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- 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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| 2. |
- 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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| 5. |
- Kelly, Adrian B., et al.
(författare)
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Polydrug use in Australian 12-14 year olds from 2006 to 2017 : an examination of drug use profiles, emotional control problems, and family relationship characteristics
- 2023
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Ingår i: Australian journal of psychology. - : Taylor & Francis. - 0004-9530 .- 1742-9536. ; 75:1
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Tidskriftsartikel (refereegranskat)abstract
- Objective: This study examined the nature and prevalence of polydrug use in 12–14 year old Australians.Method: Three Australian school surveys (2006, n=4091; 2009, n=5635; 2017, n=1539; age 12–14 years) spanning 11 years were used. Substances included alcohol, tobacco, cannabis, inhalant, and other illicit substances. Risk factors included depressed mood, low emotional control, poor family management and conflict, and academic performance. Latent class analysis was used to discern classes. Regression analyses were used to test the association of risk factors with classes.Results: Consistent across surveys, there was a class of adolescents who engaged in wide-ranging polydrug use, with prevalences ranging from 0.44% (2006) to 1.78% (2017). Emotional control problems, low academic performance, and poor family management were elevated in the polydrug class.Conclusion: A small proportion of 12–14-year-old adolescents engage in polydrug use. Interventions focusing on family risks and emotional control problems may be beneficial.
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| 6. |
- Mageroy, Melissa H., et al.
(författare)
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Molecular underpinnings of methyl jasmonate-induced resistance in Norway spruce
- 2020
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Ingår i: Plant, Cell and Environment. - : Blackwell Publishing. - 0140-7791 .- 1365-3040. ; 43:8, s. 1827-1843
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Tidskriftsartikel (refereegranskat)abstract
- In response to various stimuli, plants acquire resistance against pests and/or pathogens. Such acquired or induced resistance allows plants to rapidly adapt to their environment. Spraying the bark of mature Norway spruce (Picea abies) trees with the phytohormone methyl jasmonate (MeJA) enhances resistance to tree-killing bark beetles and their associated phytopathogenic fungi. Analysis of spruce chemical defenses and beetle colonization success suggests that MeJA treatment both directly induces immune responses and primes inducible defenses for a faster and stronger response to subsequent beetle attack. We used metabolite and transcriptome profiling to explore the mechanisms underlying MeJA-induced resistance in Norway spruce. We demonstrated that MeJA treatment caused substantial changes in the bark transcriptional response to a triggering stress (mechanical wounding). Profiling of mRNA expression showed a suite of spruce inducible defenses are primed following MeJA treatment. Although monoterpenes and diterpene resin acids increased more rapidly after wounding in MeJA-treated than control bark, expression of their biosynthesis genes did not. We suggest that priming of inducible defenses is part of a complex mixture of defense responses that underpins the increased resistance against bark beetle colonization observed in Norway spruce. This study provides the most detailed insights yet into the mechanisms underlying induced resistance in a long-lived gymnosperm.
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| 7. |
- Manchaiah, Vinaya, et al.
(författare)
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Social Representation of "Loud Music" in Young Adults : A Cross-Cultural Study
- 2017
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Ingår i: Journal of american academy of audiology. - Reston, VA, United States : American Academy of Audiology. - 1050-0545 .- 2157-3107. ; 28:6, s. 522-533
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Tidskriftsartikel (refereegranskat)abstract
- Background: Exposure to recreational noise, particularly music exposure, is considered one of the biggest public health hazards of our time. Some important influencing factors such as socioeconomic status, educational background, and cross-cultural perspectives have previously been found to be associated with attitudes toward loud music and the use of hearing protection. Although culture seems to play an important role, there is relatively little known about how it influences perceptions regarding loud music exposure in young adults.Purpose: The present study was aimed to explore cross-cultural perceptions of and reactions to loud music in young adults (18-25 yr) using the theory of social representations.Research Design: The study used a cross-sectional survey design.Study Sample: The study sample included young adults (n = 534) from five different countries (India, Iran, Portugal, the United States, and the United Kingdom) who were recruited using convenience sampling.Data Collection and Analysis: Data were collected using a questionnaire. Data were analyzed using a content analysis, co-occurrence analysis, and also x(2) analysis.Results: Fairly equal numbers of positive and negative connotations (similar to 40%) were noted in all countries. However, the x(2) analysis showed significant differences between the countries (most positive connotations were found in India and Iran, whereas the most negative connotations were found in the United Kingdom and Portugal) regarding the informants' perception of loud music. The co-occurrence analysis results generally indicate that the category "negative emotions and actions" occurred most frequently, immediately followed by the category "positive emotions and actions." The other most frequently occurring categories included "acoustics," "physical aliment," "location," and "ear and hearing problems." These six categories formed the central nodes of the social representation of loud music exposure in the global index. Although some similarities and differences were noted among the social representations toward loud music among countries, it is noteworthy that more similarities than differences were noted among countries.Conclusions: The study results suggest that "loud music" is perceived to have both positive and negative aspects within society and culture. We suggest that the health promotion strategies should focus on changing societal norms and regulations to be more effective in decreasing the noise-and/or music induced auditory symptoms among young adults.
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| 8. |
- Manchaiah, Vinaya, et al.
(författare)
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Social representation of "music" in young adults : A cross-cultural study
- 2017
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Ingår i: International Journal of Audiology. - Oxfordshire, United Kingdom : Taylor & Francis. - 1499-2027 .- 1708-8186. ; 56:1, s. 24-32
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Tidskriftsartikel (refereegranskat)abstract
- Objective: The present study was aimed to explore perceptions of and reactions to music in young adults (18-25 years) using the theory of social representations (TSR).Design: The study used a cross-sectional survey design and included participants from India, Iran, Portugal, United States, and United Kingdom. Data were analyzed using various qualitative and quantitative methods.Study sample: The study sample included 534 young adults.Results: The Chi-square analysis showed significant differences between the countries regarding the informants’ perception of music. The most positive connotations about music were found in the responses obtained from Iranian participants (82.2%), followed by Portuguese participants (80.6%), while the most negative connotations about music were found in the responses obtained from Indian participants (18.2%), followed by Iranian participants (7.3%). The participants’ responses fell into 19 main categories based on their meaning; however, not all categories were found in all five countries. The co-occurrence analysis results generally indicate that the category “positive emotions or actions” was the most frequent category occurring in all five countries.Conclusions: The results indicate that music is generally considered to bring positive emotions for people within these societies, although a small percentage of responses indicate some negative consequences of music.
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