| 1. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 2. |
- Kuliński, Karol, et al.
(författare)
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Biogeochemical functioning of the Baltic Sea
- 2022
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Ingår i: Earth System Dynamics. - : Copernicus GmbH. - 2190-4979 .- 2190-4987. ; 13, s. 633-685
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Forskningsöversikt (refereegranskat)abstract
- Location, specific topography, and hydrographic setting together with climate change and strong anthropogenic pressure are the main factors shaping the biogeochemical functioning and thus also the ecological status of the Baltic Sea. The recent decades have brought significant changes in the Baltic Sea. First, the rising nutrient loads from land in the second half of the 20th century led to eutrophication and spreading of hypoxic and anoxic areas, for which permanent stratification of the water column and limited ventilation of deep-water layers made favourable conditions. Since the 1980s the nutrient loads to the Baltic Sea have been continuously decreasing. This, however, has so far not resulted in significant improvements in oxygen availability in the deep regions, which has revealed a slow response time of the system to the reduction of the land-derived nutrient loads. Responsible for that is the low burial efficiency of phosphorus at anoxic conditions and its remobilization from sediments when conditions change from oxic to anoxic. This results in a stoichiometric excess of phosphorus available for organic-matter production, which promotes the growth of N2-fixing cyanobacteria and in turn supports eutrophication. This assessment reviews the available and published knowledge on the biogeochemical functioning of the Baltic Sea. In its content, the paper covers the aspects related to changes in carbon, nitrogen, and phosphorus (C, N, and P) external loads, their transformations in the coastal zone, changes in organic-matter production (eutrophication) and remineralization (oxygen availability), and the role of sediments in burial and turnover of C, N, and P. In addition to that, this paper focuses also on changes in the marine CO2 system, the structure and functioning of the microbial community, and the role of contaminants for biogeochemical processes. This comprehensive assessment allowed also for identifying knowledge gaps and future research needs in the field of marine biogeochemistry in the Baltic Sea. Copyright:
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| 3. |
- Gröger, Matthias, et al.
(författare)
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Coupled regional Earth system modeling in the Baltic Sea region
- 2021
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Ingår i: Earth System Dynamics. - : Copernicus GmbH. - 2190-4979 .- 2190-4987. ; 12:3, s. 939-973
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Forskningsöversikt (refereegranskat)abstract
- Nonlinear responses to externally forced climate change are known to dampen or amplify the local climate impact due to complex cross-compartmental feedback loops in the Earth system. These feedbacks are less well represented in the traditional stand-alone atmosphere and ocean models on which many of today's regional climate assessments rely (e.g., EURO-CORDEX, NOSCCA and BACC II). This has promoted the development of regional climate models for the Baltic Sea region by coupling different compartments of the Earth system into more comprehensive models. Coupled models more realistically represent feedback loops than the information imposed on the region by prescribed boundary conditions and, thus, permit more degrees of freedom. In the past, several coupled model systems have been developed for Europe and the Baltic Sea region. This article reviews recent progress on model systems that allow two-way communication between atmosphere and ocean models; models for the land surface, including the terrestrial biosphere; and wave models at the air-sea interface and hydrology models for water cycle closure. However, several processes that have mostly been realized by one-way coupling to date, such as marine biogeochemistry, nutrient cycling and atmospheric chemistry (e.g., aerosols), are not considered here. In contrast to uncoupled stand-alone models, coupled Earth system models can modify mean near-surface air temperatures locally by up to several degrees compared with their stand-alone atmospheric counterparts using prescribed surface boundary conditions. The representation of small-scale oceanic processes, such as vertical mixing and sea-ice dynamics, appears essential to accurately resolve the air-sea heat exchange over the Baltic Sea, and these parameters can only be provided by online coupled high-resolution ocean models. In addition, the coupling of wave models at the ocean-atmosphere interface allows for a more explicit formulation of small-scale to microphysical processes with local feedbacks to water temperature and large-scale processes such as oceanic upwelling. Over land, important climate feedbacks arise from dynamical terrestrial vegetation changes as well as the implementation of land-use scenarios and afforestation/deforestation that further alter surface albedo, roughness length and evapotranspiration. Furthermore, a good representation of surface temperatures and roughness length over open sea and land areas is critical for the representation of climatic extremes such as heavy precipitation, storms, or tropical nights (defined as nights where the daily minimum temperature does not fall below 20gC), and these parameters appear to be sensitive to coupling. For the present-day climate, many coupled atmosphere-ocean and atmosphere-land surface models have demonstrated the added value of single climate variables, in particular when low-quality boundary data were used in the respective stand-alone model. This makes coupled models a prospective tool for downscaling climate change scenarios from global climate models because these models often have large biases on the regional scale. However, the coupling of hydrology models to close the water cycle remains problematic, as the accuracy of precipitation provided by atmosphere models is, in most cases, insufficient to realistically simulate the runoff to the Baltic Sea without bias adjustments. Many regional stand-alone ocean and atmosphere models are tuned to suitably represent present-day climatologies rather than to accurately simulate climate change. Therefore, more research is required into how the regional climate sensitivity (e.g., the models' response to a given change in global mean temperature) is affected by coupling and how the spread is altered in multi-model and multi-scenario ensembles of coupled models compared with uncoupled ones.
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| 4. |
- Meier, H. E.Markus, et al.
(författare)
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Overview : The Baltic Earth Assessment Reports (BEAR)
- 2023
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Ingår i: Earth System Dynamics. - 2190-4979. ; 14:2, s. 519-531
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Forskningsöversikt (refereegranskat)abstract
- Baltic Earth is an independent research network of scientists from all Baltic Sea countries that promotes regional Earth system research. Within the framework of this network, the Baltic Earth Assessment Reports (BEARs) were produced in the period 2019-2022. These are a collection of 10 review articles summarising current knowledge on the environmental and climatic state of the Earth system in the Baltic Sea region and its changes in the past (palaeoclimate), present (historical period with instrumental observations) and prospective future (until 2100) caused by natural variability, climate change and other human activities. The division of topics among articles follows the grand challenges and selected themes of the Baltic Earth Science Plan, such as the regional water, biogeochemical and carbon cycles; extremes and natural hazards; sea-level dynamics and coastal erosion; marine ecosystems; coupled Earth system models; scenario simulations for the regional atmosphere and the Baltic Sea; and climate change and impacts of human use. Each review article contains an introduction, the current state of knowledge, knowledge gaps, conclusions and key messages; the latter are the bases on which recommendations for future research are made. Based on the BEARs, Baltic Earth has published an information leaflet on climate change in the Baltic Sea as part of its outreach work, which has been published in two languages so far, and organised conferences and workshops for stakeholders, in collaboration with the Baltic Marine Environment Protection Commission (Helsinki Commission, HELCOM).
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| 5. |
- Moros, Matthias, et al.
(författare)
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Giant saltwater inflow in AD 1951 triggered Baltic Sea hypoxia
- 2024
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Ingår i: Boreas. - : John Wiley & Sons. - 0300-9483 .- 1502-3885. ; 53:2, s. 125-138
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Tidskriftsartikel (refereegranskat)abstract
- A marked sedimentological change in subsurface sediments from the entire Baltic Proper, the Baltic Sea, has been previously noted. Our detailed work on a variety of multi-cores from basin-wide transects indicates that this sedimentological change was caused by a large shift in environmental conditions during the 1950s. Until the 1950s, the water column was rather weakly stratified and winter-time convection - although weakened during the post Little Ice Age warming - was still able to ventilate the bottom waters of the Baltic Proper. Therefore, complete sediment sequences only accumulated in calm waters deeper than 150-160 m. High-resolution benthic foraminiferal records of subsurface sediments obtained along the saline water inflow pathway in combination with historical data indicate that the depositional environment changed drastically owing to the giant saline water inflow in AD 1951. The accompanied sharpening of the halo(pycno)cline triggered a collapse in the ventilation of the basin, resulting in oxygen-deficient bottom waters. This deficiency, in turn, caused the onset of phosphate release from the sediments, which accelerated primary production. The ventilation collapse also enabled the onset of deposition of organic carbon-rich sediments also in shallower water areas as calm conditions prevailed up to the modern winter mixing depth (60-70 m). A slight return to Little Ice Age-type conditions was observed during the late 1980s when temperatures decreased and stratification weakened. These conditions gave rise to a reduction in hypoxic areas and to a bottom-water ventilation, most pronounced in the north of the so-called Baltic Sea Klint, a hydrographic and topographic barrier. However, the general environmental conditions essentially have not changed since the 1950s. Remarkably, external (temperature and stratification) in combination with internal factors (e.g. ventilation collapse and phosphate release) were able to change the redox conditions of the Baltic Proper from oxic to hypoxic within less than 10 years. A marked sedimentological change seen in sub-recent seabed sediment cores from the entire Baltic proper can be attributed to large hydrographic and environmental changes that started at the end of the Little Ice Age and were accelerated by a rapid change in stratification resulting from the massive inflow of saline water in AD 1951. The increase in stratification caused a collapse of the already weakened vertical winter-time deep water convection leading to hypoxia in the bottom waters, which in turn forced a sudden phosphate release from the sediments and increased primary production in the late 1950s.image
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| 6. |
- Moros, Matthias, et al.
(författare)
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Is 'deep-water formation' in the Baltic Sea a key to understanding seabed dynamics and ventilation changes over the past 7,000 years?
- 2020
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Ingår i: Quaternary International. - : Elsevier BV. - 1040-6182 .- 1873-4553. ; 550, s. 55-65
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Tidskriftsartikel (refereegranskat)abstract
- Numerous hydro-acoustic studies of the seabed of the Baltic Sea have revealed the unusual occurrence of sediment contourite drifts and re-suspension at greater water depths. In addition, radiocarbon dating of bulk sediments indicates significant age reversals. We present new geophysical, sediment proxy data (including extensive radiocarbon dating) and hydrographic measurements, which are combined with results of numerous marine geological studies performed during the last decades. These data indicate that a deep-water formation process significantly affected the seabed dynamics during regional climatically cold phases during the last c. 7,000 years. We propose that, during the colder periods (e.g. the Little Ice Age), newly formed bottom waters likely caused widespread re-suspension of organic carbon-rich laminated sediments that were deposited during the preceding warm periods in shallower areas, and this material was transported to and re-deposited in the deeper parts of the Baltic Sea sub-basins. In our scenario, a topographic feature, known as the Baltic Sea Klint, acted as a hydrographic barrier for deep-water formed in the northern Baltic. Thus, during the cold periods increased lateral matter influx from the northern Baltic led to the accumulation of much thicker macroscopically homogenous clayey sediments in sub-basins north of the Klint. Moreover, deep-water formation produced bottom currents that led to the formation of sediment contourite drifts at water depths of> 200 m in the Bothnian Sea, the Aland Deep and northern central Baltic Sea sub-basins. Bottom water ventilation in the Baltic Sea is generally assumed to be determined solely by the inflow of oxygen-rich, saline water from the North Sea, but we challenge this assumption and postulate that deep-water formation is a key process that ventilates the bottom waters of the Baltic Sea during climatically cold periods with substantial implications for its sedimentary archive.
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