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| 2. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 4. |
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| 5. |
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| 7. |
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- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:2
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Tidskriftsartikel (refereegranskat)
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| 8. |
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| 9. |
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| 10. |
- Romagnoni, A, et al.
(författare)
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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
- 2019
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 10351-
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Tidskriftsartikel (refereegranskat)abstract
- Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.
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| 11. |
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| 12. |
- Craddock, Nick, et al.
(författare)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Tidskriftsartikel (refereegranskat)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 13. |
- Lexén, Jenny, et al.
(författare)
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ProScale - A life cycle oriented method to assess toxicological potentials of product systems (2017) : Guidance Document version 1.5
- 2021
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The ProScale method was developed in an industrial consortium with expertise both from the Life Cycle Assessment and Risk Assessment areas. ProScale is intended as an easy-to-use and widely applicable method that can cover both human and eco-toxicity aspects. Currently available in this report is a module for assessing direct exposure related Human Toxicity Potentials in a life cycle perspective compatible with Life Cycle Assessments including Product Environmental Footprint (PEF).The ProScale methodology is based on chemical hazard described by substance classification (H-phrases) in the GHS/CLP classification system, occupational exposure limits (OEL) or Derived No Effect Levels (DNEL), and an exposure dose based on ECETOC Tiered Risk Assessment (TRA). ProScale scores are derived separately for inhalative, oral and dermal exposure routes. The document provides scientific background as well as practical guidance to the practitioner to carry out a ProScale assessment.
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| 14. |
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| 15. |
- Learmonth, T., et al.
(författare)
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Observation of multiple Zhang-Rice excitations in a correlated solid : Resonant inelastic X-ray scattering study of Li2CuO2
- 2007
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Ingår i: Europhysics letters. - : IOP Publishing. - 0295-5075 .- 1286-4854. ; 79:4, s. 47012-
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Tidskriftsartikel (refereegranskat)abstract
- Multiple Zhang-Rice type spectral features have been observed in resonant inelastic X-ray scattering (RIXS) from the quasi -one-dimensional cuprate charge transfer insulator Li2CuO2. The first feature appears at constant emission energy, and is associated with a Zhang-Rice singlet final state. The second is an interplaquette charge transfer excitation that results in a novel triplet Zhang-Rice -type final state. It is accompanied by the presence of a O 2p nonbonding to upper Hubbard band excitation at an energy close to that of a calculated triplet charge transfer Zhang-Rice -type excitation. The site selectivity and polarization rules associated with RIXS allows these two excitations to be distinguished.
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| 16. |
- Søgaard Jørgensen, Peter, et al.
(författare)
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Antibiotic and pesticide susceptibility and the Anthropocene operating space
- 2018
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Ingår i: Nature Sustainability. - : Springer Science and Business Media LLC. - 2398-9629. ; 1:11, s. 632-641
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Forskningsöversikt (refereegranskat)abstract
- Rising levels of antimicrobial and pesticide resistance increasingly undermine human health and systems for biomass production, and emphasize the sustainability challenge of preserving organisms susceptible to these biocides. In this Review, we introduce key concepts and examine dynamics of biocide susceptibility that must be governed to address this challenge. We focus on the impact of biocides on the capacity of susceptible organisms to prevent spread of resistance, and we then review how biocide use affects a broader suite of ecosystem services. Finally, we introduce and assess the state of what we term the Anthropocene operating space of biocide susceptibility, a framework for assessing the potential of antibiotic and pesticide resistance to undermine key functions of human society. Based on current trends in antibiotic, insecticide and herbicide resistance, we conclude that the states of all six assessed variables are beyond safe zones, with three variables surpassed regionally or globally.
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