| 1. |
- 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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| 2. |
- Momozawa, Y, et al.
(författare)
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IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes
- 2018
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9:1, s. 2427-
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Tidskriftsartikel (refereegranskat)abstract
- GWAS have identified >200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis-eQTL. We show that these are determined by ∼9720 regulatory modules, of which ∼3000 operate in multiple tissues and ∼970 on multiple genes. We identify regulatory modules that drive the disease association for 63 of the 200 risk loci, and show that these are enriched in multigenic modules. Based on these analyses, we resequence 45 of the corresponding 100 candidate genes in 6600 Crohn disease (CD) cases and 5500 controls, and show with burden tests that they include likely causative genes. Our analyses indicate that ≥10-fold larger sample sizes will be required to demonstrate the causality of individual genes using this approach.
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| 3. |
- Hegde, Gurumurthy, 1979, et al.
(författare)
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Photo Induced Effects in Nematic Liquid Crystals
- 2005
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Ingår i: Phase Transitions. - 1029-0338. ; 78:6
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Forskningsöversikt (refereegranskat)abstract
- Temperature, concentration of the solvent and pressure are the parameters that are well known to bring about phase transitions in liquid-crystalline systems. In recent years a new parameter has been added to this list: light. The principle behind these photoinduced transitions is the light-driven shape transformation of certain photoactive materials like, e.g., azobenzene. In this article, we present results of various aspects of our recent investigations on such photoinduced transitions in the nematic phase and highlight the feature that light is a new tool to study phase transitions and the associated critical phenomena
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| 4. |
- Krishnaprasad, R, et al.
(författare)
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Mechanical and thermal properties of bamboo microfibril reinforced polyhydroxybutyrate biocomposites
- 2009
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Ingår i: Journal of Polymers and the Environment. - : Springer New York LLC. - 1566-2543 .- 1572-8919 .- 1572-8900. ; 17:2, s. 109-114
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Tidskriftsartikel (refereegranskat)abstract
- In the present investigation, microfibrils were extracted from raw bamboo and characterized using scanning electron microscope. Composites based on polyhydroxybutyrate (PHB) and bamboo microfibril were prepared with various microfibril loading. The mechanical and thermal properties of the resulting composites were measured. Tensile strength and impact strength of the composites were found to be increasing with increase in the loading of bamboo microfibrils, reached an optimum and thereafter decreased with further increase in microfibril loading. Percentage crystallinity was found to be increasing with increase in fibril loading. Thermal stability of the composite was higher than that of pure PHB. The composite could be developed further for various structural applications.
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