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  • 1
    Publication Date: 2021-02-10
    Description: The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)1. In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%.
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 2
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    PANGAEA
    In:  Supplement to: Lichtschlag, Anna; Cevatoglu, Melis; Connelly, Douglas P; James, Rachael H; Bull, Jonathan M (2018): Increased Fluid Flow Activity in Shallow Sediments at the 3 km Long Hugin Fracture in the Central North Sea. Geochemistry, Geophysics, Geosystems, 19(1), 2-20, https://doi.org/10.1002/2017GC007181
    Publication Date: 2023-02-24
    Description: The North Sea hosts a wide variety of seafloor seeps that may be important for transfer of chemical species, such as methane, from the Earth's interior to its exterior. Here we provide geochemical and geophysical evidence for fluid flow within shallow sediments at the recently discovered, 3 -km long Hugin Fracture in the Central North Sea. Although venting of gas bubbles was not observed, concentrations of dissolved methane were significantly elevated (up to six-times background values) in the water column at various locations above the fracture, and microbial mats that form in the presence of methane were observed at the seafloor. Seismic amplitude anomalies revealed a bright spot at a fault bend that may be the source of the water column methane. Sediment porewaters recovered in close proximity to the Hugin Fracture indicate the presence of fluids from two different shallow (〈500 m) sources: (i) a reduced fluid characterized by elevated methane concentrations and/or high levels of dissolved sulfide (up to 6 mmol L-1), and (ii) a low-chlorinity fluid (Cl ~305 mmol L-1) that has low levels of dissolved methane and/or sulfide. The area of the seafloor affected by the presence of methane-enriched fluids is similar to the footprint of seepage from other morphological features in the North Sea.
    Keywords: ECO2; Sub-seabed CO2 Storage: Impact on Marine Ecosystems
    Type: Dataset
    Format: application/zip, 25 datasets
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  • 3
    Publication Date: 2023-02-24
    Keywords: AA; Alkalinity, total; Autoanalyzer; Carbon, inorganic, dissolved; Cast number; CTD/Rosette; CTD-RO; Date/Time of event; DEPTH, water; ECO2; Elevation of event; Event label; Gas chromatography; James Cook; JC077; JC077-CTD1; JC077-CTD10; JC077-CTD11; JC077-CTD12; JC077-CTD13; JC077-CTD14; JC077-CTD15; JC077-CTD16; JC077-CTD17; JC077-CTD18; JC077-CTD19; JC077-CTD2; JC077-CTD20; JC077-CTD21; JC077-CTD22; JC077-CTD23; JC077-CTD24; JC077-CTD25; JC077-CTD26; JC077-CTD27; JC077-CTD28; JC077-CTD29; JC077-CTD3; JC077-CTD30; JC077-CTD31; JC077-CTD32; JC077-CTD33; JC077-CTD34; JC077-CTD35; JC077-CTD36; JC077-CTD37; JC077-CTD38; JC077-CTD39; JC077-CTD4; JC077-CTD40; JC077-CTD41; JC077-CTD42; JC077-CTD43; JC077-CTD44; JC077-CTD45; JC077-CTD46; JC077-CTD47; JC077-CTD48; JC077-CTD49; JC077-CTD5; JC077-CTD50; JC077-CTD51; JC077-CTD52; JC077-CTD53; JC077-CTD54; JC077-CTD55; JC077-CTD56; JC077-CTD57; JC077-CTD58; JC077-CTD59; JC077-CTD6; JC077-CTD60; JC077-CTD61; JC077-CTD62; JC077-CTD63; JC077-CTD64; JC077-CTD7; JC077-CTD8; JC077-CTD9; Latitude of event; Longitude of event; Methane; Nitrate and Nitrite; Oxygen; Phosphate; Silicate; Sub-seabed CO2 Storage: Impact on Marine Ecosystems; Titration; Titration, Winkler
    Type: Dataset
    Format: text/tab-separated-values, 1874 data points
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  • 4
    Publication Date: 2024-01-26
    Keywords: Biomass as carbon per individual; EXP; Experiment; Growth rate as carbon per carbon biomass; Growth rate as carbon per individual; M_peninsulae_GROWTH; Santa Rosa Sound; Taxon/taxa; Treatment: temperature; Uniform resource locator/link to reference
    Type: Dataset
    Format: text/tab-separated-values, 24 data points
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  • 5
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    PANGAEA
    In:  Supplement to: Munday, Philip L; McCormick, Mark I; Meekan, Mark; Dixson, Danielle L; Watson, Sue-Ann; Chivers, Douglas P; Ferrari, Maud C O (2012): Selective mortality associated with variation in CO2 tolerance in a marine fish. Ocean Acidification, 1, 1-5, https://doi.org/10.2478/oac-2012-0001
    Publication Date: 2024-03-15
    Description: Predicted future CO2 levels can affect reproduction, growth, and behaviour of many marine organisms. However, the capacity of species to adapt to predicted changes in ocean chemistry is largely unknown. We used a unique field-based experiment to test for differential survival associated with variation in CO2 tolerance in a wild population of coral-reef fishes. Juvenile damselfish exhibited variation in their response to elevated (700 µatm) CO2 when tested in the laboratory and this influenced their behaviour and risk of mortality in the wild. Individuals that were sensitive to elevated CO2 were more active and move further from shelter in natural coral reef habitat and, as a result, mortality from predation was significantly higher compared with individuals from the same treatment that were tolerant of elevated CO2. If individual variation in CO2 tolerance is heritable, this selection of phenotypes tolerant to elevated CO2 could potentially help mitigate the effects of ocean acidification.
    Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Behaviour; Bicarbonate ion; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); Distance; Distance, standard error; Distance from shelter; Distance from shelter, standard error; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Group; Laboratory experiment; Lizard_Island; Lizard Island, northern Great Barrier Reef; Mortality/Survival; Nekton; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; pH, standard deviation; Pomacentrus wardi; Potentiometric; Potentiometric titration; Salinity; Single species; South Pacific; Species; Survival; Temperature, water; Temperature, water, standard deviation; Time in hours; Tropical
    Type: Dataset
    Format: text/tab-separated-values, 627 data points
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  • 6
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    PANGAEA
    In:  Supplement to: Ferrari, Maud C O; McCormick, Mark I; Munday, Philip L; Meekan, Mark; Dixson, Danielle L; Lonnstedt, Öona; Chivers, Douglas P (2012): Effects of ocean acidification on visual risk assessment in coral reef fishes. Functional Ecology, 26(3), 553-558, https://doi.org/10.1111/j.1365-2435.2011.01951.x
    Publication Date: 2024-03-15
    Description: 1. With the global increase in CO2 emissions, there is a pressing need for studies aimed at understanding the effects of ocean acidification on marine ecosystems. Several studies have reported that exposure to CO2 impairs chemosensory responses of juvenile coral reef fishes to predators. Moreover, one recent study pointed to impaired responses of reef fish to auditory cues that indicate risky locations. These studies suggest that altered behaviour following exposure to elevated CO2 is caused by a systemic effect at the neural level. 2. The goal of our experiment was to test whether juvenile damselfish Pomacentrus amboinensis exposed to different levels of CO2 would respond differently to a potential threat, the sight of a large novel coral reef fish, a spiny chromis, Acanthochromis polyancanthus, placed in a watertight bag. 3. Juvenile damselfish exposed to 440 (current day control), 550 or 700 µatm CO2 did not differ in their response to the chromis. However, fish exposed to 850 µatm showed reduced antipredator responses; they failed to show the same reduction in foraging, activity and area use in response to the chromis. Moreover, they moved closer to the chromis and lacked any bobbing behaviour typically displayed by juvenile damselfishes in threatening situations. 4. Our results are the first to suggest that response to visual cues of risk may be impaired by CO2 and provide strong evidence that the multi-sensory effects of CO2 may stem from systematic effects at the neural level.
    Keywords: Alkalinity, total; Alkalinity, total, standard error; Animalia; Aragonite saturation state; Behaviour; Bicarbonate ion; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Change; Change, standard error; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); Distance; Distance, standard error; EXP; Experiment; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Laboratory experiment; Lizard_Island_OA; Nekton; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Partial pressure of carbon dioxide (water) at sea surface temperature (wet air), standard error; Pelagos; pH; pH, standard error; Pomacentrus amboinensis; Potentiometric; Potentiometric titration; Salinity; Single species; South Pacific; Species; Temperature, water; Temperature, water, standard error; Treatment; Tropical
    Type: Dataset
    Format: text/tab-separated-values, 116 data points
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  • 7
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    PANGAEA
    In:  Supplement to: Hawkes, Jeffrey A; Rossel, Pamela E; Stubbins, Aron; Butterfield, David A; Connelly, Douglas P; Achterberg, Eric Pieter; Koschinsky, Andrea; Chavagnac, Valerie; Hansen, Christian T; Bach, Wolfgang; Dittmar, Thorsten (2015): Efficient removal of recalcitrant deep-ocean dissolved organic matter during hydrothermal circulation. Nature Geoscience, 8(11), 856-860, https://doi.org/10.1038/ngeo2543
    Publication Date: 2024-02-17
    Description: Oceanic dissolved organic carbon (DOC) is an important carbon pool, similar in magnitude to atmospheric CO2, but the fate of its oldest forms is not well understood (Dittmar and Stubbins, 2014; Hansell, 2013, doi:10.1146/annurev-marine-120710-100757). Hot hydrothermal circulation may facilitate the degradation of otherwise un-reactive dissolved organic matter, playing an important role in the long-term global carbon cycle. The oldest, most recalcitrant forms of DOC, which make up most of oceanic DOC, can be recovered by solid-phase extraction. Here we present measurements of solid-phase extractable DOC from samples collected between 2009 and 2013 at seven vent sites in the Atlantic, Pacific and Southern oceans, along with magnesium concentrations, a conservative tracer of water circulation through hydrothermal systems. We find that magnesium and solid-phase extractable DOC concentrations are correlated, suggesting that solid-phase extractable DOC is almost entirely lost from solution through mineralization or deposition during circulation through hydrothermal vents with fluid temperatures of 212-401 °C. In laboratory experiments, where we heated samples to 380 °C for four days, we found a similar removal efficiency. We conclude that thermal degradation alone can account for the loss of solid-phase extractable DOC in natural hydrothermal systems, and that its maximum lifetime is constrained by the timescale of hydrothermal cycling, at about 40 million years (Elderfield and Schultz, 1996, doi:10.1146/annurev.earth.24.1.191).
    Keywords: Akademik Mstislav Keldysh; AMK47; AMK47-Lost_City; AT18-08; Atlantis (1997); Carbon, organic, dissolved; Carbon, organic, dissolved, extracted; Comment; Comment 2 (continued); Contamination; CTD/Rosette; CTD-RO; Description; Error; Event label; Factor; Identification; ISIS; ISIS MS2000; J2-574; J2-575; J2-576; J2-579; J2-580; J2-581; J2-583; James Cook; JC042; JC080; JC082; JC42_ISIS_130; JC42_ISIS_133; JC42_ISIS_134; JC42_ISIS_141; JC80_015_CTD; JC80_ISIS_189; JC80_ISIS_190; JC80_ISIS_194; JC82_ISIS_198; JC82_ISIS_200; JC82_ISIS_202; JC82_ISIS_204; JC82_ISIS_206; JC82_ISIS_207; Juan_de_Fuca_Ridge_Axial; Juan_de_Fuca_Ridge_Endeavour; Latitude of event; Lithology/composition/facies; Longitude of event; Lost City Hydrothermal Field, Mid-Atlantic Ridge; M82/3; M82/3_719-1; M82/3_722-1; M82/3_739-1; M82/3_756-1; Magnesium; Maria S. Merian; Meteor (1986); MIR; MIR deep-sea manned submersible; MSM10/3; MSM10/3_290ROV-11; MSM10/3_300; MSM10/3_313ROV-12; Name; Ocean and sea region; Percentage; Precision; Remote operated vehicle; Remote operated vehicle Jason II; ROV; ROVJ; Sample type; Sample volume; Sampling date; Site; Solid phase extractable; South Atlantic Ocean; tropical/subtropical North Atlantic; Type; Volume; Wakamiko_Crater
    Type: Dataset
    Format: text/tab-separated-values, 4130 data points
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  • 8
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    PANGAEA
    In:  Supplement to: Chivers, Douglas P; McCormick, Mark I; Nilsson, Göran E; Munday, Philip L; Watson, Sue-Ann; Meekan, Mark; Mitchell, Matthew D; Corkill, Katherine C; Ferrari, Maud C O (2014): Impaired learning of predators and lower prey survival under elevated CO2: a consequence of neurotransmitter interference. Global Change Biology, 20(2), 515-522, https://doi.org/10.1111/gcb.12291
    Publication Date: 2024-03-15
    Description: Ocean acidification is one of the most pressing environmental concerns of our time, and not surprisingly, we have seen a recent explosion of research into the physiological impacts and ecological consequences of changes in ocean chemistry. We are gaining considerable insights from this work, but further advances require greater integration across disciplines. Here, we showed that projected near-future CO2 levels impaired the ability of damselfish to learn the identity of predators. These effects stem from impaired neurotransmitter function; impaired learning under elevated CO2 was reversed when fish were treated with gabazine, an antagonist of the GABA-A receptor - a major inhibitory neurotransmitter receptor in the brain of vertebrates. The effects of CO2 on learning and the link to neurotransmitter interference were manifested as major differences in survival for fish released into the wild. Lower survival under elevated CO2 , as a result of impaired learning, could have a major influence on population recruitment.
    Keywords: Alkalinity, total; Alkalinity, total, standard error; Animalia; Aragonite saturation state; Behaviour; Bicarbonate ion; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); EXP; Experiment; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Laboratory experiment; Lizard_Island_OA; Nekton; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Partial pressure of carbon dioxide (water) at sea surface temperature (wet air), standard error; Pelagos; pH; pH, standard error; Pomacentrus amboinensis; Potentiometric; Potentiometric titration; Proportion; Proportion, standard error; Salinity; South Pacific; Species; Species interaction; Temperature, water; Temperature, water, standard error; Time in days; Treatment; Tropical
    Type: Dataset
    Format: text/tab-separated-values, 416 data points
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  • 9
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    PANGAEA
    In:  Supplement to: Ferrari, Maud C O; Manassa, Rachel; Dixson, Danielle L; Munday, Philip L; McCormick, Mark I; Meekan, Mark; Sihler, H; Chivers, Douglas P (2012): Effects of ocean acidification on learning in coral reef fishes. PLoS ONE, 7(2), e31478, https://doi.org/10.1371/journal.pone.0031478
    Publication Date: 2024-03-15
    Description: Ocean acidification has the potential to cause dramatic changes in marine ecosystems. Larval damselfish exposed to concentrations of CO2 predicted to occur in the mid- to late-century show maladaptive responses to predator cues. However, there is considerable variation both within and between species in CO2 effects, whereby some individuals are unaffected at particular CO2 concentrations while others show maladaptive responses to predator odour. Our goal was to test whether learning via chemical or visual information would be impaired by ocean acidification and ultimately, whether learning can mitigate the effects of ocean acidification by restoring the appropriate responses of prey to predators. Using two highly efficient and widespread mechanisms for predator learning, we compared the behaviour of pre-settlement damselfish Pomacentrus amboinensis that were exposed to 440 µatm CO2 (current day levels) or 850 µatm CO2, a concentration predicted to occur in the ocean before the end of this century. We found that, regardless of the method of learning, damselfish exposed to elevated CO2 failed to learn to respond appropriately to a common predator, the dottyback, Pseudochromis fuscus. To determine whether the lack of response was due to a failure in learning or rather a short-term shift in trade-offs preventing the fish from displaying overt antipredator responses, we conditioned 440 or 700 µatm-CO2 fish to learn to recognize a dottyback as a predator using injured conspecific cues, as in Experiment 1. When tested one day post-conditioning, CO2 exposed fish failed to respond to predator odour. When tested 5 days post-conditioning, CO2 exposed fish still failed to show an antipredator response to the dottyback odour, despite the fact that both control and CO2-treated fish responded to a general risk cue (injured conspecific cues). These results indicate that exposure to CO2 may alter the cognitive ability of juvenile fish and render learning ineffective.
    Keywords: Alkalinity, total; Alkalinity, total, standard error; Animalia; Aragonite saturation state; Behaviour; Bicarbonate ion; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Change; Change, standard error; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); EXP; Experiment; Experimental treatment; Figure; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Group; Laboratory experiment; Lizard_Island_OA; Nekton; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Partial pressure of carbon dioxide (water) at sea surface temperature (wet air), standard error; Pelagos; pH; pH, standard error; Pomacentrus amboinensis; Potentiometric; Potentiometric titration; Salinity; Single species; South Pacific; Species; Temperature, water; Temperature, water, standard error; Treatment; Tropical
    Type: Dataset
    Format: text/tab-separated-values, 780 data points
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  • 10
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    PANGAEA
    In:  Supplement to: Ferrari, Maud C O; McCormick, Mark I; Munday, Philip L; Meekan, Mark; Dixson, Danielle L; Lonnstedt, Öona; Chivers, Douglas P (2011): Putting prey and predator into the CO2 equation-qualitative and quantitative effects of ocean acidification on predator-prey interactions. Ecology Letters, 14(11), 1143-1148, https://doi.org/10.1111/j.1461-0248.2011.01683.x
    Publication Date: 2024-03-15
    Description: Little is known about the impact of ocean acidification on predator-prey dynamics. Herein, we examined the effect of carbon dioxide (CO(2)) on both prey and predator by letting one predatory reef fish interact for 24 h with eight small or large juvenile damselfishes from four congeneric species. Both prey and predator were exposed to control or elevated levels of CO(2). Mortality rate and predator selectivity were compared across CO(2) treatments, prey size and species. Small juveniles of all species sustained greater mortality at high CO(2) levels, while large recruits were not affected. For large prey, the pattern of prey selectivity by predators was reversed under elevated CO(2). Our results demonstrate both quantitative and qualitative consumptive effects of CO(2) on small and larger damselfish recruits respectively, resulting from CO(2)-induced behavioural changes likely mediated by impaired neurological function. This study highlights the complexity of predicting the effects of climate change on coral reef ecosystems.
    Keywords: Alkalinity, total; Alkalinity, total, standard error; Animalia; Aragonite saturation state; Behaviour; Bicarbonate ion; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); EXP; Experiment; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Group; Laboratory experiment; Lizard_Island_OA; Mortality; Mortality, standard error; Mortality/Survival; Nekton; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Partial pressure of carbon dioxide (water) at sea surface temperature (wet air), standard error; Pelagos; pH; pH, standard error; Pomacentrus amboinensis; Pomacentrus chrysurus; Pomacentrus moluccensis; Pomacentrus nagasakiensis; Potentiometric; Potentiometric titration; Prey selectivity index; Prey selectivity index, standard error; Salinity; South Pacific; Species; Species interaction; Temperature, water; Temperature, water, standard error; Tropical
    Type: Dataset
    Format: text/tab-separated-values, 416 data points
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