Marine Life Observatory (to KK), as well as the National Science Foundation’s Ocean Acidification Program (to TAM) and NSF’s Program for Innovative Development of Biological Research (to TAM, KK and KAS).
    Schlagwort(e): Jellyfish ; Cephalopod ; Activity pattern ; Activity pattern ; Climate ; High-temporal resolution ; Sensory
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  • 20
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in EvoDevo 7 (2016): 19, doi:10.1186/s13227-016-0057-3
    Beschreibung: Here we present a report on Ctenopalooza: A meeting of ctenophorologists held at the Whitney Laboratory for Marine Bioscience in St. Augustine, FL, USA, on March 14–15, 2016. In this report, we provide a summary of each of the sessions that occurred during this two-day meeting, which touched on most of the relevant areas of ctenophore biology. The report includes some major themes regarding the future of ctenophore research that emerged during Ctenopalooza. More information can be found at the meeting Web site: http://ctenopalooza.whitney.ufl.edu.
    Beschreibung: Ctenopalooza was sponsored by a grant from the National Science Foundation’s Division of Integrative Organismal Systems to Joseph Ryan (#1619712). We also acknowledge funding was provided by a grant from the University of Florida’s Office of Research to Joseph Ryan (Project #00075235). Additional funding was provided by The Whitney Laboratory for Marine Bioscience.
    Schlagwort(e): Ctenophora ; Ctenophore ; Ctenophore
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  • 21
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0146977, doi:10.1371/journal.pone.0146977 .
    Beschreibung: The article reports the radiocarbon investigation of Anzapalivoro, the largest za baobab (Adansonia za) specimen of Madagascar and of another za, namely the Big cistern baobab. Several wood samples collected from the large inner cavity and from the outer part/exterior of the tree were investigated by AMS (accelerator mass spectrometry) radiocarbon dating. For samples collected from the cavity walls, the age values increase with the distance into the wood up to a point of maximum age, after which the values decrease toward the outer part. This anomaly of age sequences indicates that the inner cavity of Anzapalivoro is a false cavity, practically an empty space between several fused stems disposed in a ring-shaped structure. The radiocarbon date of the oldest sample was 780 ± 30 bp, which corresponds to a calibrated age of around 735 yr. Dating results indicate that Anzapalivoro has a closed ring-shaped structure, which consists of 5 fused stems that close a false cavity. The oldest part of the biggest za baobab has a calculated age of 900 years. We also disclose results of the investigation of a second za baobab, the Big cistern baobab, which was hollowed out for water storage. This specimen, which consists of 4 fused stems, was found to be around 260 years old.
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  • 22
    Publikationsdatum: 2022-05-25
    Beschreibung: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The definitive version was published in PLoS One 11 (2016): e0154208, doi: 10.1371/journal.pone.0154208
    Beschreibung: Some species of butterflyfish have had preyed upon corals for millions of years, yet the mechanism of butterflyfish specialized coral feeding strategy remains poorly understood. Certain butterflyfish have the ability to feed on allelochemically rich soft corals, e.g. Sinularia maxima. Cytochrome P450 (CYP) is the predominant enzyme system responsible for the detoxification of dietary allelochemicals. CYP2-like and CYP3A-like content have been associated with butterflyfish that preferentially consumes allelochemically rich soft corals. To investigate the role of butterflyfish CYP2 and CYP3A enzymes in dietary preference, we conducted oral feeding experiments using homogenates of S. maxima and a toxin isolated from the coral in four species of butterflyfish with different feeding strategies. After oral exposure to the S. maxima toxin 5-episinulaptolide (5ESL), which is not normally encountered in the Hawaiian butterflyfish diet, an endemic specialist, Chaetodon multicinctus experienced 100% mortality compared to a generalist, Chaetodon auriga, which had significantly more (3–6 fold higher) CYP3A-like basal content and catalytic activity. The specialist, Chaetodon unimaculatus, which preferentially feed on S. maxima in Guam, but not in Hawaii, had 100% survival, a significant induction of 8–12 fold CYP3A-like content, and an increased ability (2-fold) to metabolize 5ESL over other species. Computer modeling data of CYP3A4 with 5ESL were consistent with microsomal transformation of 5ESL to a C15-16 epoxide from livers of C. unimaculatus. Epoxide formation correlated with CYP3A-like content, catalytic activity, induction, and NADPH-dependent metabolism of 5ESL. These results suggest a potentially important role for the CYP3A family in butterflyfish-coral diet selection through allelochemical detoxification.
    Beschreibung: This work received support from the following sources: Resource Allocation Program of the Agricultural Research Station for UCR to DS; Summer funding by Hilda and George Liebig Environmental Sciences Summer Fellowship and travel grant Albert March Environmental Sciences Scholarship from the University of California, Riverside; and the Chemistry and DMPK CORE of COBRE, P20GM104932 from the National Institute of General Medical Sciences (NIGMS), a component of the National Institutes of Health (NIH) supported the chemistry studies.
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  • 23
    Publikationsdatum: 2022-05-25
    Beschreibung: This is an open access article, free of all copyright. The definitive version was published in PLoS ONE 11 (2016): e0164979, doi: 10.1371/journal.pone.0164979.
    Beschreibung: Understanding and managing dynamic coastal landscapes for beach-dependent species requires biological and geological data across the range of relevant environments and habitats. It is difficult to acquire such information; data often have limited focus due to resource constraints, are collected by non-specialists, or lack observational uniformity. We developed an open-source smartphone application called iPlover that addresses these difficulties in collecting biogeomorphic information at piping plover (Charadrius melodus) nest sites on coastal beaches. This paper describes iPlover development and evaluates data quality and utility following two years of collection (n = 1799 data points over 1500 km of coast between Maine and North Carolina, USA). We found strong agreement between field user and expert assessments and high model skill when data were used for habitat suitability prediction. Methods used here to develop and deploy a distributed data collection system have broad applicability to interdisciplinary environmental monitoring and modeling.
    Beschreibung: This work was supported by the North Atlantic Landscape Conservation Cooperative through the U.S. Department of the Interior Hurricane Sandy recovery program under the Disaster Relief Appropriations Act of 2013, and the U.S. Geological Survey Coastal and Marine Geology Program.
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  • 24
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0149998, doi:10.1371/journal.pone.0149998.
    Beschreibung: Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irreversible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate CF lung disease, to examine the relationship between the local microbiota and local damage, and to determine the relationships between microbiota in samples taken directly from the lung and the microbiota in spontaneously expectorated sputum. In this initial study, nine stable, adult CF patients with an FEV1〉50% underwent regional sampling of different lobes of the right lung by bronchoalveolar lavage (BAL) and protected brush (PB) sampling of mucus plugs. Sputum samples were obtained from six of the nine subjects immediately prior to the procedure. Microbial community analysis was performed on DNA extracted from these samples and the extent of damage in each lobe was quantified from a recent CT scan. The extent of damage observed in regions of the right lung did not correlate with specific microbial genera, levels of community diversity or composition, or bacterial genome copies per ml of BAL fluid. In all subjects, BAL fluid from different regions of the lung contained similar microbial communities. In eight out of nine subjects, PB samples from different regions of the lung were also similar in microbial community composition, and were similar to microbial communities in BAL fluid from the same lobe. Microbial communities in PB samples were more diverse than those in BAL samples, suggesting enrichment of some taxa in mucus plugs. To our knowledge, this study is the first to examine the microbiota in different regions of the CF lung in clinically stable individuals with mild-to-moderate CF-related lung disease.
    Beschreibung: Support from the Cystic Fibrosis Foundation Research Development Program (STANTO07R0) as a pilot grant to DAH and AA. Research reported in this publication was also supported by grants from the National Institutes of Health to DAH (R01 AI091702 to DAH) and the American Asthma Foundation Scholars Award and CFFT-ASHARE15A0 and R01HL122372 to AA and R01 HL074175 (BAS). The Dartmouth Lung Biology Center and CF Translational Research Core was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P30GM106394 and by the CFF RDP (CFRDP STANTO11R0).
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  • 25
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0150660, doi:10.1371/journal.pone.0150660.
    Beschreibung: Sperm whales are present in the Canary Islands year-round, suggesting that the archipelago is an important area for this species in the North Atlantic. However, the area experiences one of the highest reported rates of sperm whale ship-strike in the world. Here we investigate if the number of sperm whales found in the archipelago can sustain the current rate of ship-strike mortality. The results of this study may also have implications for offshore areas where concentrations of sperm whales may coincide with high densities of ship traffic, but where ship-strikes may be undocumented. The absolute abundance of sperm whales in an area of 52933 km2, covering the territorial waters of the Canary Islands, was estimated from 2668 km of acoustic line-transect survey using Distance sampling analysis. Data on sperm whale diving and acoustic behaviour, obtained from bio-logging, were used to calculate g(0) = 0.92, this is less than one because of occasional extended periods when whales do not echolocate. This resulted in an absolute abundance estimate of 224 sperm whales (95% log-normal CI 120–418) within the survey area. The recruitment capability of this number of whales, some 2.5 whales per year, is likely to be exceeded by the current ship-strike mortality rate. Furthermore, we found areas of higher whale density within the archipelago, many coincident with those previously described, suggesting that these are important habitats for females and immature animals inhabiting the archipelago. Some of these areas are crossed by active shipping lanes increasing the risk of ship-strikes. Given the philopatry in female sperm whales, replacement of impacted whales might be limited. Therefore, the application of mitigation measures to reduce the ship-strike mortality rate seems essential for the conservation of sperm whales in the Canary Islands.
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  • 26
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0151089, doi: 10.1371/journal.pone.0151089 .
    Beschreibung: The majority of ovarian tumors eventually recur in a drug resistant form. Using cisplatin sensitive and resistant cell lines assembled into 3D spheroids we profiled gene expression and identified candidate mechanisms and biological pathways associated with cisplatin resistance. OVCAR-8 human ovarian carcinoma cells were exposed to sub-lethal concentrations of cisplatin to create a matched cisplatin-resistant cell line, OVCAR-8R. Genome-wide gene expression profiling of sensitive and resistant ovarian cancer spheroids identified 3,331 significantly differentially expressed probesets coding for 3,139 distinct protein-coding genes (Fc 〉2, FDR 〈 0.05) (S2 Table). Despite significant expression changes in some transporters including MDR1, cisplatin resistance was not associated with differences in intracellular cisplatin concentration. Cisplatin resistant cells were significantly enriched for a mesenchymal gene expression signature. OVCAR-8R resistance derived gene sets were significantly more biased to patients with shorter survival. From the most differentially expressed genes, we derived a 17-gene expression signature that identifies ovarian cancer patients with shorter overall survival in three independent datasets. We propose that the use of cisplatin resistant cell lines in 3D spheroid models is a viable approach to gain insight into resistance mechanisms relevant to ovarian tumors in patients. Our data support the emerging concept that ovarian cancers can acquire drug resistance through an epithelial-to-mesenchymal transition.
    Beschreibung: This work was funded by the NIH NCRR supplement grant P41 RR001395-27S1 (J.W.H.), NSF DBI-1005378 “REU Site: Biological Discovery in Woods Hole”, faculty startup funds from the Office of Research at Oklahoma State University (W.C.), and the Mary Kay Foundation (A.S.B.).
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  • 27
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 4 (2016): 16, doi:10.1186/s40168-016-0161-6.
    Beschreibung: The epidemiology of bacterial vaginosis (BV) suggests it is sexually transmissible, yet no transmissible agent has been identified. It is probable that BV-associated bacterial communities are transferred from male to female partners during intercourse; however, the microbiota of sexual partners has not been well-studied. Pyrosequencing analysis of PCR-amplified 16S rDNA was used to examine BV-associated bacteria in monogamous couples with and without BV using vaginal, male urethral, and penile skin specimens. The penile skin and urethral microbiota of male partners of women with BV was significantly more similar to the vaginal microbiota of their female partner compared to the vaginal microbiota of non-partner women with BV. This was not the case for male partners of women with normal vaginal microbiota. Specific BV-associated species were concordant in women with BV and their male partners. In monogamous heterosexual couples in which the woman has BV, the significantly higher similarity between the vaginal microbiota and the penile skin and urethral microbiota of the male partner, supports the hypothesis that sexual exchange of BV-associated bacterial taxa is common.
    Beschreibung: This work was supported by National Institute of Health Grant R01 AI079071-01A1.
    Schlagwort(e): Bacterial vaginosis ; Microbiome ; Sexual transmission ; Penile skin ; Urethra ; Vagina
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  • 28
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 16 (2016): 149, doi:10.1186/s12862-016-0703-3.
    Beschreibung: As a result of vendor errors being introduced during processing, the original version of this article was published with some duplication errors in Table 1.
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  • 29
    Publikationsdatum: 2022-05-26
    Beschreibung: This article is distributed under the terms of the Creative Commons public domain dedication. The definitive version was published in PLoS One 11 (2016): e0158495, doi:10.1371/journal.pone.0158495.
    Beschreibung: The number of fluorescent labels that can unambiguously be distinguished in a single image when acquired through band pass filters is severely limited by the spectral overlap of available fluorophores. The recent development of spectral microscopy and the application of linear unmixing algorithms to spectrally recorded image data have allowed simultaneous imaging of fluorophores with highly overlapping spectra. However, the number of distinguishable fluorophores is still limited by the unavoidable decrease in signal to noise ratio when fluorescence signals are fractionated over multiple wavelength bins. Here we present a spectral image analysis algorithm to greatly expand the number of distinguishable objects labeled with binary combinations of fluorophores. Our algorithm utilizes a priori knowledge about labeled specimens and imposes a binary label constraint on the unmixing solution. We have applied our labeling and analysis strategy to identify microbes labeled by fluorescence in situ hybridization and here demonstrate the ability to distinguish 120 differently labeled microbes in a single image.
    Beschreibung: This work was supported by Grant 2007-3- 13 from the Alfred P. Sloan Foundation (to GGB), National Institutes of Health Grant 1RC1-DE020630 from the National Institute of Dental and Craniofacial Research (NIDCR) (to GGB) and by National Institutes of Health Fellowship 1F31-DE019576 from NIDCR (to AMV).
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  • 30
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 33, doi:10.1186/s13742-016-0138-1.
    Beschreibung: Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (〉10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host–symbiont interactions. A de novo transcriptome for the P. astreoides holobiont (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867 255 transcript elements with an average length of 685 bases. The isolated P. astreoides assembly consists of 129 718 transcript elements with an average length of 811 bases, and the isolated Symbiodinium sp. assembly had 186 177 transcript elements with an average length of 1105 bases. This contribution to coral transcriptome data provides a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.
    Beschreibung: Bioinformatic analysis was performed in part on computing resources at the University of Puerto Rico (UPR) Puerto Rico Center for Environmental Neuroscience (PRCEN)’s High Performance Computing Facility, which is supported by: Institutional Development Award Networks of Biomedical Research Excellent (INBRE) grant P20GM103475 from the National Institute of General Medical Sciences, National Institutes of Health; the Institute for Functional Nanomaterials (IFN) award from the Experimental Program to Stimulate Competitive Research (EPSCoR) Track 1 program of the National Science Foundation (NSF); and EPSCoR Track 2 awards for computational nanoscience (EPS 1002410, EPS 1010094). Funding and support of the research was provided by PRCEN thanks to an NSF Centers of Research Excellent in Science and Technology (CREST) award, number HRD-1137725.
    Schlagwort(e): Porites astreoides ; Calcification ; Biomineralization ; Coral ; Symbiodinium ; Dinoflagellate ; Zooxanthellae ; Symbiosis ; Swimming larvae ; Larval settlement
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  • 31
    facet.materialart.
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    Public Library of Science
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0150820, doi:10.1371/journal.pone.0150820.
    Beschreibung: Methanol is a major volatile organic compound on Earth and serves as an important carbon and energy substrate for abundant methylotrophic microbes. Previous geochemical surveys coupled with predictive models suggest that the marine contributions are exceedingly large, rivaling terrestrial sources. Although well studied in terrestrial ecosystems, methanol sources are poorly understood in the marine environment and warrant further investigation. To this end, we adapted a Purge and Trap Gas Chromatography/Mass Spectrometry (P&T-GC/MS) method which allowed reliable measurements of methanol in seawater and marine phytoplankton cultures with a method detection limit of 120 nanomolar. All phytoplankton tested (cyanobacteria: Synechococcus spp. 8102 and 8103, Trichodesmium erythraeum, and Prochlorococcus marinus), and Eukarya (heterokont diatom: Phaeodactylum tricornutum, coccolithophore: Emiliania huxleyi, cryptophyte: Rhodomonas salina, and non-diatom heterokont: Nannochloropsis oculata) produced methanol, ranging from 0.8–13.7 micromolar in culture and methanol per total cellular carbon were measured in the ranges of 0.09–0.3%. Phytoplankton culture time-course measurements displayed a punctuated production pattern with maxima near early stationary phase. Stabile isotope labeled bicarbonate incorporation experiments confirmed that methanol was produced from phytoplankton biomass. Overall, our findings suggest that phytoplankton are a major source of methanol in the upper water column of the world’s oceans.
    Beschreibung: This project was solely supported by a grant to TJM from the National Science Foundation (Award# CHE-OCE 1131415).
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  • 32
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 14, doi:10.1186/s13742-016-0118-5.
    Beschreibung: Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine–terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.
    Beschreibung: Work was supported in part by: the Institute of Theoretical Physics and the Pauli Center at ETH Zurich; the US National Science Foundation (NSF Moorea Coral Reef Long Term Ecological Research Site, OCE-1236905; Socio-Ecosystem Dynamics of Natural-Human Networks on Model Islands, CNH-1313830; Coastal SEES: Adaptive Capacity, Resilience, and Coral Reef State Shifts in Social-ecological Systems, OCE-1325652, OCE-1325554); the Gordon and Betty Moore Foundation (Berkeley Initiative in Global Change Biology; Genomic Standards Consortium); Courtney Ross and the Ross Institute; UC Berkeley Vice Chancellor for Research; CRIOBE; and the France Berkeley Fund (FBF 2014-0015).
    Schlagwort(e): Computational ecology ; Biodiversity ; Genomics ; Biocode ; Earth observations ; Social-ecological system ; Ecosystem dynamics ; Climate change scenarios ; Predictive modeling
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  • 33
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0160080, doi: 10.1371/journal.pone.0160080 .
    Beschreibung: Pilot whales are two cetacean species (Globicephala melas and G. macrorhynchus) whose distributions are correlated with water temperature and partially overlap in some areas like the North Atlantic Ocean. In the context of global warming, distribution range shifts are expected to occur in species affected by temperature. Consequently, a northward displacement of the tropical pilot whale G. macrorynchus is expected, eventually leading to increased secondary contact areas and opportunities for interspecific hybridization. Here, we describe genetic evidences of recurrent hybridization between pilot whales in northeast Atlantic Ocean. Based on mitochondrial DNA sequences and microsatellite loci, asymmetric introgression of G. macrorhynchus genes into G. melas was observed. For the latter species, a significant correlation was found between historical population growth rate estimates and paleotemperature oscillations. Introgressive hybridization, current temperature increases and lower genetic variation in G. melas suggest that this species could be at risk in its northern range. Under increasing environmental and human-mediated stressors in the North Atlantic Ocean, it seems recommendable to develop a conservation program for G. melas.
    Beschreibung: LM had a PCTI Grant from the Asturias Regional Government, referenced BP 10-004. MAS was supported by a 2013 FCT Investigator contract through POPH, QREN European Social Fund and the Portuguese Ministry for Science and Education. This study was also supported by a grant from the Principality of Asturias (reference: GRUPIN-2014-093).
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  • 34
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 4 (2016): 8, doi:10.1186/s40168-016-0154-5.
    Beschreibung: Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.
    Beschreibung: This work was supported by the US Dept. of Energy under Contract DE-AC02-06CH11357.
    Schlagwort(e): Metagenomics ; Genotype ; Assembly ; Binning ; Curation
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  • 35
    Publikationsdatum: 2024-04-29
    Beschreibung: Coastal erosion and flooding transform terrestrial landscapes into marine environments. In the Arctic, these processes inundate terrestrial permafrost with seawater and create submarine permafrost. Permafrost begins to warm under marine conditions, which can destabilize the sea floor and may release greenhouse gases. We report on the transition of terrestrial to submarine permafrost at a site where the timing of inundation can be inferred from the rate of coastline retreat. On Muostakh Island in the central Laptev Sea, East Siberia, changes in annual coastline position have been measured for decades and vary highly spatially. We hypothesize that these rates are inversely related to the inclination of the upper surface of submarine ice-bonded permafrost (IBP) based on the consequent duration of inundation with increasing distance from the shoreline. We compared rapidly eroding and stable coastal sections of Muostakh Island and find permafrost-table inclinations, determined using direct current resistivity, of 1 and 5 %, respectively. Determinations of submarine IBP depth from a drilling transect in the early 1980s were compared to resistivity profiles from 2011. Based on borehole observations, the thickness of unfrozen sediment overlying the IBP increased from 0 to 14m below sea level with increasing distance from the shoreline. The geoelectrical profiles showed thickening of the unfrozen sediment overlying ice-bonded permafrost over the 28 years since drilling took place. We use geoelectrical estimates of IBP depth to estimate permafrost degradation rates since inundation. Degradation rates decreased from over 0.4ma-1 following inundation to around 0.1ma-1 at the latest after 60 to 110 years and remained constant at this level as the duration of inundation increased to 250 years. We suggest that long-term rates are lower than these values, as the depth to the IBP increases and thermal and porewater solute concentration gradients over depth decrease. For the study region, recent increases in coastal erosion rate and changes in benthic temperature and salinity regimes are expected to affect the depth to submarine permafrost, leading to coastal regions with shallower IBP.
    Repository-Name: EPIC Alfred Wegener Institut
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  • 36
    Publikationsdatum: 2016-03-10
    Print ISSN: 0716-078X
    Digitale ISSN: 0717-6317
    Thema: Biologie , Geologie und Paläontologie
    Publiziert von BioMed Central
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  • 37
  • 38
    Publikationsdatum: 2016-09-01
    Print ISSN: 0716-078X
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    Thema: Biologie , Geologie und Paläontologie
    Publiziert von BioMed Central
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  • 39
    Publikationsdatum: 2016-09-13
    Print ISSN: 0716-078X
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    Thema: Biologie , Geologie und Paläontologie
    Publiziert von BioMed Central
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  • 40
    Publikationsdatum: 2016-03-31
    Print ISSN: 0716-078X
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    Thema: Biologie , Geologie und Paläontologie
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  • 41
    Publikationsdatum: 2016-09-01
    Print ISSN: 0716-078X
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    Thema: Biologie , Geologie und Paläontologie
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  • 42
    Publikationsdatum: 2016-07-22
    Print ISSN: 0716-078X
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    Thema: Biologie , Geologie und Paläontologie
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  • 43
    Publikationsdatum: 2016-05-06
    Print ISSN: 0716-078X
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    Thema: Biologie , Geologie und Paläontologie
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  • 44
    Publikationsdatum: 2016-04-29
    Print ISSN: 0716-078X
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    Thema: Biologie , Geologie und Paläontologie
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  • 45
    Publikationsdatum: 2016-03-14
    Print ISSN: 0716-078X
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    Thema: Biologie , Geologie und Paläontologie
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  • 46
    Publikationsdatum: 2016-04-04
    Print ISSN: 0716-078X
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    Thema: Biologie , Geologie und Paläontologie
    Publiziert von BioMed Central
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  • 47
    Publikationsdatum: 2016-03-08
    Print ISSN: 0716-078X
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    Thema: Biologie , Geologie und Paläontologie
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  • 48
    Publikationsdatum: 2016-03-10
    Print ISSN: 0716-078X
    Digitale ISSN: 0717-6317
    Thema: Biologie , Geologie und Paläontologie
    Publiziert von BioMed Central
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  • 49
    Publikationsdatum: 2016-07-12
    Beschreibung: Sources and Transformations of Anthropogenic Nitrogen along an Urban River-Estuarine Continuum Michael J. Pennino, Sujay S. Kaushal, Sudhir Murthy, Joel Blomquist, Jeff Cornwell, and Lora Harris Biogeosciences Discuss., doi:10.5194/bg-2016-264,2016 Manuscript under review for BG (discussion: open, 0 comments) The results of this manuscript report the analysis of the fate and transport of wastewater and anthropogenic nitrogen along the Potomac River Estuary, from Washington D.C. to the Chesapeake Bay. In conjunction with a mass balance approach, nitrate isotopes were used to estimate fluxes and trace the sources and transformations N along the estuary. This study shows that estuaries have a large capacity to transform N inputs, but with large seasonal variability due to hydrological extremes.
    Print ISSN: 1810-6277
    Digitale ISSN: 1810-6285
    Thema: Biologie , Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
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  • 50
    Publikationsdatum: 2016-07-10
    Beschreibung: Resistance amongst the commensal flora is a serious threat because a very highly populated ecosystem like the gut, may at a later stage, be a source of extra intestinal infections, resistant strains may spread...
    Digitale ISSN: 1471-2180
    Thema: Biologie
    Publiziert von BioMed Central
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  • 51
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    Publikationsdatum: 2016-07-12
    Beschreibung: Boreal fire records in Northern Hemisphere ice cores: A review Michel Legrand, Joseph McConnell, Hubertus Fischer, Eric W. Wolff, Susanne Preunkert, Nathan Chellman, Daiana Leuenberger, Olivia Maselli, Michael Sigl, Simon Schüpbach, and Mike Flannigan Clim. Past Discuss., doi:10.5194/cp-2016-70,2016 Manuscript under review for CP (discussion: open, 0 comments) Here we review previous attempts made to reconstruct past forest fire using chemical signals recorded in Greenland ice. We showed that the Greenland ice records of ammonium, found to be a good fire proxy, consistently indicate changing fire activity in Canada in response to past climatic conditions that occurred since the last 15 000 years including the little ice age and the last large climatic transition.
    Print ISSN: 1814-9324
    Digitale ISSN: 1814-9332
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
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  • 52
    Publikationsdatum: 2016-07-10
    Beschreibung: As increasingly fragmented and isolated populations of threatened species become subjected to climate change, invasive species and other stressors, there is an urgent need to consider adaptive potential when m...
    Digitale ISSN: 1742-9994
    Thema: Biologie
    Publiziert von BioMed Central
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  • 53
    Publikationsdatum: 2016-07-12
    Beschreibung: Tectonothermal evolution in the core of an arcuate fold and thrust belt: the south-eastern sector of the Cantabrian Zone (Variscan belt, north-western Spain) María Luz Valín, Susana García-López, Covadonga Brime, Fernando Bastida, and Jesús Aller Solid Earth, 7, 1003-1022, doi:10.5194/se-7-1003-2016, 2016 The tectonothermal evolution of an area located in the core of the Ibero-Armorican Arc (Variscan belt) has been determined by using the conodont colour alteration index (CAI), Kübler index of illite (KI), the Árkai index of chlorite (AI) and the analysis of clay minerals and rock cleavage. The area is part of the Cantabrian Zone (CZ), which represents the foreland fold and thrust belt of the orogen. It has been thrust by several large units of the CZ, what resulted in the generation of a large number of synorogenic Carboniferous sediments. CAI, KI and AI values show an irregular distribution of metamorphic grade, independent of stratigraphic position. Two tectonothermal events have been distinguished in the area. The first one, poorly defined, is mainly located in the northern part. It gave rise to very-low-grade metamorphism in some areas and it was associated with a deformation event that resulted in the emplacement of the last large thrust unit and development of upright folds and associated cleavage ( S 1 ). The second tectonothermal event gave rise to low-grade metamorphism and cleavage ( S 2 ) crosscutting earlier upright folds in the central, western and southern parts of the study area. The event continued with the intrusion of small igneous rock bodies, which gave rise to contact metamorphism and hydrothermal alteration. This event was linked to an extensional episode due to a gravitational instability at the end of the Variscan deformation. This tectonothermal evolution occurred during the Gzhelian–Sakmarian. Subsequently, several hydrothermal episodes took place and local crenulation cleavage developed during the Alpine deformation.
    Digitale ISSN: 1869-9537
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
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  • 54
    Publikationsdatum: 2016-07-12
    Beschreibung: Microstructures and deformation mechanisms in Opalinus Clay: insights from scaly clay from the Main Fault in the Mont Terri Rock Laboratory (CH) Ben Laurich, Janos L. Urai, and Christophe Nussbaum Solid Earth Discuss., doi:10.5194/se-2016-94,2016 Manuscript under review for SE (discussion: open, 0 comments) Scaly clay is a well-known rock fabric that can develop in tectonic systems and that can alter the physical rock properties of a formation. However, internal microstructure and evolution of this fabric remains poorly understood. We examined the scaly microstructure of progressively faulted Opalinus Clay using optical as well as scanning electron microscopy. We present an evolutionary model for scaly clay that is of interest in the evaluation of Opalinus Clay to host radioactive waste.
    Digitale ISSN: 1869-9537
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
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  • 55
    Publikationsdatum: 2016-07-12
    Beschreibung: Microstructures and deformation mechanisms in Opalinus Clay: insights from scaly clay from the Main Fault in the Mont Terri Rock Laboratory (CH) Ben Laurich, Janos L. Urai, and Christophe Nussbaum Solid Earth Discuss., doi:10.5194/se-2016-94,2016 Manuscript under review for SE (discussion: open, 0 comments) Scaly clay is a well-known rock fabric that can develop in tectonic systems and that can alter the physical rock properties of a formation. However, internal microstructure and evolution of this fabric remains poorly understood. We examined the scaly microstructure of progressively faulted Opalinus Clay using optical as well as scanning electron microscopy. We present an evolutionary model for scaly clay that is of interest in the evaluation of Opalinus Clay to host radioactive waste.
    Print ISSN: 1869-9510
    Digitale ISSN: 1869-9529
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
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  • 56
    Publikationsdatum: 2016-07-12
    Beschreibung: Fixation kinetics of chelated and non-chelated zinc in semi-arid alkaline soils: application to zinc management Theophilus K. Udeigwe, Madeleine Eichmann, and Matthew C. Menkiti Solid Earth, 7, 1023-1031, doi:10.5194/se-7-1023-2016, 2016 Micronutrient fixation leads to the reduction of plant-available portions. This study examined the fixation kinetics of chelated and non-chelated zinc (Zn) in semi-arid soils. About 30 % more Zn was fixed in the non-chelated system in the first 14 days. Slope of change of Zn to Cu (i.e., Cu–Zn) was higher than other micronutrients. Zn fixation kinetics were better described by a power-function model. Tools developed from this study will be used to advance micronutrient management.
    Print ISSN: 1869-9510
    Digitale ISSN: 1869-9529
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
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  • 57
    Publikationsdatum: 2016-07-13
    Beschreibung: Lentiviral vectors (LV) are widely used for various gene transfer or gene therapy applications. The effects of LV on target cells are expected to be limited to gene delivery. Yet, human hematopoietic CD34+ cel...
    Digitale ISSN: 1756-8935
    Thema: Biologie , Medizin
    Publiziert von BioMed Central
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  • 58
    Publikationsdatum: 2016-07-13
    Beschreibung: Improved MODIS Dark Target Aerosol Optical Depth algorithm over land: Angular effect Correction Yerong Wu, Martin de Graaf, and Massimo Menenti Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-185,2016 Manuscript under review for AMT (discussion: open, 0 comments) In this paper, we developed a new algorithm to improve the retrieval of Aerosol Optical Depth (AOD) over land with satellite measurement, by refining the shape of the spectral surface reflectance to improve the estimated background reflectance in the channel used for AOD retrieval. The results show that the angular effects of the retrievals are largely reduced, including fewer occurrences of negative retrievals. This implies that the users can get more accurate data without angular bias.
    Print ISSN: 1867-1381
    Digitale ISSN: 1867-8548
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
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  • 59
    Publikationsdatum: 2016-07-13
    Beschreibung: Investigation of processes controlling summertime gaseous elemental mercury oxidation at midlatitudinal marine, coastal, and inland sites Zhuyun Ye, Huiting Mao, Che-Jen Lin, and Su Youn Kim Atmos. Chem. Phys., 16, 8461-8478, doi:10.5194/acp-16-8461-2016, 2016 In this study, a state-of-the-art chemical mechanism was incorporated into a box model to investigate the atmospheric Hg cycling in different environments. As a result, for each of the three environments, GOM diurnal cycles of over half the selected cases were reasonably represented by the box model. A realistic model can be a powerful tool, providing important information on atmospheric Hg cycling and implications for policy makers.
    Print ISSN: 1680-7367
    Digitale ISSN: 1680-7375
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
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  • 60
    Publikationsdatum: 2016-07-13
    Beschreibung: Effects of polar stratospheric clouds in the Nimbus 7 LIMS Version 6 data set Ellis Remsberg and V. Lynn Harvey Atmos. Meas. Tech., 9, 2927-2946, doi:10.5194/amt-9-2927-2016, 2016 Emissions from polar stratospheric cloud (PSC) particles affect the retrieved ozone and water vapor from the Limb Infrared Monitor of the Stratosphere (LIMS) satellite experiment. Threshold criteria are applied to the retrieved ozone for the detection and screening of those effects. The PSC effects correlate very well with regions of coldest temperatures (
    Digitale ISSN: 1867-8610
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
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  • 61
    Publikationsdatum: 2016-07-13
    Beschreibung: Dengue hemorrhagic fever (DHF) is a severe life-threatening form of dengue infection. Low platelet count is one of the characteristic clinical manifestations in patients with severe dengue. However, little is ...
    Digitale ISSN: 1471-2350
    Thema: Biologie , Medizin
    Publiziert von BioMed Central
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  • 62
    Publikationsdatum: 2016-07-13
    Beschreibung: Health information is increasingly being digitally stored and exchanged. The public is regularly collecting and storing health-related data on their own electronic devices and in the cloud. Diabetes prevention...
    Digitale ISSN: 1472-6947
    Thema: Informatik , Medizin
    Publiziert von BioMed Central
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  • 63
    Publikationsdatum: 2016-07-13
    Beschreibung: Plant cell wall degrading enzymes (PCWDEs) are a subset of carbohydrate-active enzymes (CAZy) produced by plant pathogens to degrade plant cell walls. To counteract PCWDEs, plants release PCWDEs inhibitor prot...
    Digitale ISSN: 1471-2180
    Thema: Biologie
    Publiziert von BioMed Central
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  • 64
    Publikationsdatum: 2016-07-13
    Beschreibung: Pseudomonas aeruginosa is the predominant pathogen associated with the decline of pulmonary function in cystic fibrosis (CF) patients. Both environment-to-host acquisition and patient-...
    Digitale ISSN: 1471-2180
    Thema: Biologie
    Publiziert von BioMed Central
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  • 65
    Publikationsdatum: 2016-07-13
    Beschreibung: Similar to Gram-negative organisms, Borrelia spirochetes are dual-membrane organisms with both an inner and outer membrane. Although the outer membrane contains integral membrane proteins, few of the borrelial ou...
    Digitale ISSN: 1471-2180
    Thema: Biologie
    Publiziert von BioMed Central
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  • 66
    facet.materialart.
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    Copernicus
    Publikationsdatum: 2016-07-13
    Beschreibung: The 1816 ‘year without a summer’ in an atmospheric reanalysis Philip Brohan, Gilbert P. Compo, Stefan Brönnimann, Robert J. Allan, Renate Auchmann, Yuri Brugnara, Prashant D. Sardeshmukh, and Jeffrey S. Whitaker Clim. Past Discuss., doi:10.5194/cp-2016-78,2016 Manuscript under review for CP (discussion: open, 0 comments) We have used modern weather forecasting tools to reconstruct the dreadful European weather of 200 years ago – 1816 was the ‘year without a summer’; harvests failed, and people starved. We can show that 1816’s extreme climate was caused by the eruption of the Tambora volcano the previous year. This means we have some chance of predicting such extreme summers if they occur in future, though this is still a challenge to today’s forecast models.
    Print ISSN: 1814-9340
    Digitale ISSN: 1814-9359
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
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  • 67
    Publikationsdatum: 2016-07-13
    Beschreibung: Palynological evidence for late Miocene stepwise aridification on the northeastern Tibetan Plateau Jia Liu, Ji Jun Li, Chun Hui Song, Hao Yu, Ting Jiang Peng, Zheng Chuang Hui, and Xi Yan Ye Clim. Past, 12, 1473-1484, doi:10.5194/cp-12-1473-2016, 2016 The late Cenozoic basins in the northeastern Tibetan Plateau document both the tectonic uplift process and its associated environmental changes. Here, we investigated a late Miocene sporopollen record from the Tianshui Basin in the northeastern Tibetan Plateau. The results show that a persistent aridification trend parallels the global cooling of the late Miocene, and the stepwise vegetation succession is consistent with the major uplift events of the Tibetan Plateau.
    Print ISSN: 1814-9324
    Digitale ISSN: 1814-9332
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
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  • 68
    Publikationsdatum: 2016-07-13
    Beschreibung: Gone or just out of sight? The apparent disappearance of aromatic litter components in soils Thimo Klotzbücher, Karsten Kalbitz, Chiara Cerli, Peter J. Hernes, and Klaus Kaiser SOIL, 2, 325-335, doi:10.5194/soil-2-325-2016, 2016 Uncertainties concerning stabilization of organic compounds in soil limit our basic understanding on soil organic matter (SOM) formation and our ability to model and manage effects of global change on SOM stocks. One controversially debated aspect is the contribution of aromatic litter components, such as lignin and tannins, to stable SOM forms. Here, we summarize and discuss the inconsistencies and propose research options to clear them.
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 69
    Publikationsdatum: 2016-07-13
    Beschreibung: Structure of Suasselkä Postglacial Fault in northern Finland obtained by analysis of local events and ambient seismic noise Nikita Afonin, Elena Kozlovskaya, Ilmo Kukkonen, and DAFNE/FINLAND Working Group Solid Earth Discuss., doi:10.5194/se-2016-90,2016 Manuscript under review for SE (discussion: open, 0 comments) Understanding inner structure of seismogenic faults and their ability to reactivate is particularly important in investigating continental intraplate seismicity regime. In our study we address this problem using analysis of local seismic events and ambient seismic noise recorded by the temporary DAFNE array in northern Fennoscandian Shield. The main purpose of the DAFNE/FINLAND passive seismic array experiment was to characterize the present-day seismicity of the Suasselkä post-glacial fault (SPGF) that was proposed as one potential target for the DAFNE (Drilling Active Faults in Northern Europe) project. The DAFNE/FINLAND array comprised the area of about 20 to 100 km and consisted of 8 short-period and 4 broad-band 3-component autonomous seismic stations installed in the close vicinity of the fault area. The array recorded continuous seismic data during September, 2011–May, 2013. Recordings of the array have being analyzed in order to identify and locate natural earthquakes from the fault area and to discriminate them from the blasts in the Kittilä Gold Mine. As a result, we found several dozens of natural seismic events originating from the fault area, which proves that the fault is still seismically active. In order to study the inner structure of the SPGF we use cross-correlation of ambient seismic noise recorded by the array. Analysis of azimuthal distribution of noise sources demonstrated that during the time interval under consideration the distribution of noise sources is close to the uniform one. The continuous data were processed in several steps including single station data analysis, instrument response removal and time-domain stacking. The data were used to estimate empirical Green’s functions between pairs of stations in the frequency band of 0.1–1 Hz and to calculate correspondent surface wave dispersion curves. The S-wave velocity models were obtained as a result of dispersion curves inversion. The results suggest that the area of the SPGF corresponds to a narrow region of low S-wave velocities surrounded by rocks with high S-wave velocities. We interpret this low velocity region as a non-healed mechanically weak fault damage zone (FDZ) that remained after the last major earthquake that occurred after the last glaciation.
    Digitale ISSN: 1869-9537
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 70
    Publikationsdatum: 2016-07-13
    Beschreibung: Structure of Suasselkä Postglacial Fault in northern Finland obtained by analysis of local events and ambient seismic noise Nikita Afonin, Elena Kozlovskaya, Ilmo Kukkonen, and DAFNE/FINLAND Working Group Solid Earth Discuss., doi:10.5194/se-2016-90,2016 Manuscript under review for SE (discussion: open, 0 comments) Understanding inner structure of seismogenic faults and their ability to reactivate is particularly important in investigating continental intraplate seismicity regime. In our study we address this problem using analysis of local seismic events and ambient seismic noise recorded by the temporary DAFNE array in northern Fennoscandian Shield. The main purpose of the DAFNE/FINLAND passive seismic array experiment was to characterize the present-day seismicity of the Suasselkä post-glacial fault (SPGF) that was proposed as one potential target for the DAFNE (Drilling Active Faults in Northern Europe) project. The DAFNE/FINLAND array comprised the area of about 20 to 100 km and consisted of 8 short-period and 4 broad-band 3-component autonomous seismic stations installed in the close vicinity of the fault area. The array recorded continuous seismic data during September, 2011–May, 2013. Recordings of the array have being analyzed in order to identify and locate natural earthquakes from the fault area and to discriminate them from the blasts in the Kittilä Gold Mine. As a result, we found several dozens of natural seismic events originating from the fault area, which proves that the fault is still seismically active. In order to study the inner structure of the SPGF we use cross-correlation of ambient seismic noise recorded by the array. Analysis of azimuthal distribution of noise sources demonstrated that during the time interval under consideration the distribution of noise sources is close to the uniform one. The continuous data were processed in several steps including single station data analysis, instrument response removal and time-domain stacking. The data were used to estimate empirical Green’s functions between pairs of stations in the frequency band of 0.1–1 Hz and to calculate correspondent surface wave dispersion curves. The S-wave velocity models were obtained as a result of dispersion curves inversion. The results suggest that the area of the SPGF corresponds to a narrow region of low S-wave velocities surrounded by rocks with high S-wave velocities. We interpret this low velocity region as a non-healed mechanically weak fault damage zone (FDZ) that remained after the last major earthquake that occurred after the last glaciation.
    Print ISSN: 1869-9510
    Digitale ISSN: 1869-9529
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 71
    Publikationsdatum: 2016-07-13
    Beschreibung: Comparison of box counting and correlation dimension methods in well logging data analysis associate with the texture of volcanic rocks D. Mou and Z. W. Wang Nonlin. Processes Geophys. Discuss., doi:10.5194/npg-2014-85,2016 Manuscript under review for NPG (discussion: open, 0 comments) We have developed a fractal analysis method to estimate the dimension of well logging curves in Liaohe oil field, China. The box counting and correlation dimension are methods that can be applied to predict the texture of volcanic rocks with calculation the fractal dimension of well logging curves. The well logging curves are composed of gamma ray (GR), compensated neutron logs (CNL), acoustic (AC), density (DEN), Resistivity lateral log deep ( R LLD ), every curve contains a total of 6000 logging data. The dimension of well logging curves are calculated using box counting and correlation algorithms respectively. It is shown that two types of dimension of CNL, DEN and AC have the same average value. The box counting dimension of volcanic lava is lower than the pyroclastic rock obviously. The majority of correlation dimension of volcanic lava is lower than the pyroclastic rock, but a small amount of correlation dimension of volcanic lava is equal to the pyroclastic rock. It is demonstrated that the box counting dimension is more suitable for predicting the texture of volcanic rocks. Applications to logging data, A well show the relationship between the fractal dimension and the texture of volcanic rock in certain depth.
    Print ISSN: 1023-5809
    Digitale ISSN: 1607-7946
    Thema: Geologie und Paläontologie , Physik
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 72
    Publikationsdatum: 2016-07-13
    Beschreibung: First year of the new Arctic AWIPEV-COSYNA cabled Underwater Observatory in Kongsfjorden, Spitsbergen Philipp Fischer, Max Schwanitz, Reiner Loth, Uwe Posner, Markus Brand, and Friedhelm Schröder Ocean Sci. Discuss., doi:10.5194/os-2016-52,2016 Manuscript under review for OS (discussion: open, 0 comments) We observed oceanographic and community data from October 2013 to November 2014 in the shallow waters of Kongsfjorden on the west coast of Svalbard (Norway) using remote controlled hydrographic and optic sensors. Daily vertical profiles of temperature, salinity and turbidity were sampled together with stereo images of the macrobiotic community, including fish. A distinct seasonal cycle in total species abundances was found with surprisingly high animal counts during the polar winter.
    Print ISSN: 1812-0806
    Digitale ISSN: 1812-0822
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 73
    Publikationsdatum: 2016-07-14
    Beschreibung: Hill rices (Oryza sativa L.) are direct seeded rices grown on hill slopes of different gradients. These landraces have evolved under rainfed and harsh environmental conditions and may possess genes governing adap...
    Digitale ISSN: 1471-2156
    Thema: Biologie
    Publiziert von BioMed Central
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  • 74
    Publikationsdatum: 2016-07-14
    Beschreibung: In the context of spore contamination involved in bio-terrorism and food preservation, the development of new techniques for spore inactivation is an important challenge.
    Digitale ISSN: 1471-2180
    Thema: Biologie
    Publiziert von BioMed Central
    Standort Signatur Erwartet Verfügbarkeit
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  • 75
    Publikationsdatum: 2016-07-13
    Beschreibung: Landfast ice thickness in the Canadian Arctic Archipelago from observations and models Stephen E. L. Howell, Frédéric Laliberté, Ron Kwok, Chris Derksen, and Joshua King The Cryosphere, 10, 1463-1475, doi:10.5194/tc-10-1463-2016, 2016 The Canadian Ice Service record of observed landfast ice and snow thickness represents one of the longest in the Arctic that spans over 5 decades. We analyze this record to report on long-term trends and variability of ice and snow thickness within the Canadian Arctic Archipelago (CAA). Results indicate a thinning of ice at several sites in the CAA. State-of-the-art climate models still have difficultly capturing observed ice thickness values in the CAA and should be used with caution.
    Print ISSN: 1994-0416
    Digitale ISSN: 1994-0424
    Thema: Geographie , Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 76
    Publikationsdatum: 2016-07-13
    Beschreibung: Coastal dynamics and submarine permafrost in shallow water of the central Laptev Sea, East Siberia Pier Paul Overduin, Sebastian Wetterich, Frank Günther, Mikhail N. Grigoriev, Guido Grosse, Lutz Schirrmeister, Hans-Wolfgang Hubberten, and Aleksandr Makarov The Cryosphere, 10, 1449-1462, doi:10.5194/tc-10-1449-2016, 2016 How fast does permafrost warm up and thaw after it is covered by the sea? Ice-rich permafrost in the Laptev Sea, Siberia, is rapidly eroded by warm air and waves. We used a floating electrical technique to measure the depth of permafrost thaw below the sea, and compared it to 60 years of coastline retreat and permafrost depths from drilling 30 years ago. Thaw is rapid right after flooding of the land and slows over time. The depth of permafrost is related to how fast the coast retreats.
    Print ISSN: 1994-0432
    Digitale ISSN: 1994-0440
    Thema: Geographie , Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 77
    Publikationsdatum: 2016-07-13
    Beschreibung: Age of the Mt. Ortles ice cores, the Tyrolean Iceman and glaciation of the highest summit of South Tyrol since the Northern Hemisphere Climatic Optimum Paolo Gabrielli, Carlo Barbante, Giuliano Bertagna, Michele Bertó, Daniel Binder, Alberto Carton, Luca Carturan, Federico Cazorzi, Giulio Cozzi, Giancarlo Dalla Fontana, Mary Davis, Fabrizio De Blasi, Roberto Dinale, Gianfranco Dragà, Giuliano Dreossi, Daniela Festi, Massimo Frezzotti, Jacopo Gabrieli, Stephan Galos, Patrick Ginot, Petra Heidenwolf, Theo M. Jenk, Natalie Kehrwald, Donald Kenny, Olivier Magand, Volkmar Mair, Vladimir Mikhalenko, Ping Nan Lin, Klaus Oeggl, Gianni Piffer, Mirko Rinaldi, Ulrich Schotterer, Margit Schwikowski, Roberto Seppi, Andrea Spolaor, Barbara Stenni, Davdi Tonidandel, CChiara Uglietti, Victor Zagorodnov, Thomas Zanoner, and Piero Zennaro The Cryosphere Discuss., doi:10.5194/tc-2016-159,2016 Manuscript under review for TC (discussion: open, 0 comments) New ice cores were extracted from Alto dell'Ortles, the highest glacier of South Tyrol in the Italian Alps, to check whether prehistoric ice, that is coeval to the famous 5200 years old Tyrolean Iceman, is still preserved in this region. Dating of the ice cores confirms the hypothesis and indicates that the drilling site was glaciated since the end of the Northern Hemisphere Climatic Optimum (7000 BP). We also infer that an unprecedented acceleration of the glacier flow has just recently begun.
    Print ISSN: 1994-0432
    Digitale ISSN: 1994-0440
    Thema: Geographie , Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 78
    Publikationsdatum: 2016-07-13
    Beschreibung: Combined diurnal variations of discharge and hydrochemistry of the Isunnguata Sermia outlet of the Greenland Ice Sheet give in sight on sub glacial conditions Joseph Graly, Joel Harrington, and Neil Humphrey The Cryosphere Discuss., doi:10.5194/tc-2016-137,2016 Manuscript under review for TC (discussion: open, 0 comments) At a major outlet of the Greenland Ice Sheet in West Greenland, we find that the chemical solutes is the emerging subglacial waters are out of phase with water discharge and can spike in concentration during waning flow. This suggests that the subglacial waters are spreading out across a large area of the glacial bed throughout the day, stimulating chemical weathering beyond the major water distribution channels.
    Print ISSN: 1994-0432
    Digitale ISSN: 1994-0440
    Thema: Geographie , Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 79
    Publikationsdatum: 2016-07-14
    Beschreibung: Individuals with a severe mental illness (SMI) are at least two times more likely to suffer from metabolic co-morbidities, leading to excessive and premature deaths. In spite of the many physical and mental he...
    Digitale ISSN: 1756-0500
    Thema: Biologie , Medizin
    Publiziert von BioMed Central
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  • 80
    Publikationsdatum: 2016-07-14
    Beschreibung: Why did the storm ex-Gaston (2010) fail to redevelop during the PREDICT experiment? Thomas M. Freismuth, Blake Rutherford, Mark A. Boothe, and Michael T. Montgomery Atmos. Chem. Phys., 16, 8511-8519, doi:10.5194/acp-16-8511-2016, 2016 Numerical model analyses are used to investigate the role of dry, environmental air in the failed redevelopment of a tropical cyclone (ex-Gaston, 2010). As early as 12:00 UTC 2 September 2010, a dry layer at and above 600 hPa results in a decrease in the vertical mass flux and vertical, relative vorticity. The intrusion of dry air led to a reduction in vorticity and a compromised pouch at these middle levels. This study supports work looking at the role of dry air in moist convection.
    Print ISSN: 1680-7316
    Digitale ISSN: 1680-7324
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 81
    Publikationsdatum: 2016-07-14
    Beschreibung: A comparative analysis of UV nadir-backscatter and infrared limb-emission ozone data assimilation Rossana Dragani Atmos. Chem. Phys., 16, 8539-8557, doi:10.5194/acp-16-8539-2016, 2016 We present an assessment of ultraviolet nadir-backscatter and infrared limb-emission ozone data assimilation. Understanding the differences in the impact produced by the assimilation of limb and nadir ozone data is relevant to many applications, including climate reanalysis and air quality. The results show the potential and limitations of each dataset and support the need for a more balanced long-term availability of both types of sensors than currently envisaged.
    Print ISSN: 1680-7316
    Digitale ISSN: 1680-7324
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 82
    Publikationsdatum: 2016-07-14
    Beschreibung: Continuous measurements of isotopic composition of water vapour on the East Antarctic Plateau Mathieu Casado, Amaelle Landais, Valérie Masson-Delmotte, Christophe Genthon, Erik Kerstel, Samir Kassi, Laurent Arnaud, Ghislain Picard, Frederic Prie, Olivier Cattani, Hans-Christian Steen-Larsen, Etienne Vignon, and Peter Cermak Atmos. Chem. Phys., 16, 8521-8538, doi:10.5194/acp-16-8521-2016, 2016 Climatic conditions in Concordia are very cold (−55 °C in average) and very dry, imposing difficult conditions to measure the water vapour isotopic composition. New developments in infrared spectroscopy enable now the measurement of isotopic composition in water vapour traces (down to 20 ppmv). Here we present the results results of a first campaign of measurement of isotopic composition of water vapour in Concordia, the site where the 800 000 years long ice core was drilled.
    Print ISSN: 1680-7316
    Digitale ISSN: 1680-7324
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 83
    facet.materialart.
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    Copernicus
    Publikationsdatum: 2016-07-14
    Beschreibung: Surface Renewal as a Significant Mechanism for Dust Emission Jie Zhang, Zhenjiao Teng, Ning Huang, Lei Guo, and Yaping Shao Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-421,2016 Manuscript under review for ACP (discussion: open, 0 comments) In spite of the tremendous efforts, many questions remain unanswered regarding dust emission mechanisms. A series of wind-tunnel experiments are carried out on dust emissions from different soil surfaces to better understand relevant mechanisms. Here are some interesting results that demonstrate the importance of surface renewal mechanism which was normally neglected in previous researches and is strongly recommended to be considered in future dust models.
    Print ISSN: 1680-7316
    Digitale ISSN: 1680-7324
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 84
    Publikationsdatum: 2016-07-14
    Beschreibung: Variations in O 3 , CO, and CH 4 over the Bay of Bengal during the summer monsoon season: Ship-borne measurements and model simulations Imran A. Girach, Narendra Ojha, Prabha R. Nair, Andrea Pozzer, Yogesh K. Tiwari, K. Ravi Kumar, and Jos Lelieveld Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-595,2016 Manuscript under review for ACP (discussion: open, 0 comments) This study presents first ship-borne measurements of trace gases over the Bay of Bengal during summer monsoon. The observed variations in trace gases are shown to be due to dynamics/transport and en-route photochemistry. Analysis of meteorological and chemical fields shows that significantly lower ozone during rainfall is associated with the downdrafts. A regional model reproduces the observed variations and revealed the rapid transport of ozone across the Bay of Bengal during an event.
    Print ISSN: 1680-7316
    Digitale ISSN: 1680-7324
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 85
    Publikationsdatum: 2016-07-14
    Beschreibung: Chemical Characteristics of Marine Fine Aerosols over Sea and at Offshore Islands during Three Cruise Sampling Campaigns in the Taiwan Strait– Sea Salts and Anthropogenic Particles Tsung-Chang Li, Chung-Shin Yuan, Chung-Hsuang Hung, Hsun-Yu Lin, Hu-Ching Huang, and Chon-Lin Lee Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-384,2016 Manuscript under review for ACP (discussion: open, 0 comments) This manuscript is significant because it is important to establish data on the background physicochemical characteristics of atmospheric fine particles, as well as their spatial distributions and seasonal variations given various meteorological conditions, and the results of this study will be very much valuable for clarifying the transportation PM 2.5 over sea and at the offshore islands at the Taiwan Strait, which can further fill the the important blank for the global atmospheric research.
    Print ISSN: 1680-7316
    Digitale ISSN: 1680-7324
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 86
    Publikationsdatum: 2016-07-14
    Beschreibung: Continuous measurements of isotopic composition of water vapour on the East Antarctic Plateau Mathieu Casado, Amaelle Landais, Valérie Masson-Delmotte, Christophe Genthon, Erik Kerstel, Samir Kassi, Laurent Arnaud, Ghislain Picard, Frederic Prie, Olivier Cattani, Hans-Christian Steen-Larsen, Etienne Vignon, and Peter Cermak Atmos. Chem. Phys., 16, 8521-8538, doi:10.5194/acp-16-8521-2016, 2016 Climatic conditions in Concordia are very cold (−55 °C in average) and very dry, imposing difficult conditions to measure the water vapour isotopic composition. New developments in infrared spectroscopy enable now the measurement of isotopic composition in water vapour traces (down to 20 ppmv). Here we present the results results of a first campaign of measurement of isotopic composition of water vapour in Concordia, the site where the 800 000 years long ice core was drilled.
    Print ISSN: 1680-7367
    Digitale ISSN: 1680-7375
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 87
    Publikationsdatum: 2016-07-14
    Beschreibung: On the role of tropopause folds in summertime tropospheric ozone over the eastern Mediterranean and the Middle East Dimitris Akritidis, Andrea Pozzer, Prodromos Zanis, Evangelos Tyrlis, Bojan Škerlak, Michael Sprenger, and Jos Lelieveld Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-547,2016 Manuscript under review for ACP (discussion: open, 0 comments) We investigate the contribution of tropopause folds in the summertime tropospheric ozone pool over the eastern Mediterranean and the Middle East. For this purpose we use the EMAC atmospheric chemistry climate model and a fold identification algorithm. A clear increase of ozone is found in the middle troposphere due to fold activity. The interannual variability of near surface ozone over the eastern Mediterranean is related to that of both tropopause folds and ozone in the free troposphere.
    Print ISSN: 1680-7367
    Digitale ISSN: 1680-7375
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 88
    Publikationsdatum: 2016-07-14
    Beschreibung: A Polarimetric Scattering Database for Non-spherical Ice Particles at MicrowaveWavelengths Yinghui Lu, Zhiyuan Jiang, Kultegin Aydin, Johannes Verlinde, Eugene E. Clothiaux, and Giovanni Botta Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-228,2016 Manuscript under review for AMT (discussion: open, 0 comments) The database contains the complete(polarimatric) scattering information for different types of ice particles at different incident and scattered radiation directions at 4 microwave wavelengths. These results are useful for understanding the dependence of ice-particle scattering properties on ice-particle orientation with respect to the incident and scattered radiation. It is also useful in ice property retrievals, radar forward simulation.
    Print ISSN: 1867-1381
    Digitale ISSN: 1867-8548
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 89
    Publikationsdatum: 2016-07-14
    Beschreibung: Variations in O 3 , CO, and CH 4 over the Bay of Bengal during the summer monsoon season: Ship-borne measurements and model simulations Imran A. Girach, Narendra Ojha, Prabha R. Nair, Andrea Pozzer, Yogesh K. Tiwari, K. Ravi Kumar, and Jos Lelieveld Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-595,2016 Manuscript under review for ACP (discussion: open, 0 comments) This study presents first ship-borne measurements of trace gases over the Bay of Bengal during summer monsoon. The observed variations in trace gases are shown to be due to dynamics/transport and en-route photochemistry. Analysis of meteorological and chemical fields shows that significantly lower ozone during rainfall is associated with the downdrafts. A regional model reproduces the observed variations and revealed the rapid transport of ozone across the Bay of Bengal during an event.
    Print ISSN: 1680-7367
    Digitale ISSN: 1680-7375
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 90
    Publikationsdatum: 2016-07-14
    Beschreibung: A comparative analysis of UV nadir-backscatter and infrared limb-emission ozone data assimilation Rossana Dragani Atmos. Chem. Phys., 16, 8539-8557, doi:10.5194/acp-16-8539-2016, 2016 We present an assessment of ultraviolet nadir-backscatter and infrared limb-emission ozone data assimilation. Understanding the differences in the impact produced by the assimilation of limb and nadir ozone data is relevant to many applications, including climate reanalysis and air quality. The results show the potential and limitations of each dataset and support the need for a more balanced long-term availability of both types of sensors than currently envisaged.
    Print ISSN: 1680-7367
    Digitale ISSN: 1680-7375
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 91
    Publikationsdatum: 2016-07-14
    Beschreibung: Why did the storm ex-Gaston (2010) fail to redevelop during the PREDICT experiment? Thomas M. Freismuth, Blake Rutherford, Mark A. Boothe, and Michael T. Montgomery Atmos. Chem. Phys., 16, 8511-8519, doi:10.5194/acp-16-8511-2016, 2016 Numerical model analyses are used to investigate the role of dry, environmental air in the failed redevelopment of a tropical cyclone (ex-Gaston, 2010). As early as 12:00 UTC 2 September 2010, a dry layer at and above 600 hPa results in a decrease in the vertical mass flux and vertical, relative vorticity. The intrusion of dry air led to a reduction in vorticity and a compromised pouch at these middle levels. This study supports work looking at the role of dry air in moist convection.
    Print ISSN: 1680-7367
    Digitale ISSN: 1680-7375
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 92
    Publikationsdatum: 2016-07-14
    Beschreibung: Thermal infrared laser heterodyne spectro-radiometry for solar occultation atmospheric CO 2 measurements Alex Hoffmann, Neil A. Macleod, Marko Huebner, and Damien Weidmann Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-142,2016 Manuscript under review for AMT (discussion: open, 0 comments) This paper focuses on the demonstration and assessment of thermal infrared laser heterodyne spectro-radiometry for the remote sensing of carbon dioxide (CO 2 ). A research instrument has been developed and operated from the ground using direct sunlight to measure CO 2 to a high precision. This technology would enable the development of high-performance miniature ground-based sounders to complement existing measurement networks and contribute to the improvement of global carbon emission assessment.
    Print ISSN: 1867-1381
    Digitale ISSN: 1867-8548
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 93
    Publikationsdatum: 2016-07-14
    Beschreibung: A Polarimetric Scattering Database for Non-spherical Ice Particles at MicrowaveWavelengths Yinghui Lu, Zhiyuan Jiang, Kultegin Aydin, Johannes Verlinde, Eugene E. Clothiaux, and Giovanni Botta Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-228,2016 Manuscript under review for AMT (discussion: open, 0 comments) The database contains the complete(polarimatric) scattering information for different types of ice particles at different incident and scattered radiation directions at 4 microwave wavelengths. These results are useful for understanding the dependence of ice-particle scattering properties on ice-particle orientation with respect to the incident and scattered radiation. It is also useful in ice property retrievals, radar forward simulation.
    Digitale ISSN: 1867-8610
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 94
    Publikationsdatum: 2016-07-14
    Beschreibung: Chemical Characteristics of Marine Fine Aerosols over Sea and at Offshore Islands during Three Cruise Sampling Campaigns in the Taiwan Strait– Sea Salts and Anthropogenic Particles Tsung-Chang Li, Chung-Shin Yuan, Chung-Hsuang Hung, Hsun-Yu Lin, Hu-Ching Huang, and Chon-Lin Lee Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-384,2016 Manuscript under review for ACP (discussion: open, 0 comments) This manuscript is significant because it is important to establish data on the background physicochemical characteristics of atmospheric fine particles, as well as their spatial distributions and seasonal variations given various meteorological conditions, and the results of this study will be very much valuable for clarifying the transportation PM 2.5 over sea and at the offshore islands at the Taiwan Strait, which can further fill the the important blank for the global atmospheric research.
    Print ISSN: 1680-7367
    Digitale ISSN: 1680-7375
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 95
    Publikationsdatum: 2016-07-14
    Beschreibung: Evaluation of Machine Learning Algorithms for Classification of Primary Biological Aerosol using a new UV-LIF spectrometer Simon Ruske, David O. Topping, Virginia E. Foot, Paul H. Kaye, Warren R. Stanley, Ian Crawford, Andrew P. Morse, and Martin W. Gallagher Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-214,2016 Manuscript under review for AMT (discussion: open, 0 comments) Particles such as Bacteria, Pollen and Fungal spores have important implications within the environment and public health sectors. Here we evaluate the performance of various different methods for distinguishing between these different types of particles using a new instrument. We demonstrate that there may be better alternatives to the currently used methods which can be further investigated in future research.
    Print ISSN: 1867-1381
    Digitale ISSN: 1867-8548
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 96
    Publikationsdatum: 2016-07-14
    Beschreibung: Identification of the cloud base height over the central Himalayan region: Intercomparison of Ceilometer and Doppler Lidar K. K. Shukla, K. Niranjan Kumar, D. V. Phanikumar, R. K. Newsom, V. R. Kotamarthi, T. B. M. J. Ouarda, and M. V. Ratnam Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-162,2016 Manuscript under review for AMT (discussion: open, 0 comments) Estimation of Cloud base height was carried out by using various ground based instruments (Doppler Lidar and Ceilometer) and satellite datasets (MODIS) over central Himalayan region for the first time. The present study demonstrates the potential of Doppler Lidar in precise estimation of cloud base height and updraft velocities. More such deployments will be invaluable inputs for regional weather prediction models over complex Himalayan terrains.
    Digitale ISSN: 1867-8610
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 97
    Publikationsdatum: 2016-07-14
    Beschreibung: On the role of tropopause folds in summertime tropospheric ozone over the eastern Mediterranean and the Middle East Dimitris Akritidis, Andrea Pozzer, Prodromos Zanis, Evangelos Tyrlis, Bojan Škerlak, Michael Sprenger, and Jos Lelieveld Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-547,2016 Manuscript under review for ACP (discussion: open, 0 comments) We investigate the contribution of tropopause folds in the summertime tropospheric ozone pool over the eastern Mediterranean and the Middle East. For this purpose we use the EMAC atmospheric chemistry climate model and a fold identification algorithm. A clear increase of ozone is found in the middle troposphere due to fold activity. The interannual variability of near surface ozone over the eastern Mediterranean is related to that of both tropopause folds and ozone in the free troposphere.
    Print ISSN: 1680-7316
    Digitale ISSN: 1680-7324
    Thema: Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 98
    Publikationsdatum: 2016-07-14
    Beschreibung: Increased nitrate and decreased δ 15 N–NO 3 − in the Greenland Arctic after 1940 attributed to North American oil burning Nathan J. Chellman, Meredith G. Hastings, and Joseph R. McConnell The Cryosphere Discuss., doi:10.5194/tc-2016-163,2016 Manuscript under review for TC (discussion: open, 0 comments) This manuscript analyzes the changing sources of nitrate deposition to Greenland since 1760 CE using a dataset consisting of sub-seasonally resolved nitrogen isotopes of nitrate and source tracers. Correlations amongst ion concentration, source tracers, and the δ 15 N–NO 3 − provide evidence of the impact of biomass burning and fossil fuel combustion emissions of nitrogen oxides and suggest that oil combustion is the likely driver of increased nitrate concentration in Greenland ice since 1940 CE.
    Print ISSN: 1994-0416
    Digitale ISSN: 1994-0424
    Thema: Geographie , Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 99
    Publikationsdatum: 2016-07-14
    Beschreibung: Inversion of geothermal heat flux in a thermomechanically coupled nonlinear Stokes ice sheet model Hongyu Zhu, Noemi Petra, Georg Stadler, Tobin Isaac, Thomas J. R. Hughes, and Omar Ghattas The Cryosphere, 10, 1477-1494, doi:10.5194/tc-10-1477-2016, 2016 We study how well the basal geothermal heat flux can be inferred from surface velocity observations using a thermomechanically coupled nonlinear Stokes ice sheet model. The prospects and limitations of this inversion is studied in two and three dimensional model problems. We also argue that a one-way coupled approach for the adjoint equations motivated by staggered solvers for forward multiphysics problems can lead to an incorrect gradient and premature termination of the optimization iteration.
    Print ISSN: 1994-0432
    Digitale ISSN: 1994-0440
    Thema: Geographie , Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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  • 100
    Publikationsdatum: 2016-07-14
    Beschreibung: Increased nitrate and decreased δ 15 N–NO 3 − in the Greenland Arctic after 1940 attributed to North American oil burning Nathan J. Chellman, Meredith G. Hastings, and Joseph R. McConnell The Cryosphere Discuss., doi:10.5194/tc-2016-163,2016 Manuscript under review for TC (discussion: open, 0 comments) This manuscript analyzes the changing sources of nitrate deposition to Greenland since 1760 CE using a dataset consisting of sub-seasonally resolved nitrogen isotopes of nitrate and source tracers. Correlations amongst ion concentration, source tracers, and the δ 15 N–NO 3 − provide evidence of the impact of biomass burning and fossil fuel combustion emissions of nitrogen oxides and suggest that oil combustion is the likely driver of increased nitrate concentration in Greenland ice since 1940 CE.
    Print ISSN: 1994-0432
    Digitale ISSN: 1994-0440
    Thema: Geographie , Geologie und Paläontologie
    Publiziert von Copernicus im Namen von The European Geosciences Union (EGU).
    Standort Signatur Erwartet Verfügbarkeit
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