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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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| 6. |
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| 7. |
- 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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| 8. |
- 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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| 9. |
- Cichocka, Magdalena Ola, 1986-, et al.
(författare)
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Aluminosilicate Zeolite EMM-28 Containing Supercavities Determined by Continuous Rotation Electron Diffraction
- 2022
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 61:29, s. 11103-11109
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Tidskriftsartikel (refereegranskat)abstract
- A new aluminosilicate zeolite, denoted EMM-28, has been successfully synthesized on a large scale using 1,1-(3,3-(1,3-phenylene)bis(propane-3,1-diyl))bis(1-methylpyrrolidinium) hydroxide as an organic structure directing agent (OSDA), which was scaled up to an ∼20 g scale with a yield of 77%. It crystallizes as thin plates (40–100 nm in thickness), and the corresponding powder X-ray diffraction (PXRD) pattern shows significant peak broadening which makes it insufficient for structure determination. Continuous rotation electron diffraction (cRED) data collected from 13 crystals were successfully used to solve and refine the structure of EMM-28. This illustrates that cRED data are capable of performing structure determination despite limited PXRD data quality. EMM-28 has a unique framework structure containing supercavities, >21 Å in size, connected by one-dimensional 10-ring channels. High-resolution transmission electron microscopy (HRTEM) confirmed the structure model. The structure of EMM-28 is related to several known zeolite structures with large cavities.
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| 11. |
- Willhammar, Tom, et al.
(författare)
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EMM-23 : A Stable High-Silica Multidimensional Zeolite with Extra-Large Trilobe-Shaped Channels.
- 2014
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 136:39, s. 13570-3
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Tidskriftsartikel (refereegranskat)abstract
- Stable, multidimensional, and extra-large pore zeolites are desirable by industry for catalysis and separation of bulky molecules. Here we report EMM-23, the first stable, three-dimensional extra-large pore aluminosilicate zeolite. The structure of EMM-23 was determined from submicron-sized crystals by combining electron crystallography, solid-state nuclear magnetic resonance (NMR), and powder X-ray diffraction. The framework contains highly unusual trilobe-shaped pores that are bound by 21-24 tetrahedral atoms. These extra-large pores are intersected perpendicularly by a two-dimensional 10-ring channel system. Unlike most ideal zeolite frameworks that have tetrahedral sites with four next-nearest tetrahedral neighbors (Q(4) species), this unusual zeolite possesses a high density of Q(2) and Q(3) silicon species. It is the first zeolite prepared directly with Q(2) species that are intrinsic to the framework. EMM-23 is stable after calcination at 540 °C. The formation of this highly interrupted structure is facilitated by the high density of extra framework positive charge introduced by the dicationic structure directing agent.
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| 12. |
- Zhang, L, et al.
(författare)
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An MPER antibody neutralizes HIV-1 using germline features shared among donors
- 2019
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 5389-
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Tidskriftsartikel (refereegranskat)abstract
- The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic CDRH3s, lack activity as inferred germline precursors, are often from the minor IgG3 subclass, and some are polyreactive, such as 4E10. Here we describe an MPER broadly neutralizing antibody from the major IgG1 subclass, PGZL1, which shares germline V/D-region genes with 4E10, has a shorter CDRH3, and is less polyreactive. A recombinant sublineage variant pan-neutralizes a 130-isolate panel at 1.4 μg/ml (IC50). Notably, a germline revertant with mature CDR3s neutralizes 12% of viruses and still binds MPER after DJ reversion. Crystal structures of lipid-bound PGZL1 variants and cryo-EM reconstruction of an Env-PGZL1 complex reveal how these antibodies recognize MPER and viral membrane. Discovery of common genetic and structural elements among MPER antibodies from different patients suggests that such antibodies could be elicited using carefully designed immunogens.
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