| 1. |
- Benson, Mikael, 1954, et al.
(författare)
-
A network-based analysis of allergen-challenged CD4+T cells from patients with allergic rhinitis
- 2006
-
Ingår i: Genes and Immunity. - : Springer Science and Business Media LLC. - 1466-4879 .- 1476-5470. ; 7:6, s. 514-521
-
Tidskriftsartikel (refereegranskat)abstract
- We performed a network-based analysis of DNA microarray data from allergen-challenged CD4 + T cells from patients with seasonal allergic rhinitis. Differentially expressed genes were organized into a functionally annotated network using the Ingenuity Knowledge Database, which is based on manual review of more than 200000 publications. The main function of this network is the regulation of lymphocyte apoptosis, a role associated with several genes of the tuber necrosis factor superfamily. The expression of TNFRSF4, one of the genes in this family, was found to be 48 times higher in allergen-challenged cells than in diluent-challenged cells. TNFRSF4 is known to inhibit apoptosis and to enhance Th2 proliferation. Examination of a different material of allergen-stimulated peripheral blood mononuclear cells showed a higher number of interleukin-4 + type 2 CD4 + T (Th2) cells in patients than in controls (P
|
|
| 2. |
- Franck, Niclas, et al.
(författare)
-
Identification of adipocyte genes regulated by caloric intake
- 2011
-
Ingår i: Journal of Clinical Endocrinology and Metabolism. - : Endocrine society. - 0021-972X .- 1945-7197. ; 96:2, s. E413-E418
-
Tidskriftsartikel (refereegranskat)abstract
- CONTEXT: Changes in energy intake have marked and rapid effects on metabolic functions and some of the effects may be due to changes in adipose tissue gene expression that precede alterations in body weight. OBJECTIVE: To identify genes in adipose tissue regulated by changes in caloric intake independent of changes in body weight. RESEARCH DESIGN AND METHODS: Obese subjects were given a very-low calorie diet (VLCD; 450 kcal/day) for 16 weeks. After the diet, ordinary food was gradually reintroduced during 2 weeks while there were minimal changes in body weight. Adipose tissue gene expression was measured by microarray analysis. First, genes regulated during caloric restriction and in the opposite direction during the weight stable re-feeding phase were identified. To verify opposite regulation to that observed during caloric restriction, identified genes were further analyzed using adipocyte expression profiles from healthy subjects before and after overfeeding. Results were confirmed using real time PCR or immunoassay. RESULTS: Using a significance level of p<0.05 for all comparisons, 52 genes were downregulated and 50 were up-regulated by caloric restriction and regulated in the opposite direction by re-feeding and overfeeding. Among these were genes that affect lipogenesis (ACLY, ACACA, FASN, SCD), protein synthesis (4EBP1, 4EBP2), beta-oxidation (CPT1B), liberation of fatty acids (CIDEA) and glyceroneogenesis (PCK2). Interestingly, several of these are under control of the master regulator mTOR. CONCLUSIONS: The observed transcriptional changes indicate that mTOR plays a central role in the control of diet-regulated adipocyte genes involved in lipogenesis and protein synthesis.
|
|
| 3. |
- Guillot, Gilles, 1972, et al.
(författare)
-
Correcting for ascertainment bias in the inference of population structure
- 2009
-
Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 25:4, s. 552-554
-
Tidskriftsartikel (refereegranskat)abstract
- Background: The ascertainment process of molecular markers amounts to disregard loci carrying alleles with low frequencies. This can result in strong biases in inferences under population genetics models if not properly taken into account by the inference algorithm. Attempting to model this censoring process in view of making inference of population structure (i.e. identifying clusters of individuals) brings up challenging numerical difficulties. Method: These difficulties are related to the presence of intractable normalizing constants in Metropolis-Hastings acceptance ratios. This can be solved via an Markov chain Monte Carlo (MCMC) algorithm known as single variable exchange algorithm (SVEA). Result: We show how this general solution can be implemented for a class of clustering models of broad interest in population genetics that includes the models underlying the computer programs STRUCTURE, GENELAND and GESTE. We also implement the method proposed for a simple example and show that it allows us to reduce the bias substantially.
|
|
| 4. |
|
|
| 5. |
- Guillot, Gilles, et al.
(författare)
-
Discrimination and scoring using small sets of genes for two-sample microarray data
- 2007
-
Ingår i: Mathematical Biosciences. - : Elsevier. - 0025-5564 .- 1879-3134. ; 205:2, s. 195-203
-
Tidskriftsartikel (refereegranskat)abstract
- Comparison of gene expression for two groups of individuals form an important subclass of microarray experiments. We study multivariate procedures, in particular use of Hotelling's T2 for discrimination between the groups with a special emphasis on methods based on few genes only. We apply the methods to data from an experiment with a group of atopic dermatitis patients compared with a control group. We also compare our methodology to other recently proposed methods on publicly available datasets. It is found that (i) use of several genes gives a much improved discrimination of the groups as compared to one gene only, (ii) the genes that play the most important role in the multivariate analysis are not necessarily those that rank first in univariate comparisons of the groups, (iii) Linear Discriminant Analysis carried out with sets of 2-5 genes selected according to their Hotelling T2 give results comparable to state-of-the-art methods using many more genes, a feature of our method which might be crucial in clinical applications. Finding groups of genes that together give optimal multivariate discrimination (given the size of the group) can identify crucial pathways and networks of genes responsible for a disease. The computer code that we developed to make computations is available as an R package.
|
|
| 6. |
- Guillot, Gilles, 1972
(författare)
-
On the inference of spatial structure from population genetics data
- 2009
-
Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 25:14, s. 1796-1801
-
Tidskriftsartikel (refereegranskat)abstract
- Motivation: In a series of recent papers, Tess, a computer program based on the concept of hidden Markov random field, has been proposed to infer the number and locations of panmictic population units from the genotypes and spatial locations of these individuals. The method seems to be of broad appeal as it is conceptually much simpler than other competing methods and it has been reported by its authors to be fast and accurate. However, this methodology is not grounded in a formal statistical inference method and seems to rely to a large extent on arbitrary choices regarding the parameters used. The present article is an investigation of the accuracy of this method and an attempt to assess whether recent results reported on the basis of this method are genuine features of the genetic process or artefacts of the method. Method: I analyse simulated data consisting of populations at Hardy-Weinberg and linkage equilibrium and also data simulated under a scenario of isolation-by-distance at mutation-migration-drift equilibrium. Arabidopsis thaliana data previously analysed with this method are also reconsidered. Results: Using the Tess program under the no-admixture model to analyse data consisting of several genuine HWLE populations with individuals of pure ancestries leads to highly inaccurate results; Using the Tess program under the admixture model to analyse data consisting of a continuous isolation-by-distance population leads to the inference of spurious HWLE populations whose number and features depend on the parameters used. Results previously reported about the A. thaliana using Tess seem to a large extent to be artefacts of the statistical methodology used. The findings go beyond population clustering models and can be an help to design more efficient algorithms based on graphs.
|
|
| 7. |
- Guillot, Gilles, 1972, et al.
(författare)
-
Spatial prediction of weed intensities from exact count data and image-based estimates
- 2009
-
Ingår i: Journal of the Royal Statistical Society Series C-Applied Statistics. - : Oxford University Press (OUP). - 0035-9254 .- 1467-9876. ; 58, s. 525-542
-
Tidskriftsartikel (refereegranskat)abstract
- Collecting weed exact counts in an agricultural field is easy but extremely time consuming. Image analysis algorithms for object extraction applied to pictures of agricultural fields may be used to estimate the weed content with a high resolution (about 1 m(2)), and pictures that are acquired at a large number of sites can be used to obtain maps of weed content over a whole field at a reasonably low cost. However, these image-based estimates are not perfect and acquiring exact weed counts also is highly useful both for assessing the accuracy of the image-based algorithms and for improving the estimates by use of the combined data. We propose and compare various models for image index and exact weed count and we use them to assess how such data should be combined to obtain reliable maps. The method is applied to a real data set from a 30-ha field. We show that using image estimates in addition to exact counts allows us to improve the accuracy of maps significantly. We also show that the relative performances of the methods depend on the size of the data set and on the specific methodology (full Bayes versus plug-in) that is implemented.
|
|
| 8. |
- Pétri, Jérôme A., et al.
(författare)
-
Constraining the magnetic field geometry of the millisecond pulsar PSRJ0030+0451 from joint radio, thermal X-ray, and γ-ray emission
- 2023
-
Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 680
-
Tidskriftsartikel (refereegranskat)abstract
- Context. With the advent of multi-wavelength electromagnetic observations of neutron stars - spanning many decades in photon energies - from radio wavelengths up to X-rays and γ-rays, it has become possible to significantly constrain the geometry and the location of the associated emission regions. Aims. In this work, we use results from the modelling of thermal X-ray observations of PSR J0030+0451 from the Neutron Star Interior Composition Explorer (NICER) mission and phase-aligned radio and γ-ray pulse profiles to constrain the geometry of an off-centred dipole that is able to reproduce the light curves in these respective bands simultaneously. Methods. To this aim, we deduced a configuration with a simple dipole off-centred from the location of the centre of the thermal X-ray hot spots. We show that the geometry is compatible with independent constraints from radio and -ray pulsations only, leading to a fixed magnetic obliquity of α ≈ 75° and a line-of-sight inclination angle of ζ ≈ 54°. Results. We demonstrate that an off-centred dipole cannot be rejected by accounting for the thermal X-ray pulse profiles. Moreover, the crescent shape of one spot is interpreted as the consequence of a small-scale surface dipole on top of the large-scale off-centred dipole.
|
|
| 9. |
- Thebault, Martin, et al.
(författare)
-
A Comparative Study Of Simulation Tools To Model The Solar Irradiation On Building Façades
- 2021
-
Ingår i: Proceedings - ISES Solar World Congress 2021. - Freiburg, Germany : International Solar Energy Society. - 9783982040875 ; , s. 1058-1069
-
Konferensbidrag (refereegranskat)abstract
- This paper presents a comparison among eight tools commonly used to evaluate the solar irradiation in urban environments. The focus is on the vertical surfaces (i.e., façades). The analysed tools have a large range of applications, from detailed microclimate studies to large-scale irradiation modelling. The benchmark tests consist of simulations using two conceptual urban designs. Two representative winter and summer days are defined. The results, obtained for the modelling of the shortwave irradiance received on the façades, are discussed together with the observed differences. This work provides an overview of some of the available tools, their features, similarities, and differences as well as a comparison of the modelled solar irradiation. This work is conducted in the framework of IEA SHC Task 63 "Solar Neighborhood Planning" where experts from five countries, in six universities, two companies and one research institute have been engaged.
|
|
