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- Haiman, Christopher A., et al.
(författare)
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A common variant at the TERT-CLPTM1L locus is associated with estrogen receptor-negative breast cancer
- 2011
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 43:12, s. 61-1210
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Tidskriftsartikel (refereegranskat)abstract
- Estrogen receptor (ER)-negative breast cancer shows a higher incidence in women of African ancestry compared to women of European ancestry. In search of common risk alleles for ER-negative breast cancer, we combined genome-wide association study (GWAS) data from women of African ancestry (1,004 ER-negative cases and 2,745 controls) and European ancestry (1,718 ER-negative cases and 3,670 controls), with replication testing conducted in an additional 2,292 ER-negative cases and 16,901 controls of European ancestry. We identified a common risk variant for ER-negative breast cancer at the TERT-CLPTM1L locus on chromosome 5p15 (rs10069690: per-allele odds ratio (OR) = 1.18 per allele, P = 1.0 x 10(-10)). The variant was also significantly associated with triple-negative (ER-negative, progesterone receptor (PR)-negative and human epidermal growth factor-2 (HER2)-negative) breast cancer (OR = 1.25, P = 1.1 x 10(-9)), particularly in younger women (<50 years of age) (OR = 1.48, P = 1.9 x 10(-9)). Our results identify a genetic locus associated with estrogen receptor negative breast cancer subtypes in multiple populations.
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- Andrikopoulos, Petros, et al.
(författare)
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Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide
- 2023
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Ingår i: Nature Communications. - 2041-1723 .- 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The host-microbiota co-metabolite trimethylamine N-oxide (TMAO) is linked to increased cardiovascular risk but how its circulating levels are regulated remains unclear. We applied "explainable" machine learning, univariate, multivariate and mediation analyses of fasting plasma TMAO concentration and a multitude of phenotypes in 1,741 adult Europeans of the MetaCardis study. Here we show that next to age, kidney function is the primary variable predicting circulating TMAO, with microbiota composition and diet playing minor, albeit significant, roles. Mediation analysis suggests a causal relationship between TMAO and kidney function that we corroborate in preclinical models where TMAO exposure increases kidney scarring. Consistent with our findings, patients receiving glucose-lowering drugs with reno-protective properties have significantly lower circulating TMAO when compared to propensity-score matched control individuals. Our analyses uncover a bidirectional relationship between kidney function and TMAO that can potentially be modified by reno-protective anti-diabetic drugs and suggest a clinically actionable intervention for decreasing TMAO-associated excess cardiovascular risk.
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- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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- Calogiuri, Tullia, et al.
(författare)
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Design and Construction of an Experimental Setup to Enhance Mineral Weathering through the Activity of Soil Organisms
- 2023
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Ingår i: Journal of Visualized Experiments. - : Journal of Visualized Experiments. - 1940-087X. ; :201
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Tidskriftsartikel (refereegranskat)abstract
- Enhanced weathering (EW) is an emerging carbon dioxide (CO2) removal technology that can contribute to climate change mitigation. This technology relies on accelerating the natural process of mineral weathering in soils by manipulating the abiotic variables that govern this process, in particular mineral grain size and exposure to acids dissolved in water. EW mainly aims at reducing atmospheric CO2 concentrations by enhancing inorganic carbon sequestration. Until now, knowledge of EW has been mainly gained through experiments that focused on the abiotic variables known for stimulating mineral weathering, thereby neglecting the potential influence of biotic components. While bacteria, fungi, and earthworms are known to increase mineral weathering rates, the use of soil organisms in the context of EW remains underexplored. This protocol describes the design and construction of an experimental setup developed to enhance mineral weathering rates through soil organisms while concurrently controlling abiotic conditions. The setup is designed to maximize weathering rates while maintaining soil organisms' activity. It consists of a large number of columns filled with rock powder and organic material, located in a climate chamber and with water applied via a downflow irrigation system. Columns are placed above a fridge containing jerrycans to collect the leachate. Representative results demonstrate that this setup is suitable to ensure the activity of soil organisms and quantify their effect on inorganic carbon sequestration. Challenges remain in minimizing leachate losses, ensuring homogeneous ventilation through the climate chamber, and avoiding flooding of the columns. With this setup, an innovative and promising approach is proposed to enhance mineral weathering rates through the activity of soil biota and disentangle the effect of biotic and abiotic factors as drivers of EW.
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- Corbett, Thomas, et al.
(författare)
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Organic carbon source controlled microbial olivine dissolution in small-scale flow-through bioreactors, for CO2 removal
- 2024
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Ingår i: NPJ MATERIALS DEGRADATION. - : Nature Publishing Group. - 2397-2106. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- The development of carbon dioxide removal methods, coupled with decreased CO2 emissions, is fundamental to achieving the targets outlined in the Paris Agreement limiting global warming to 1.5 degrees C. Here we are investigating the importance of the organic carbon feedstock to support silicate mineral weathering in small-scale flow through bioreactors and subsequent CO2 sequestration. Here, we combine two bacteria and two fungi, widely reported for their weathering potential, in simple flow through bioreactors (columns) consisting of forsterite and widely available, cheap organic carbon sources (wheat straw, bio-waste digestate of pig manure and biowaste, and manure compost), over six weeks. Compared to their corresponding abiotic controls, the inoculated straw and digestate columns release more total alkalinity (similar to 2 times more) and produce greater dissolved and solid inorganic carbon (29% for straw and 13% for digestate), suggesting an increase in CO2 sequestration because of bio-enhanced silicate weathering. Microbial biomass is higher in the straw columns compared to the digestate and manure compost columns, with a phospholipid fatty acid derived total microbial biomass 10 x greater than the other biotic columns. Scanning Electron Microscopy imaging shows the most extensive colonisation and biofilm formation on the mineral surfaces in the straw columns. The biotic straw and digestate columns sequester 50 and 14 mg C more than their abiotic controls respectively, while there is no difference in the manure columns. The selection of organic carbon sources to support microbial communities in the flow through bioreactors controlls the silicate weathering rates and CO2 sequestration.
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- Edström, Kristina, Professor, 1958-
(författare)
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Battery 2030+ Roadmap
- 2020
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Climate change is the biggest challenge facing the world today. Europe is committed to achieving a climate-neutral society by 2050, as stated in the European Green Deal.1 The transition towards a climate-neutral Europe requires fundamental changes in the way we generate and use energy. If batteries can be made simultaneously more sustainable, safe, ultrahigh performing, and affordable, they will be true enablers, “accelerating the shift towards sustainable and smart mobility; supplying clean, affordable and secure energy; and mobilizing industry for a clean and circular economy” - all of which are important elements of the UN Sustainable Development Goals.In other words, batteries are a key technology for battling carbon dioxide emissions from the transport, power, and industry sectors. However, to reach our sustainability goals, batteries must exhibit ultra-high performance beyond their capabilities today. Ultra-high performance includes energy and power performance approaching theoretical limits, outstanding lifetime and reliability, and enhanced safety and environmental sustainability. Furthermore, to be commercially successful, these batteries must support scalability that enables cost-effective large-scale production.BATTERY 2030+, is the large-scale, long-term European research initiative with the vision of inventing the sustainable batteries of the future, to enable Europe to reach the goals envisaged in the European Green Deal. BATTERY 2030+ is at the heart of a green and connected society.BATTERY 2030+ will contribute to create a vibrant battery research and development (R&D) community in Europe, focusing on long-term research that will continuously feed new knowledge and technologies throughout the value chain, resulting in new products and innovations. In addition, the initiative will attract talent from across Europe and contribute to ensure access to competences needed for ongoing societal transformation.The BATTERY 2030+ aims are:• to invent ultra-high performance batteries that are safe, affordable, and sustainable, witha long lifetime.• to provide new tools and breakthrough technologies to the European battery industrythroughout the value chain.• to enable long-term European leadership in both existing markets (e.g., transport andstationary storage) and future emerging sectors (e.g., robotics, aerospace, medical devices, and Internet of things)With this roadmap, BATTERY 2030+ advocates research directions based on a chemistry-neutral approach that will allow Europe to reach or even surpass its ambitious battery performance targets set in the European Strategic Energy Technology Plan (SET-Plan)3 and foster innovation throughout the battery value chain.
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- Forslund, Sofia K., et al.
(författare)
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Combinatorial, additive and dose-dependent drug–microbiome associations
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 600:7889, s. 500-505
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Tidskriftsartikel (refereegranskat)abstract
- During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery1–5. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the explanatory power of drugs for the variability in both host and gut microbiome features exceeds that of disease. We quantify inferred effects of single medications, their combinations as well as additive effects, and show that the latter shift the metabolome and microbiome towards a healthier state, exemplified in synergistic reduction in serum atherogenic lipoproteins by statins combined with aspirin, or enrichment of intestinal Roseburia by diuretic agents combined with beta-blockers. Several antibiotics exhibit a quantitative relationship between the number of courses prescribed and progression towards a microbiome state that is associated with the severity of cardiometabolic disease. We also report a relationship between cardiometabolic drug dosage, improvement in clinical markers and microbiome composition, supporting direct drug effects. Taken together, our computational framework and resulting resources enable the disentanglement of the effects of drugs and disease on host and microbiome features in multimedicated individuals. Furthermore, the robust signatures identified using our framework provide new hypotheses for drug–host–microbiome interactions in cardiometabolic disease.
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