| 1. |
- Bishop, Kevin, et al.
(författare)
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Effect of DEM-smoothing and -aggregation on topographically-based flow directions and catchment boundaries
- 2021
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Ingår i: Journal of Hydrology. - : Elsevier BV. - 0022-1694 .- 1879-2707. ; 602
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Tidskriftsartikel (refereegranskat)abstract
- It is generally assumed that, in humid climates, the groundwater table is a subdued copy of the surface topography. However, the general groundwater table is unlikely to be affected by the microtopography as seen in high-resolution Digital Elevation Models (DEMs). So far, there has been little guidance on the best resolution DEM to use to determine the shape of the water table or the direction of shallow groundwater flow in headwater catchments. We, therefore, looked at the effects of DEM-smoothing and -aggregation on the calculated flow directions and derived catchment boundaries, and identified areas and landscape features for which the calculated flow directions are particularly sensitive to DEM smoothing or aggregation. For > 40 % of the area of the Krycklan study catchment, the calculated flow directions depend strongly on the degree of smoothing or aggregation of the DEM. The four main landscape features for which DEM smoothing or aggregation strongly affected the calculated flow directions were: local slopes in the opposite direction of the general slope, flat areas, ridges, and incised streambanks. To determine the effects of the changing flow directions on the derived catchment boundaries for the smoothed and aggregated DEMs, we calculated the drainage area for 40 locations, representing the outlets of catchments of varying sizes. The shape and size of the catchments of first-order streams were most affected by the processing of the DEM. These streams were often almost completely smoothed out during the DEM preprocessing steps. These shifts in catchment boundaries and drainage area would have a large effect on the water balance. This study thus highlights the need to carefully consider the effects of DEM smoothing or -aggregation on the calculated flow directions and drainage areas.
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| 2. |
- Chen, Zhishan, et al.
(författare)
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Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
- 2024
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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| 3. |
- Fernandez-Rozadilla, Ceres, et al.
(författare)
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Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries
- 2023
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 55, s. 89-99
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Tidskriftsartikel (refereegranskat)abstract
- Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.
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| 4. |
- Helgadottir, Hildur, et al.
(författare)
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Multiple primary melanoma incidence trends over five decades, a nation-wide population-based study
- 2021
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 113:3, s. 318-328
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Over the past decades many regions have experienced a steady increase in the incidence of cutaneous melanoma. Here, we report on incidence trends for subsequent primary melanoma.METHODS: In this nationwide population-based study, patients diagnosed with a first primary cutaneous melanoma reported to the Swedish Cancer Registry, were followed for up to ten years for a diagnosis of subsequent primary melanoma. Patients were grouped with patients diagnosed with first melanoma in the same decade (1960s, 1970s, 1980s, 1990s and 2000s, respectively). Frequencies, incidence rates (IRs), standardized incidence ratios (SIRs) and 95% confidence intervals (CIs) for second melanomas were calculated. All tests of statistical significance were two-sided.RESULTS: 54,884 patients with melanoma were included and 2,469 were diagnosed, within ten years, with subsequent melanomas. Over the five decades there was a statistically significant steady increase in the frequency, IR and SIR for second primary melanoma. For example, in the 1960s cohort, <1% (1.0 (95% CI = 0.5-1.7) and 1.1 (95% CI = 0.5-1.9) per 1,000 person-years in women and men, respectively) had second primary melanoma and this rose to 6.4% (7.5 (95% CI = 6.8-8.3) per 1,000 person-years) in the women and 7.9% (10.3 (95% CI = 9.3-11.2) per 1,000 person-years) in the men in the 2000s cohort. This rise was seen, independent of age, sex, invasiveness or site of the melanoma. Further, in patients diagnosed with a second melanoma, the frequency of those having >2 melanomas increased statistically significantly and was 0.0% in the 1960s and rose to 18.0% in the 2000s (P <.001).CONCLUSIONS: This is the first study to evaluate and report on a rising trend for subsequent primary melanoma. Additional primary melanomas worsen the patients' survival and precautions are needed to turn this steep upgoing trend.
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| 5. |
- Karimi, Shirin, et al.
(författare)
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Local‐and network‐scale influence of peatlands on boreal catchment response to rainfall events
- 2023
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Ingår i: Hydrological Processes. - 0885-6087 .- 1099-1085. ; 37
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Tidskriftsartikel (refereegranskat)abstract
- Boreal catchments are composed of different land covers, such as forests, peatlands and lakes, which differ in their runoff response to rainfall events. Understanding the individual and combined responses to rainfall events of these different land cover types is crucial for predicting potential impacts of future climate conditions on boreal water cycling. A common assumption is that peatlands attenuate peak flows, which is used as a motivation to restore drained boreal wetlands. However, it remains unclear how and to what extent peatlands can affect peak flow response. Only a few previous studies have looked at the hydrologic dynamics of peatlands in response to specific rainfall events across a wide range of nested sub-catchments with varying peatland cover. In this study, we use nine years of hourly hydrometric data from 14 catchments within the Krycklan Catchment Study in northern Sweden to examine how peatlands contribute to flood attenuation at both local and stream network scales. Our analysis at the local scale demonstrated that during large events with low antecedent wetness conditions, peatland-dominated catchment exhibited more muted responses compared to the similar-sized forest-dominated catchment. However, during events with high antecedent wetness conditions, the peatland-dominated catchment exhibited flood magnitudes similar to the forest-dominated catchment, although the elevated flow condition at the peatland-dominated catchment persisted for longer periods. Finally, our analysis revealed no significant influence of peatlands on the attenuation or amplification of floods at the stream network scale.
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| 6. |
- Morrison, Kathleen D., et al.
(författare)
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Mapping past human land use using archaeological data : A new classification for global land use synthesis and data harmonization
- 2021
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 16:4
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Tidskriftsartikel (refereegranskat)abstract
- In the 12,000 years preceding the Industrial Revolution, human activities led to significant changes in land cover, plant and animal distributions, surface hydrology, and biochemical cycles. Earth system models suggest that this anthropogenic land cover change influenced regional and global climate. However, the representation of past land use in earth system models is currently oversimplified. As a result, there are large uncertainties in the current understanding of the past and current state of the earth system. In order to improve representation of the variety and scale of impacts that past land use had on the earth system, a global effort is underway to aggregate and synthesize archaeological and historical evidence of land use systems. Here we present a simple, hierarchical classification of land use systems designed to be used with archaeological and historical data at a global scale and a schema of codes that identify land use practices common to a range of systems, both implemented in a geospatial database. The classification scheme and database resulted from an extensive process of consultation with researchers worldwide. Our scheme is designed to deliver consistent, empirically robust data for the improvement of land use models, while simultaneously allowing for a comparative, detailed mapping of land use relevant to the needs of historical scholars. To illustrate the benefits of the classification scheme and methods for mapping historical land use, we apply it to Mesopotamia and Arabia at 6 kya (c. 4000 BCE). The scheme will be used to describe land use by the Past Global Changes (PAGES) LandCover6k working group, an international project comprised of archaeologists, historians, geographers, paleoecologists, and modelers. Beyond this, the scheme has a wide utility for creating a common language between research and policy communities, linking archaeologists with climate modelers, biodiversity conservation workers and initiatives.
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| 7. |
- Seibert, Jan, et al.
(författare)
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Aqua temporaria incognita
- 2020
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Ingår i: Hydrological Processes. - : Wiley. - 0885-6087 .- 1099-1085. ; 34, s. 5704-5711
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Tidskriftsartikel (refereegranskat)
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| 8. |
- Seibert, Jan, et al.
(författare)
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Shallow-groundwater-level time series and a groundwater chemistry survey from a boreal headwater catchment, Krycklan, Sweden
- 2023
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Ingår i: Earth System Science Data. - 1866-3508 .- 1866-3516. ; 15, s. 1779-1800
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Tidskriftsartikel (refereegranskat)abstract
- Shallow groundwater can respond quickly to precipitation and is the main contributor to streamflow in most catchments in humid, temperate climates. Therefore, it is important to have high-spatiotemporal-resolution data on groundwater levels and groundwater chemistry to test spatially distributed hydrological models. However, currently, there are few datasets on groundwater levels with a high spatiotemporal resolution because of the large effort required to collect these data. To better understand shallow groundwater dynamics in a boreal headwater catchment, we installed a network of groundwater wells in two areas in the Krycklan catchment in northern Sweden for a small headwater catchment (3.5 ha; 54 wells) and a hillslope (1 ha; 21 wells). The average well depth was 274 cm (range of 70-581 cm). We recorded the groundwater-level variation at 10-30 min intervals between 18 July 2018-1 November 2020. Manual water-level measurements (0-26 per well) during the summers of 2018 and 2019 were used to confirm and re-calibrate the automatic water-level measurements. The groundwater-level data for each well was carefully processed using six data quality labels. The absolute and relative positions of the wells were measured with a high-precision GPS and terrestrial laser scanner to determine differences in absolute groundwater levels and calculate groundwater gradients. During the summer of 2019, all wells with sufficient water were sampled once and analyzed for electrical conductivity, pH, absorbance, and anion and cation concentrations, as well as the stable isotopes of hydrogen and oxygen. The data are available at https://doi.org/10.5880/fidgeo.2022.020 (Erdbrugger et al., 2022). This combined hydrometric and hydrochemical dataset can be useful for testing models that simulate groundwater dynamics and evaluating metrics that describe subsurface hydrological connectivity.
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| 9. |
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| 10. |
- Seibert, Jan, et al.
(författare)
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Temporal and spatial variation in shallow groundwater gradients in a boreal headwater catchment
- 2023
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Ingår i: Journal of Hydrology. - 0022-1694 .- 1879-2707. ; 626
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Tidskriftsartikel (refereegranskat)abstract
- In humid climates, shallow groundwater is often assumed to be a subdued replica of the surface topography. Nevertheless, the relation between the surface topography and groundwater table can change over time, especially when catchment wetness changes. To investigate the correlation between the surface topography and the groundwater table, we analyzed groundwater levels and gradients in a boreal headwater catchment using 1.5 years of continuous groundwater level data for 75 wells. As expected, groundwater gradients changed with catchment wetness. Gradient directions calculated over short distances (5 m) changed by up to 360 degrees; gradients calculated over larger distances (20 m) varied by up to 270 degrees. The groundwater gradient directions were generally most variable for flatter locations and locations where the local surface slope differed from the surrounding topography. Smoothed digital elevation models (DEMs) represented the groundwater surface better than high resolution DEMs. The optimal degree of smoothing varied over the year and was lowest for very wet periods, such as the snowmelt period, when groundwater tables were high.
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