| 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. |
- Amendola, L., et al.
(författare)
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Cosmology and fundamental physics with the Euclid satellite
- 2018
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Ingår i: Living Reviews in Relativity. - : Springer. - 1433-8351 .- 2367-3613. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Euclid is a European Space Agency medium-class mission selected for launch in 2020 within the cosmic vision 2015–2025 program. The main goal of Euclid is to understand the origin of the accelerated expansion of the universe. Euclid will explore the expansion history of the universe and the evolution of cosmic structures by measuring shapes and red-shifts of galaxies as well as the distribution of clusters of galaxies over a large fraction of the sky. Although the main driver for Euclid is the nature of dark energy, Euclid science covers a vast range of topics, from cosmology to galaxy evolution to planetary research. In this review we focus on cosmology and fundamental physics, with a strong emphasis on science beyond the current standard models. We discuss five broad topics: dark energy and modified gravity, dark matter, initial conditions, basic assumptions and questions of methodology in the data analysis. This review has been planned and carried out within Euclid’s Theory Working Group and is meant to provide a guide to the scientific themes that will underlie the activity of the group during the preparation of the Euclid mission.
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| 4. |
- Barnett, R., et al.
(författare)
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Euclid preparation V. Predicted yield of redshift 7 < z < 9 quasars from the wide survey
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 631
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Tidskriftsartikel (refereegranskat)abstract
- We provide predictions of the yield of 7 < z < 9 quasars from the Euclid wide survey, updating the calculation presented in the Euclid Red Book in several ways. We account for revisions to the Euclid near-infrared filter wavelengths; we adopt steeper rates of decline of the quasar luminosity function (QLF; Phi) with redshift, Phi proportional to 10(k(z-6)), k = 0:72, and a further steeper rate of decline, k = 0:92; we use better models of the contaminating populations (MLT dwarfs and compact early-type galaxies); and we make use of an improved Bayesian selection method, compared to the colour cuts used for the Red Book calculation, allowing the identification of fainter quasars, down to J(AB) similar to 23. Quasars at z > 8 may be selected from Euclid OYJH photometry alone, but selection over the redshift interval 7 < z < 8 is greatly improved by the addition of z-band data from, e.g., Pan-STARRS and LSST. We calculate predicted quasar yields for the assumed values of the rate of decline of the QLF beyond z = 6. If the decline of the QLF accelerates beyond z = 6, with k = 0.92, Euclid should nevertheless find over 100 quasars with 7.0 < z < 7.5, and similar to 25 quasars beyond the current record of z = 7.5, including similar to 8 beyond z = 8.0. The first Euclid quasars at z > 7.5 should be found in the DR1 data release, expected in 2024. It will be possible to determine the bright-end slope of the QLF, 7 < z < 8, M-1450 < 25, using 8m class telescopes to confirm candidates, but follow-up with JWST or E-ELT will be required to measure the faint-end slope. Contamination of the candidate lists is predicted to be modest even at J(AB) similar to 23. The precision with which k can be determined over 7 < z < 8 depends on the value of k, but assuming k = 0.72 it can be measured to a 1 sigma uncertainty of 0.07.
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| 5. |
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| 6. |
- Volpati, D., et al.
(författare)
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Exploring the alignment of carbon nanotubes dispersed in a liquid crystal matrix using coplanar electrodes
- 2015
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 117:12
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Tidskriftsartikel (refereegranskat)abstract
- We report on the use of a liquid crystalline host medium to align single-walled carbon nanotubes in an electric field using an in-plane electrode configuration. Electron microscopy reveals that the nanotubes orient in the field with a resulting increase in the DC conductivity in the field direction. Current versus voltage measurements on the composite show a nonlinear behavior, which was modelled by using single-carrier space-charge injection. The possibility of manipulating the conductivity pathways in the same sample by applying the electrical field in different (in-plane) directions has also been demonstrated. Raman spectroscopy indicates that there is an interaction between the nanotubes and the host liquid crystal molecules that goes beyond that of simple physical mixing.
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| 7. |
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| 8. |
- Massey, D., et al.
(författare)
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What factors influence ward nurses' recognition of and response to patient deterioration? An integrative review of the literature
- 2017
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Ingår i: Nursing Open. - : Wiley. - 2054-1058. ; 4:1, s. 6-23
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Tidskriftsartikel (refereegranskat)abstract
- AimIn this integrative review, we aimed to: first, identify and summarize published studies relating to ward nurses' recognition of and response to patient deterioration; second, to critically evaluate studies that described or appraised the practice of ward nurses in recognizing and responding to patient deterioration; and third, identify gaps in the literature for further research. MethodsThe Cumulative Index to Nursing and Allied Health Literature (CINAHL) Ovid Medline, Informit and Google Scholar databases were accessed for the years 1990-2014. Data were extracted and summarized in tables and then appraised using the Mixed Method Appraisal Tool. Data were grouped into two domains; recognizing and responding to deterioration and then thematic analysis was used to identify the emerging themes. ResultsSeventeen studies were reviewed and appraised. Recognizing patient deterioration was encapsulated in four themes: (1) assessing the patient; (2) knowing the patient; (3) education and (4) environmental factors. Responding to patient deterioration was encapsulated in three themes; (1) non-technical skills; (2) access to support and (3) negative emotional responses. ConclusionIssues involved in timely recognition of and response to clinical deterioration remain complex, yet patient safety relies on nurses' timely assessments and actions.
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| 9. |
- Massey, M. K., et al.
(författare)
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Computing with carbon nanotubes : Optimization of threshold logic gates using disordered nanotube/polymer composites
- 2015
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 117:13
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Tidskriftsartikel (refereegranskat)abstract
- This paper explores the use of single-walled carbon nanotube (SWCNT)/poly(butyl methacrylate) composites as a material for use in unconventional computing. The mechanical and electrical properties of the materials are investigated. The resulting data reveal a correlation between the SWCNT concentration/viscosity/conductivity and the computational capability of the composite. The viscosity increases significantly with the addition of SWCNTs to the polymer, mechanically reinforcing the host material and changing the electrical properties of the composite. The electrical conduction is found to depend strongly on the nanotube concentration; Poole-Frenkel conduction appears to dominate the conductivity at very low concentrations (0.11% by weight). The viscosity and conductivity both show a threshold point around 1% SWCNT concentration; this value is shown to be related to the computational performance of the material. A simple optimization of threshold logic gates shows that satisfactory computation is only achieved above a SWCNT concentration of 1%. In addition, there is some evidence that further above this threshold the computational efficiency begins to decrease. (C) 2015 AIP Publishing LLC.
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| 10. |
- Massey, M.K., et al.
(författare)
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Evolution of Electronic Circuits using Carbon Nanotube Composites
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6:32197
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Tidskriftsartikel (refereegranskat)abstract
- volution-in-materio concerns the computer controlled manipulation of material systems using external stimuli to train or evolve the material to perform a useful function. In this paper we demonstrate the evolution of a disordered composite material, using voltages as the external stimuli, into a form where a simple computational problem can be solved. The material consists of single-walled carbon nanotubes suspended in liquid crystal; the nanotubes act as a conductive network, with the liquid crystal providing a host medium to allow the conductive network to reorganise when voltages are applied. We show that the application of electric fields under computer control results in a significant change in the material morphology, favouring the solution to a classification task.
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