| 1. |
- Lembrechts, Jonas J., et al.
(författare)
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Global maps of soil temperature
- 2022
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 28:9, s. 3110-3144
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Tidskriftsartikel (refereegranskat)abstract
- Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean=3.0±2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6±2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7±2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications.
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| 2. |
- Dahlberg, C. Johan, et al.
(författare)
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Correlations between plant climate optima across different spatial scales
- 2020
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Ingår i: Environmental and Experimental Botany. - : Elsevier BV. - 0098-8472 .- 1873-7307. ; 170
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Tidskriftsartikel (refereegranskat)abstract
- Identifying the factors determining the abundance and distribution of species is a fundamental question in ecology. One key issue is how similar the factors determining species' distributions across spatial scales are (here we focus especially on spatial extents). If the factors are similar across extents, then the large scale distribution pattern of a species may provide information about its local habitat requirements, and vice versa. We assessed the relationships between landscape and national optima as well as landscape and continental optima for growing degree days, maximum temperature and minimum temperature for 96 bryophytes and 50 vascular plants. For this set of species, we derived landscape optima from abundance weighted temperature data using species inventories in central Sweden and a fine-grained temperature model (50 m), national optima from niche centroid modelling based on GBIF data from Sweden and the same fine-grained climate model, and continental optima using the same method as for the national optima but from GBIF data from Europe and Worldclim temperatures (c. 1000 m). The landscape optima of all species were positively correlated with national as well as continental optima for maximum temperature (r = 0.45 and 0.46, respectively), weakly so for growing degree days (r = 0.30 and r = 0.28), but sometimes absent for minimum temperature (r = 0.26 and r = 0.04). The regression slopes of national or continental optima on local optima did not differ between vascular plants and bryophytes for GDD and Tmax. However, the relationship between the optima of Tmin differed between groups, being positive in vascular plants but absent in bryophytes. Our results suggest that positive correlations between optima at different spatial scales are present for some climatic variables but not for others. Moreover, our results for vascular plants and bryophytes suggest that correlations might differ between organism groups and depend on the ecology of the focal organisms. This implies that it is not possible to routinely up- or downscale distribution patterns based on environmental correlations, since drivers of distribution patterns might differ across spatial extents.
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| 3. |
- Dahlberg, C. Johan, 1978-, et al.
(författare)
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Performance of Forest Bryophytes with Different Geographical Distributions Transplanted across a Topographically Heterogeneous Landscape
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:11
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Tidskriftsartikel (refereegranskat)abstract
- Most species distribution models assume a close link between climatic conditions and species distributions. Yet, we know little about the link between species’ geographical distributions and the sensitivity of performance to local environmental factors. We studied the performance of three bryophyte species transplanted at south- and north-facing slopes in a boreal forest landscape in Sweden. At the same sites, we measured both air and ground temperature. We hypothesized that the two southerly distributed species Eurhynchium angustirete and Herzogiella seligeri perform better on south-facing slopes and in warm conditions, and that the northerly distributed species Barbilophozia lycopodioides perform better on north-facing slopes and in relatively cool conditions. The northern, but not the two southern species, showed the predicted relationship with slope aspect. However, the performance of one of the two southern species was still enhanced by warm temperatures. An important reason for the inconsistent results can be that microclimatic gradients across landscapes are complex and influenced by many climate-forcing factors. Therefore, comparing only north- and south-facing slopes might not capture the complexity of microclimatic gradients. Population growth rates and potential distributions are the integrated results of all vital rates. Still, the study of selected vital rates constitutes an important first step to understand the relationship between population growth rates and geographical distributions and is essential to better predict how climate change influences species distributions.
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| 4. |
- Dahlberg, C. Johan, 1978-, et al.
(författare)
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Plant landscape climatic optima correlate with their continental range optima
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Aim Factors determining species’ distributions at smaller scales may inform us about larger scale distributions, and vice versa. We predicted that landscape and continental climatic optima for plants are positively correlated, and that species that have their optima outside a given focal landscape will cluster at the warmest or coldest landscape patches. Also, we predicted that the correlations of temperature optima are stronger for vascular plants than for bryophytes, since bryophytes may be regulated also by air moisture.LocationÅngermanland, Sweden (landscape scale); Europe (continental scale).MethodsWe derived landscape optima from fine-grained temperature models (50 m) and species inventories, and continental optima from MaxEnt niche modelling based on GBIF occurrences and Worldclim temperatures (c. 1000 m), for 96 bryophytes and 50 vascular plants. Optima were derived for growing degree days, and maximum and minimum temperature.ResultsThe landscape and continental optima of all species were positively correlated for growing degree days and maximum temperature (r = 0.19 and r = 0.44), but not for minimum temperature (r = -0.010). Species with their continental optima outside the focal landscape did not clearly cluster in the most extreme parts of the landscape. For vascular plants the correlation was positive for both growing degree days and maximum temperature (r = 0.50 and r = 0.64), but for bryophytes only for maximum temperature (r = 0.34).Main conclusionsThe optima correlations for maximum temperature and growing degree days indicate that we can infer large scale distribution patterns of plants from their local scale distributions, and suggest in which environments species occur if we only know their continental scale optima. The lack of clustering of southern and northern species limits the possibility for conservation actions targeting microrefugia. Lastly, the correlations indicate that the distributions of vascular plants were more influenced by temperature than bryophytes.
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| 5. |
- Dahlberg, C. Johan, 1978-, et al.
(författare)
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Population dynamics of moss transplants across microclimatic gradients
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In order to determine the response of a species to climatic change it is important to study how climatic factors influence its vital rates and population growth rate across climatic gradients. We investigated how microclimate influence the population dynamics of transplants from northern and more southern populations of the forest bryophyte Hylocomiastrum umbratum. We predicted that its population growth rate is favored by moist microclimates with colder maximum temperatures, longer snow cover duration and less evaporation, and that annual shoots (segments) will be shorter under drier conditions. We also predicted that northern populations will have higher population growth rate and larger segments than southern populations when transplanted to the northern range. We placed transplants from three northern and three southern populations of H. umbratum at 30 forested sites in central Sweden differing in microclimate. We marked and followed the growth of individual shoots during two years, and calculated population growth rates and stable stage distributions of segment size classes using transition matrix models for northern and southern transplants, respectively, at each locality. Population growth rate was lower and shorter segments developed at sites with higher evaporation, corresponding to our hypothesis. There were no significant difference in population growth rate and stable stage segment length between southern and northern populations. Higher evaporation during the summer result in lower population growth rates of H. umbratum by affecting vital rates, in terms of less segment growth. Both climate change and forestry may alter evaporation conditions across the landscape and, thus, the future distribution of the species.
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| 6. |
- Dahlberg, C. Johan, 1978-
(författare)
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The role of microclimate for the performance and distribution of forest plants
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Microclimatic gradients may have large influence on individual vital rates and population growth rates of species, and limit their distributions. Therefore, I focused on the influence of microclimate on individual performance and distribution of species. Further, I examined differences in how microclimate affect species with contrasting distributions or different ecophysiological traits, and populations within species. More specifically, I investigated the performance of northern and southern distributed forest bryophytes that were transplanted across microclimatic gradients, and the timing of vegetative and reproductive development among northern, marginal and more southern populations of a forest herb in a common garden. Also, I compared the landscape and continental distributions across forest bryophytes and vascular plants and, thus, their distribution limiting factors at different spatial scales. Lastly, I examined the population dynamics across microclimatic gradients of transplants from northern and southern populations of a forest moss. The effects of microclimatic conditions on performance differed among bryophytes with contrasting distributions. There were no clear differences between northern and southern populations in the timing of development of a forest herb or in the population dynamics of a moss. However, within each region there was a differentiation of the forest herb populations, related to variation in local climatic conditions and in the south also to proportion of deciduous trees. The continental distributions of species were reflected in their landscape distributions and vice versa, in terms of their occurrence optima for climatic variables. The variation in landscape climatic optima was, however, larger than predicted, which limit the precision for predictions of microrefugia. Probably, the distributions of vascular plants were more affected by temperature than the distributions of bryophytes. Bryophytes are sensitive to moisture conditions, which was demonstrated by a correlation between evaporation and the population growth rate of a forest moss. We might be able to predict species’ landscape scale distributions by linking microclimatic conditions to their population growth rates, via their vital rates, and infer larger scale distribution patterns.
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| 7. |
- Lembrechts, Jonas J., et al.
(författare)
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SoilTemp : A global database of near-surface temperature
- 2020
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 26:11, s. 6616-6629
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Tidskriftsartikel (refereegranskat)abstract
- Current analyses and predictions of spatially explicit patterns and processes in ecology most often rely on climate data interpolated from standardized weather stations. This interpolated climate data represents long-term average thermal conditions at coarse spatial resolutions only. Hence, many climate-forcing factors that operate at fine spatiotemporal resolutions are overlooked. This is particularly important in relation to effects of observation height (e.g. vegetation, snow and soil characteristics) and in habitats varying in their exposure to radiation, moisture and wind (e.g. topography, radiative forcing or cold-air pooling). Since organisms living close to the ground relate more strongly to these microclimatic conditions than to free-air temperatures, microclimatic ground and near-surface data are needed to provide realistic forecasts of the fate of such organisms under anthropogenic climate change, as well as of the functioning of the ecosystems they live in. To fill this critical gap, we highlight a call for temperature time series submissions to SoilTemp, a geospatial database initiative compiling soil and near-surface temperature data from all over the world. Currently, this database contains time series from 7,538 temperature sensors from 51 countries across all key biomes. The database will pave the way toward an improved global understanding of microclimate and bridge the gap between the available climate data and the climate at fine spatiotemporal resolutions relevant to most organisms and ecosystem processes.
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| 8. |
- Lindqvist, C Mårten, et al.
(författare)
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The Mutational Landscape in Pediatric Acute Lymphoblastic Leukemia Deciphered by Whole Genome Sequencing
- 2015
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Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 36:1, s. 118-128
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Tidskriftsartikel (refereegranskat)abstract
- Genomic characterization of pediatric acute lymphoblastic leukemia (ALL) has identified distinct patterns of genes and pathways altered in patients with well-defined genetic aberrations. To extend the spectrum of known somatic variants in ALL, we performed whole genome and transcriptome sequencing of three B-cell precursor patients, of which one carried the t(12;21)ETV6-RUNX1 translocation and two lacked a known primary genetic aberration, and one T-ALL patient. We found that each patient had a unique genome, with a combination of well-known and previously undetected genomic aberrations. By targeted sequencing in 168 patients, we identified KMT2D and KIF1B as novel putative driver genes. We also identified a putative regulatory non-coding variant that coincided with overexpression of the growth factor MDK. Our results contribute to an increased understanding of the biological mechanisms that lead to ALL and suggest that regulatory variants may be more important for cancer development than recognized to date. The heterogeneity of the genetic aberrations in ALL renders whole genome sequencing particularly well suited for analysis of somatic variants in both research and diagnostic applications.
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| 9. |
- Merinero, Sonia, et al.
(författare)
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Intraspecific variation influences performance of moss transplants along microclimate gradients
- 2020
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 101:5
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Tidskriftsartikel (refereegranskat)abstract
- Identifying the environmental drivers of population dynamics is crucial to predict changes in species abundances and distributions under climate change. Populations of the same species might differ in their responses as a result of intraspecific variation. Yet the importance of such differences remains largely unexplored. We examined the responses of latitudinally distant populations of the forest moss Hylocomiastrum umbratum along microclimate gradients in Sweden. We transplanted moss mats from southern and northern populations to 30 sites with contrasting microclimates (i.e., replicated field common gardens) within a forest landscape, and recorded growth and survival of individual shoots over 3 yr. To evaluate the importance of intraspecific variation in responses to environmental factors, we assessed effects of the interactions between population origin and microclimate drivers on growth and survival. Effects on overall performance of transplanted populations were estimated using the product of survival and growth. We found differences between southern and northern populations in the response to summer temperature and snowmelt date in one of three yearly transitions. In this year, southern populations performed better in warm, southern-like conditions than in cold, northern-like conditions; and the reverse pattern was true for northern populations. Survival of all populations decreased with evaporation, consistent with the high hydric demands and poikilohydric nature of mosses. Our results are consistent with population adaptation to local climate, and suggest that intraspecific variation among populations can have important effects on the response of species to microclimate drivers. These findings highlight the need to account for differential responses in predictions of species abundance and distribution under climate change.
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| 10. |
- Callaghan, Terry, et al.
(författare)
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Multi-Decadal Changes in Tundra Environments and Ecosystems : Synthesis of the International Polar Year-Back to the Future Project (IPY-BTF)
- 2011
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Ingår i: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 40:6, s. 705-716
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the responses of tundra systemsto global change has global implications. Most tundraregions lack sustained environmental monitoring and oneof the only ways to document multi-decadal change is toresample historic research sites. The International PolarYear (IPY) provided a unique opportunity for such researchthrough the Back to the Future (BTF) project (IPY project#512). This article synthesizes the results from 13 paperswithin this Ambio Special Issue. Abiotic changes includeglacial recession in the Altai Mountains, Russia; increasedsnow depth and hardness, permafrost warming, andincreased growing season length in sub-arctic Sweden;drying of ponds in Greenland; increased nutrient availabilityin Alaskan tundra ponds, and warming at mostlocations studied. Biotic changes ranged from relativelyminor plant community change at two sites in Greenland tomoderate change in the Yukon, and to dramatic increasesin shrub and tree density on Herschel Island, and in subarcticSweden. The population of geese tripled at one sitein northeast Greenland where biomass in non-grazed plotsdoubled. A model parameterized using results from a BTFstudy forecasts substantial declines in all snowbeds andincreases in shrub tundra on Niwot Ridge, Colorado overthe next century. In general, results support and provideimproved capacities for validating experimental manipulation,remote sensing, and modeling studies.
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| 11. |
- Dahlberg, C. Johan, 1978-, et al.
(författare)
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Population differentiation in timing of development in a forest herb associated with local climate and canopy closure
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Our knowledge of how plant seasonal development is related to local versus larger-scale environmental variation is limited. We investigated differentiation in the timing of vegetative and reproductive development among populations of the forest herb Lathyrus vernus over different spatial scales. We predicted earlier development and shorter development time for populations from a colder, northern region compared to populations from a warmer, southern region. Also, we predicted earlier and shorter development within regions to be associated with colder temperatures and higher proportions of deciduous trees at their sites of origin. Lastly, we predicted that earlier flowering is strongly correlated with earlier start of development. To examine these predictions, we conducted a common garden study, and compared the development of 10 northern and 10 southern Swedish L. vernus populations. Start of development, development time and start of flowering did not differ between populations from the two regions in contrast to our prediction. Within the southern region, start of flowering was earlier in populations from colder sites, while start of development was earlier with colder temperatures within the northern region. Start of flowering occurred earlier in southern populations from sites with higher proportion of deciduous trees. Thus, the prediction for the timing of development within regions was partly confirmed. However, vegetative and reproductive development was not simultaneously influenced by temperature and proportion of deciduous trees within regions, possibly due to the negative correlation between vegetative growth and development time. This implies that earlier start of development or shorter development time not necessarily correspond to earlier start of flowering or vice versa. Overall, the results suggest that smaller scale effects within region, such as temperature and interspecific competition for light, was more important for the timing of development than the larger scale gradients between regions. Lastly, the population differentiation across gradients of temperature and proportion of deciduous trees implies that populations may adapt to long-term changes in light or climatic conditions, and differ in their short-term response to climate change.
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| 12. |
- Dahlberg, Johan, 1988-
(författare)
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Genetic Cartography at Massively Parallel Scale
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Massively parallel sequencing (MPS) is revolutionizing genomics. In this work we use, refine, and develop new tools for the discipline.MPS has led to the discovery of multiple novel subtypes in Acute Lymphoblastic Leukemia (ALL). In Study I we screen for fusion genes in 134 pediatric ALL patients, including patients without an assigned subtype. In approximately 80% of these patients we detect novel or known fusion gene families, most of which display distinct methylation and expression patterns. This shows the potential for improvements in the clinical stratification of ALL. Large sample sizes are important to detect recurrent somatic variation. In Study II we investigate if a non-index overlapping pooling schema can be used to increase sample size and detect somatic variation. We designed a schema for 172 ALL samples and show that it is possible to use this method to call somatic variants.Around the globe there are many ongoing and completed genome projects. In Study III we sequenced the genome of 1000 Swedes to create a reference data set for the Swedish population. We identified more than 10 million variants that were not present in publicly available databases, highlighting the need for population-specific resources. Data, and the tools developed during this study, have been made publicly available as a resource for genomics in Sweden and abroad.The increased amount of sequencing data has created a greater need for automation. In Study IV we present Arteria, a computational automation system for sequencing core facilities. This system has been adopted by multiple facilities and has been used to analyze thousands of samples. In Study V we developed CheckQC, a program that provides automated quality control of Illumina sequencing runs. These tools make scaling up MPS less labour intensive, a key to unlocking the full future potential of genomics.The tools, and data presented here are a valuable contribution to the scientific community. Collectively they showcase the power of MPS and genomics to bring about new knowledge of human health and disease.
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| 13. |
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| 14. |
- Marincevic-Zuniga, Yanara, et al.
(författare)
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Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles
- 2017
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Ingår i: Journal of Hematology & Oncology. - : Springer Science and Business Media LLC. - 1756-8722. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Background: Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. Methods: We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes. Results: We identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations. Conclusion: Our study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.
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| 15. |
- Meineri, Eric, et al.
(författare)
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Using Gaussian Bayesian Networks to disentangle direct and indirect associations between landscape physiography, environmental variables and species distribution
- 2015
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Ingår i: Ecological Modelling. - : Elsevier BV. - 0304-3800 .- 1872-7026. ; 313, s. 127-136
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Tidskriftsartikel (refereegranskat)abstract
- Landscape physiography affects temperature, soil moisture and solar radiation. In turn, these variables are thought to determine how species are distributed across landscapes. Systems involving direct and indirect associations between variables can be described using path models. However, studies applying these to species distribution modelling are rare. Bayesian Networks are path models designed to represent associations across observed variables. Here, we demonstrate the use of Bayesian Networks to disentangle the direct and indirect associations between landscape physiography, soil moisture, solar radiation, temperature and the distribution patterns of four plants at their northern range limit in Sweden. Fine scale variations in maximum temperatures were associated with variations in elevation, distance to coast and solar radiation. In contrast, fine scale variations in minimum temperature were associated with distance to coast, cold air drainage and soil moisture. These associations between landscape physiography and minimum and maximum temperature were predicted, furthermore, to be associated with growing season length, growing degree day and ultimately species distributions. All species were indirectly associated with aspect through their responses to either solar radiation or temperature. The models demonstrated strong indirect associations between landscape physiography and species distributions. The models suggested that local variation in light can be as important as temperature for species distributions. Disentangling the direct and indirect associations between landscape physiography, environmental variables and species distribution can provide new and important insights into how landscape components are linked to species distributions.
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| 16. |
- Neuman, Paul, et al.
(författare)
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Longitudinal assessment of femoral knee cartilage quality using contrast enhanced MRI (dGEMRIC) in patients with anterior cruciate ligament injury - comparison with asymptomatic volunteers.
- 2011
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Ingår i: Osteoarthritis and Cartilage. - : Elsevier BV. - 1063-4584. ; 19, s. 977-983
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: In this observational longitudinal study we estimate knee joint cartilage glycosaminoglycan (GAG) content, in patients with an acute anterior cruciate ligament (ACL) injury, with or without a concomitant meniscus injury. METHODS: 29 knees (19 men/10 women) were prospectively examined by repeat delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC), approximately 3 weeks and 2.3±1.3 (range 4.5) years after the injury. We estimated the GAG content (T1Gd) in the central weight-bearing parts of the medial and lateral femoral cartilage and compared results with a reference cohort (n=24) with normal knees and no history of injury examined by dGEMRIC at one occasion previously. RESULTS: The healthy reference group had longer T1Gd values compared with the ACL-injured patients at follow-up both medially: 428±38 vs 363±61ms (P<0.0001) and laterally: 445±41 vs 396±48ms (P=0.0002). At follow-up T1Gd was lower in meniscectomized patients compared to those without a meniscectomy, both medially (-84ms, P=0.002) and laterally (-38ms, P=0.05). In the injured group, the medial femoral cartilage showed similar T1Gd at the two dGEMRIC investigations: 357±50 vs 363±61ms (P=0.57), whereas the lateral femoral cartilage T1Gd increased: 374±48 vs 396±48ms (P=0.04). CONCLUSIONS: The general decrease in cartilage T1Gd in ACL-injured patients compared with references provide evidence for structural matrix GAG changes that seem more pronounced if a concomitant meniscal injury is present. The fact that post-traumatic OA commonly develops in ACL-injured patients, in particularly those with meniscectomy, suggests that shorter T1Gd may be an early biomarker for OA.
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