| 1. |
- Milham, Michael P., et al.
(författare)
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An Open Resource for Non-human Primate Imaging
- 2018
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Ingår i: Neuron. - : Elsevier BV. - 0896-6273 .- 1097-4199. ; 100:1, s. 61-74
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Tidskriftsartikel (refereegranskat)abstract
- Non-human primate neuroimaging is a rapidly growing area of research that promises to transform and scale translational and cross-species comparative neuroscience. Unfortunately, the technological and methodological advances of the past two decades have outpaced the accrual of data, which is particularly challenging given the relatively few centers that have the necessary facilities and capabilities. The PRIMatE Data Exchange (PRIME-DE) addresses this challenge by aggregating independently acquired non-human primate magnetic resonance imaging (MRI) datasets and openly sharing them via the International Neuroimaging Data-sharing Initiative (INDI). Here, we present the rationale, design, and procedures for the PRIME-DE consortium, as well as the initial release, consisting of 25 independent data collections aggregated across 22 sites (total = 217 non-human primates). We also outline the unique pitfalls and challenges that should be considered in the analysis of non-human primate MRI datasets, including providing automated quality assessment of the contributed datasets.
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| 2. |
- Wienberg, C., et al.
(författare)
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The giant Mauritanian cold-water coral mound province: Oxygen control on coral mound formation
- 2018
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Ingår i: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791. ; 185, s. 135-152
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Tidskriftsartikel (refereegranskat)abstract
- The largest coherent cold-water coral (CWC) mound province in the Atlantic Ocean exists along the Mauritanian margin, where up to 100 m high mounds extend over a distance of similar to 400 km, arranged in two slope-parallel chains in 400-550 m water depth. Additionally, CWCs are present in the numerous submarine canyons with isolated coral mounds being developed on some canyon flanks. Seventy-seven Uranium-series coral ages were assessed to elucidate the timing of CWC colonisation and coral mound development along the Mauritanian margin for the last similar to 120,000 years. Our results show that CWCs were present on the mounds during the Last Interglacial, though in low numbers corresponding to coral mound aggradation rates of 16 cm kyr(-1). Most prolific periods for CWC growth are identified for the last glacial and deglaciation, resulting in enhanced mound aggradation (>1000 cm kyr(-1)), before mound formation stagnated along the entire margin with the onset of the Holocene. Until today, the Mauritanian mounds are in a dormant state with only scarce CWC growth. In the canyons, live CWCs are abundant since the Late Holocene at least. Thus, the canyons may serve as a refuge to CWCs potentially enabling the observed modest re-colonisation pulse on the mounds along the open slope. The timing and rate of the pre-Holocene coral mound aggradation, and the cessation of mound formation varied between the individual mounds, which was likely the consequence of vertical/lateral changes in water mass structure that placed the mounds near or out of oxygen-depleted waters, respectively. (C) 2018 The Authors. Published by Elsevier Ltd.
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| 4. |
- Demichev, Vadim, et al.
(författare)
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A time-resolved proteomic and prognostic map of COVID-19
- 2021
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Ingår i: Cell Systems. - : Elsevier BV. - 2405-4712 .- 2405-4720. ; 12:8, s. 780-794.e7
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Tidskriftsartikel (refereegranskat)abstract
- COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.
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| 7. |
- Wisshak, M., et al.
(författare)
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Bioerosion along a bathymetric gradient in a cold-temperate setting (Kosterfjord, SW Sweden): an experimental study
- 2005
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Ingår i: Facies. - : Springer Science and Business Media LLC. - 0172-9179 .- 1612-4820. ; 51:1-4, s. 99-123
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Tidskriftsartikel (refereegranskat)abstract
- In the cold-temperate setting of the Swedish Kosterfjord, a 2-year experiment was launched in order to assess bioerosion rates and to investigate the endolithic borer communities in relation to light availability (relative bathymetry), hydrography and exposure time. The inventory of microendolithic traces, studied by SEM analysis of epoxy resin casts of planted bivalve shells, yields diverse ichnocoenoses comprising a total of 21 traces produced by boring cyanobacteria (7), chlorophytes (4), fungi (6) and traces of uncertain affinity (4). The link between the endoliths (biotaxa) and the traces they leave (ichnotaxa) is evaluated by the study of the boring organisms in situ by transmission light microscopy of planted Iceland spar and bivalve shells. Additionally, the activity of various macroborers (foraminiferans, polychaetes, echinoids, gastropods and sponges) is documented, adding to a distinct diversity maximum at 7 m water depth. A highly condensed photic zonation, due to the high latitude (59 degrees) and eutrophic conditions, is recorded by the measurement of the Photosynthetically Active Radiation (PAR) and is confirmed by the bathymetric range of the photic related ichnocoenoses. At 1 m water depth, a mature shallow euphotic ichnocoenosis dominated by cyanobacteria and at 7 m, a deep euphotic ichnocoenosis dominated by chlorophytes, respectively, is developed after as little as 12 months exposure. With the vanishing light availability from 15 m downwards, the ichnocoenoses development is significantly slowed and only immature dysphotic and aphotic borer communities (dominated by fungi) are encountered. Strong fluctuations of salinity (down to 8%) and temperature (0-20 degrees C) in the euphotic zone indicate most phototrophs present to be considerably euryhaline and eurytherm, while most endolithic fungi appear preferentially in the deeper, more stable marine waters.
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| 8. |
- Wisshak, M., et al.
(författare)
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The physical niche of the bathyal Lophelia pertusa in a non-bathyal setting: environmental controls and palaeoecological implications
- 2005
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Ingår i: In Freiwald A, Roberts JM (eds), Cold-water Corals and Ecosystems. Springer-Verlag, Berlin Heidelberg. - 9783540276739 ; , s. 979-1001
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- The habitat-forming scleractinian coral Lophelia pertusa supports an ecosystem that is widely known to occur in the bathyal marine ecologic realm along deep shelves, oceanic banks, seamounts and continental margins. Therefore, L. pertusa is generally considered a ʻdeep-waterʼ or ʻdeep-seaʼ coral. In contrast, this study analyses the environmental controls of this bathyal ecosystem where it is thriving well in the non-bathyal shallow-water setting of the Swedish Kosterfjord area (NE Skagerrak). This is one of several shallow-water L. pertusa occurrences in Scandinavian waters where saline and temperature stable oceanic waters intrude as topographically-guided underflows onto the inner shelf and adjacent fjords, driven by an estuarine circulation. The L. pertusa occurrence of the Säcken site in the northern Kosterfjord exists at 80-90 m water depth and only a few tens of metres beneath a permanently brackish surface water layer. At the depth of the coral patches, however, the hydrographic data reveal fully marine conditions, which are ensured by a deeper inflow of Atlantic water through the Norwegian Trench into the Skagerrak. SEM analyses of resin casts taken from dead L. pertusa skeletons yield an endolith assemblage dominated by boring sponges such as Cliona spp. (trace: Entobia ispp.), the boring bryozoan Spathipora, the fungus Dodgella priscus (trace Saccomorpha clava) and an unknown fungus (trace: Orthogonum lineare). Such a composition exclusively of heterotroph organisms resembles the Saccomorpha clava / Orthogonum lineare ichnocoenosis which is regarded as indicative for fossil and Recent, open marine, aphotic environments. This interpretation is supported by direct light measurements at the Säcken site, which indicate aphotic conditions for at least most of the year. The finding of bathyal communities in comparatively shallow waters is linked to factors that force deeper oceanic water masses to surface. Such situations are likely to be expected where an estuarine circulation prevails, or in deep-sea basins bordered by narrow shelves and with local upwelling cells driven by the wind regime, facilitating the intrusion of eutrophic deeper waters to shallow depths – including the benthic communities. This circumstance reveals a major potential pitfall in the palaeobathymetric interpretation of fossil L. pertusa occurrences, which tend to be interpreted as bathyal palaeoenvironments. Strikingly, almost all known exposed ancient L. pertusa locations (e.g. Rhodes and Messina Strait in the Mediterranean Sea or the Cook Strait, New Zealand) derive from tectonically active regions with steep bathymetric gradients and a specific confined topography which could have forced deep water to the near surface.
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