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| 2. |
- Alam, Moudud, 1976-, et al.
(författare)
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Fitting conditional and simultaneous autoregressive spatial models in hglm
- 2015
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Ingår i: The R Journal. - 2073-4859. ; 7:2, s. 5-18
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Tidskriftsartikel (refereegranskat)abstract
- We present a new version (> 2.0) of the hglm package for fitting hierarchical generalized linear models (HGLMs) with spatially correlated random effects. CAR() and SAR() families for conditional and simultaneous autoregressive random effects were implemented. Eigen decomposition of the matrix describing the spatial structure (e.g., the neighborhood matrix) was used to transform the CAR/SAR random effects into an independent, but eteroscedastic, Gaussian random effect. A linear predictor is fitted for the random effect variance to estimate the parameters in the CAR and SAR models. This gives a computationally efficient algorithm for moderately sized problems.
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| 3. |
- Alvarez-Castro, Jose, et al.
(författare)
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Estimation and interpretation of genetic effects with epistasis using the NOIA model.
- 2012
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Ingår i: Methods in Molecular Biology. - Totowa, NJ : Humana Press. - 1064-3745 .- 1940-6029. ; 871, s. 191-204
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Tidskriftsartikel (refereegranskat)abstract
- We introduce this communication with a brief outline of the historical landmarks in genetic modeling, especially concerning epistasis. Then, we present methods for the use of genetic modeling in QTL analyses. In particular, we summarize the essential expressions of the natural and orthogonal interactions (NOIA) model of genetic effects. Our motivation for reviewing that theory here is twofold. First, this review presents a digest of the expressions for the application of the NOIA model, which are often mixed with intermediate and additional formulae in the original articles. Second, we make the required theory handy for the reader to relate the genetic concepts to the particular mathematical expressions underlying them. We illustrate those relations by providing graphical interpretations and a diagram summarizing the key features for applying genetic modeling with epistasis in comprehensive QTL analyses. Finally, we briefly review some examples of the application of NOIA to real data and the way it improves the interpretability of the results.
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| 5. |
- Anglart, D, et al.
(författare)
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Detecting and predicting changes in milk homogeneity using data from automatic milking systems.
- 2021
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Ingår i: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 104:10, s. 11009-11017
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Tidskriftsartikel (refereegranskat)abstract
- To ensure milk quality and detect cows with signs of mastitis, visual inspection of milk by prestripping quarters before milking is recommended in many countries. An objective method to find milk changed in homogeneity (i.e., with clots) is to use commercially available inline filters to inspect the milk. Due to the required manual labor, this method is not applicable in automatic milking systems (AMS). We investigated the possibility of detecting and predicting changes in milk homogeneity using data generated by AMS. In total, 21,335 quarter-level milk inspections were performed on 5,424 milkings of 624 unique cows on 4 farms by applying visual inspection of inline filters that assembled clots from the separate quarters during milking. Images of the filters with clots were scored for density, resulting in 892 observations with signs of clots for analysis (77% traces or mild cases, 15% moderate cases, and 8% heavy cases). The quarter density scores were combined into 1 score indicating the presence of clots during a single cow milking and into 2 scores summarizing the density scores in cow milkings during a 30-h sampling period. Data generated from the AMS, such as milk yield, milk flow, conductivity, and online somatic cell counts, were used as input to 4 multilayer perceptron models to detect or predict single milkings with clots and to detect milking periods with clots. All models resulted in high specificity (98-100%), showing that the models correctly classified cow milkings or cow milking periods with no clots observed. The ability to successfully classify cow milkings or cow periods with observed clots had a low sensitivity. The highest sensitivity (26%) was obtained by the model that detected clots in a single milking. The prevalence of clots in the data was low (2.4%), which was reflected in the results. The positive predictive value depends on the prevalence and was relatively high, with the highest positive predictive value (72%) reached in the model that detected clots during the 30-h sampling periods. The misclassification rate for cow milkings that included higher-density scores was lower, indicating that the models that detected or predicted clots in a single milking could better distinguish the heavier cases of clots. Using data from AMS to detect and predict changes in milk homogeneity seems to be possible, although the prediction performance for the definitions of clots used in this study was poor.
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| 6. |
- Berglund‐snodgrass, Lina, et al.
(författare)
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A Healthy City for All? Social Services’ Roles in Collaborative Urban Development
- 2022
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Ingår i: Urban Planning. - : Cogitatio Press. - 2183-7635. ; 7:4, s. 113-123
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Tidskriftsartikel (refereegranskat)abstract
- There is broad consensus among policymakers about the urgency of developing healthy, inclusive, and socially sustainable cities. In the Swedish context, social services are considered to have knowledge that needs to be integrated into the broader urban development processes in order to accomplish such ends. This article aims to better understand the ways in which social service officials collaborate in urban development processes for developing the social dimensions of healthy cities. We draw from neo‐institutional theories, which set out actors (e.g., social service officials) as acting according to a logic of appropriateness, which means that actors do what they see as appropriate for themselves in a specific type of situation. Based on semi‐structured interviews with social services officials in 10 Swedish municipalities on their experiences of collaboration in the development of housing and living environments for people with psychiatric disabilities, we identified that they act based on (a) a pragmatic rule of conduct through the role of the problem solver, (b) a bureaucratic rule of conduct through the role of the knowledge provider, and (c) activist rule of conduct through the role of the advo-cator. In these roles, they have little authority in the development processes, and are unable to set the agenda for the social dimensions of healthy cities but act as the moral consciousness by looking out for everyone’s right to equal living conditions in urban development. © 2022 by the author(s); licensee Cogitatio (Lisbon, Portugal).
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| 7. |
- Besnier, Francois, et al.
(författare)
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Fine mapping and replication of QTL in outbred chicken advanced intercross lines
- 2011
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Ingår i: Genetics Selection Evolution. - Paris : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 43, s. 3-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature.METHODS: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight.RESULTS: Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL.CONCLUSIONS: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.
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| 8. |
- Bjorvang, Richelle D., et al.
(författare)
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Follicular fluid and blood levels of persistent organic pollutants and reproductive outcomes among women undergoing assisted reproductive technologies
- 2022
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Ingår i: Environmental Research. - : Elsevier. - 0013-9351 .- 1096-0953. ; 208
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Tidskriftsartikel (refereegranskat)abstract
- Persistent organic pollutants (POPs) are industrial chemicals resistant to degradation and have been shown to have adverse effects on reproductive health in wildlife and humans. Although regulations have reduced their levels, they are still ubiquitously present and pose a global concern. Here, we studied a cohort of 185 women aged 21-43 years with a median of 2 years of infertility who were seeking assisted reproductive technology (ART) treatment at the Carl von Linne Clinic in Uppsala, Sweden. We analyzed the levels of 9 organochlorine pesticides (OCPs), 10 polychlorinated biphenyls (PCBs), 3 polybrominated diphenyl ethers (PBDEs), and 8 perfluoroalkyl substances (PFASs) in the blood and follicular fluid (FF) samples collected during ovum pick-up. Impact of age on chemical transfer from blood to FF was analyzed. Associations of chemicals, both individually and as a mixture, to 10 ART endpoints were investigated using linear, logistic, and weighted quantile sum regression, adjusted for age, body mass index, parity, fatty fish intake and cause of infertility. Out of the 30 chemicals, 20 were detected in more than half of the blood samples and 15 in FF. Chemical transfer from blood to FF increased with age. Chemical groups in blood crossed the blood-follicle barrier at different rates: OCPs > PCBs > PFASs. Hexachlorobenzene, an OCP, was associated with lower anti-Miillerian hormone, clinical pregnancy, and live birth. PCBs and PFASs were associated with higher antral follicle count and ovarian response as measured by ovarian sensitivity index, but also with lower embryo quality. As a mixture, similar findings were seen for the sum of PCBs and PFASs. Our results suggest that age plays a role in the chemical transfer from blood to FF and that exposure to POPs significantly associates with ART outcomes. We strongly encourage further studies to elucidate the underlying mechanisms of reproductive effects of POPs in humans.
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| 9. |
- Cedervall, Ylva, et al.
(författare)
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Timed Up-and-Go Dual-Task Testing in the Assessment of Cognitive Function : A Mixed Methods Observational Study for Development of the UDDGait Protocol
- 2020
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Ingår i: International Journal of Environmental Research and Public Health. - : MDPI. - 1661-7827 .- 1660-4601. ; 17:5
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Tidskriftsartikel (refereegranskat)abstract
- New methods to screen for and identify early-stage dementia disorders are highly sought after. The purpose of this pilot study is to develop a study protocol for a dual-task test aimed at aiding the early detection of dementia disorders. We used the Timed Up-and-Go (TUG) test, which is a mobility task involving starting in a sitting position, standing up, walking three meters to cross a line on the floor, turning around, walking back and sitting down again. We combined TUG with the verbal task of naming different animals. Pilot study participants were 43 individuals with and without established dementia diagnoses who attended a clinic for memory assessment. Video-recorded test performances were systematically analysed. Deviant test performances concerning the interplay between test administration and participants' responses to the assessment instructions were revealed and led to refinements being made to the final study protocol. Exploration of the dual-task test outcome measures in a sub-sample of 22 persons, ten with and twelve without dementia, indicated that step-length and number of named animals after the turning point of the dual-task test might constitute appropriate measures for examining this kind of sample. We concluded that the refined study protocol is feasible for testing individuals undergoing initial memory assessments and healthy controls. Follow-up studies with larger samples are being carried out and will bring new knowledge to this area of research. It may also provide an opportunity for further studies exploring possibilities for broad clinical implementation.
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| 10. |
- Chozas, A., et al.
(författare)
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Family history of breast cancer is associated with elevated risk of prostate cancer : evidence for shared genetic risks
- 2022
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Ingår i: Human Heredity. - : S. Karger AG. - 0001-5652 .- 1423-0062. ; 87, s. 12-19
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Although breast and prostate cancers arise in different organs and are more frequent in the opposite sex, multiple studies have reported an association between their family history. Analysis of single nucleotide polymorphism data, based on distant relatives, has revealed a small positive genetic correlation between these cancers explained by common variants. The estimate of genetic correlation based on close relatives reveals the extent to which shared genetic risks are explained by both common and rare variants. This estimate is unknown for breast and prostate cancer. Method: We estimated the relative risks, heritability, and genetic correlation of breast cancer and prostate cancer, based on the Minnesota Breast and Prostate Cancer Study, a family study of 141 families ascertained for breast cancer. Results: Heritability of breast cancer was 0.34 (95% credible interval: 0.23-0.49) and 0.65 (95% credible interval: 0.36-0.97) for prostate cancer, and the genetic correlation was 0.23. In terms of odds ratios, these values correspond to a 1.3 times higher odds of breast cancer among probands, given that the brother has prostate cancer. Conclusion: This study shows the inherent relation between prostate cancer and breast cancer; an incident of one in a family increases the risk of developing the other. The large difference between estimates of genetic correlation from distant and close relatives, if replicated, suggests that rare variants contribute to the shared genetic risk of breast and prostate cancer. However, the difference could steam from genotype-by-family effects shared between the two types of cancers. ©; 2021 The Author(s).
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