| 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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| 4. |
- Båth, Klara, et al.
(författare)
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Microbiota of an unpasteurised cellar-stored goat cheese from northern Sweden
- 2012
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Ingår i: Agricultural and Food Science. - Helsinki, Finland : M T T / Agrifood Research Finland. - 1459-6067 .- 1795-1895. ; 21:2, s. 197-203
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Tidskriftsartikel (refereegranskat)abstract
- This qualitative study reports on lactic acid bacteria (LAB), yeasts and moulds isolated from three artisanal Swedish cellar-stored goat cheeses aged for 1, 3 and 5 months. Starter culture LAB dominated in the younger cheeses, and Leuconostoc pseudomesenteroides, common in raw goats' milk, had persisted from the unpasteurised milk into all the cheeses. Non-starter LAB dominated in the 5 month cheese, in particular, Lactobacillus sakei, a meat-associated LAB not previously isolated from cheese. Debaryomyces hansenii, and Penicillium and Mucor species were dominant among the yeasts and moulds, respectively. The cheese rind was not formed primarily from Penicillium species as in traditional cheeses such as Camembert - rather, mycelium from Mucor mucedo contributed to rind formation. Mould species known to produce sterigmatocystin, aflatoxins or ochratoxin A in cheese were not isolated in this study; growth of mycotoxigenic Aspergilli may have been inhibited by the cool conditions in the earth-cellar (4-6 degrees C).
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| 5. |
- Leong, Su-lin L., et al.
(författare)
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Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date
- 2015
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Ingår i: Environmental Microbiology. - Hoboken, USA : Wiley-Blackwell. - 1462-2912 .- 1462-2920. ; 17:2, s. 496-513
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Tidskriftsartikel (refereegranskat)abstract
- Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its dry' but nutrient-rich environment, X.bisporus appears to have relinquished abilities for combative interactions. Elements to sense/signal osmotic stress, e.g. HogA pathway, were present in X.bisporus. However, transcriptomes at optimal (approximate to 0.89) versus low a(w) (0.68) revealed differential expression of only a few stress-related genes; among these, certain (not all) steps for glycerol synthesis were upregulated. Xeromyces bisporus increased glycerol production during hypo- and hyper-osmotic stress, and much of its wet weight comprised water and rinsable solutes; leaked solutes may form a protective slime. Xeromyces bisporus and other food-borne moulds increased membrane fatty acid saturation as water activity decreased. Such modifications did not appear to be transcriptionally regulated in X.bisporus; however, genes modulating sterols, phospholipids and the cell wall were differentially expressed. Xeromyces bisporus was previously proposed to be a chaophile', preferring solutes that disorder biomolecular structures. Both X.bisporus and the closely related xerophile, Xerochrysium xerophilum, with low membrane unsaturation indices, could represent a phylogenetic cluster of chaophiles'.
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| 6. |
- Leong, Su-lin L., et al.
(författare)
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The extreme xerophilic mould Xeromyces bisporus : Growth and competition at various water activities
- 2011
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Ingår i: International Journal of Food Microbiology. - Amsterdam, Netherlands : Elsevier. - 0168-1605 .- 1879-3460. ; 145:1, s. 57-63
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Tidskriftsartikel (refereegranskat)abstract
- Little is known about the mould, Xeromyces bisporus, unique in its strong xerophilicity and ability to grow at water activity (a(w)) 0.62, lower than for any other known organism. The linear growth rates of one fast and one slow-growing strain of X. bisporus were assessed at 20, 25, 30 and 37 degrees C on solid agar media containing a mixture of glucose and fructose to reduce a(w) to 0.94, 0.88, 0.84, 0.80, 0.76 and 0.66. Growth rates of xerophilic species closely related to X. bisporus, viz. Chrysosporium Mops, C. xerophilum and Monascus eremophilus, were also assessed. Optimal conditions for growth of both X. bisporus strains were approx. 0.84 a(w) and 30 degrees C, despite FRR 2347 growing two- to five-fold faster than CBS 185.75. X. bisporus FRR 2347 even grew well at 0.66 a(w) (0.48 mm/day). C. Mops and C xerophilurn were more tolerant of high a(w) than X. bisporus. and could be differentiated from each other based on: the faster growth of C. xerophilum; its preference for temperatures >= 30 degrees C and a(w) >= 0.94 (c.f. <= 25 degrees C and similar to 0.88 a(w) for C Mops); and its ability to grow at 0.66 a(w), which is the lowest a(w) reported to date for this species. M. eremophilus grew slowly (max. 0.4 mm/day) even in its optimal conditions of similar to 0.88 a(w) and 25 degrees C. To investigate the competitive characteristics of X. bisporus at low a(w), both X. bisporus strains were grown in dual-culture with xerotolerant species Aspergillus flavus and Penicillium roqueforti, and xerophilic species A. penicillioides, C. Mops, C. xerophilum and Eurotium chevalieri, on glucose-fructose agar plates at 0.94, 0.84, 0.80 and 0.76 a(w) and at 25 degrees C. Growth rates and types of interactions were assessed. Excretion of inhibitory substances acting over a long-range was not observed by any species; inhibitors acting over a short-range that temporarily slowed competitors' growth or produced a protective zone around the colony were occasionally observed for A. penicillioides, C. Mops and C. xerophilum. Instead, rapid growth relative to the competitor was the most common means of dominance. The xerotolerant species. A. flavus and P. roqueforti were dominant over X. bisporus at 0.94 a(w). E. chevalieri was often dominant due to its rapid growth over the entire a(w) range. At a(w) < 0.80, X. bisporus was competitive because it grew faster than the other species examined. This supports the concept that its ideal environmental niche is sugary foods with low a(w).
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| 7. |
- Vinnere Pettersson, Olga, et al.
(författare)
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Phylogeny and intraspecific variation of the extreme xerophile, Xeromyces bisporus
- 2011
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Ingår i: Fungal Biology. - Oxon, United Kingdom : Elsevier. - 1878-6146 .- 1878-6162. ; 115:11, s. 1100-1111
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Tidskriftsartikel (refereegranskat)abstract
- The filamentous ascomycete Xeromyces bisporus is an extreme xerophile able to grow down to a water activity of 0.62. We have inferred the phylogenetic position of Xeromyces in relation to other xerophilic and xerotolerant fungi in the order Eurotiales. Using nrDNA and betatubulin sequences, we show that it is more closely related to the xerophilic food-borne species of the genus Chrysosporium, than to the genus Monascus. The taxonomy of X. bisporus and Monascus is discussed. Based on physiological, morphological, and phylogenetic distinctiveness, we suggest that Xeromyces should be retained as a separate genus.
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| 8. |
- Keiter, Su, et al.
(författare)
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Long-term effects of a binary mixture of perfluorooctane sulfonate (PFOS) and bisphenol A (BPA) in zebrafish (Danio rerio)
- 2012
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Ingår i: Aquatic Toxicology. - : Elsevier. - 0166-445X .- 1879-1514. ; 118-119, s. 116-129
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Tidskriftsartikel (refereegranskat)abstract
- Previous in vitro studies have reported the potential of perfluorooctane sulfonate (PFOS) to increase the toxicity of other compounds. Given the complex nature of mixtures of environmental pollutants in aquatic systems together with the persistent and bioaccumulative properties of PFOS, this study aimed at evaluating the long-term effects and toxicity-increasing behavior of PFOS in vivo using the zebrafish (Danio rerio). Fish were maintained in flow-through conditions and exposed to single and binary mixtures of PFOS and the endocrine disruptor bisphenol A (BPA) at nominal concentrations of 0.6, 100 and 300 mu g/L and 10, 200 and 400 mu g/L, respectively. F1 and F2 generations were evaluated from 0 to 180 days post-fertilization (dpf) and F3 generation was evaluated from 0 to 14 dpf. Survival was documented in all generations, whereas growth, fecundity, fertilization rate, histological alterations (in liver, thyroid and gonads) and vitellogenin (Vtg) induction in males were evaluated for Fl and F2 generations. Data for growth were collected at 30, 90 and 180 dpf and data for histological evaluations and Vtg induction were analyzed at 90 and 180 dpf. No significant effects on survival were seen in the Fl generation in any treatment following 180 d exposure: however, in the F2 generation, 300 mu g/L PFOS both alone and in combination with BPA (10, 200 and 400 mu g/L) induced 100% mortality within 14 dpf. PFOS (0.6 and 300 mu g/L) did not increase the Vtg-inducing potential of BPA (10, 200 and 400 mu g/L) in a binary mixture. In contrast, binary mixtures with 300 mu g/L PFOS suppressed the Vtg levels in Fl males at 90 dpf when compared to single BPA exposures. Whereas the lowest tested PFOS concentration (0.6 mu g/L) showed an estrogenic potential in terms of significant Vtg induction, Vtg levels were generally found to decrease with increasing PFOS-exposure in both Fl and F2 generations. In Fl generation, BPA-exposure was found to increase Vtg levels in a concentration-dependent manner. Histological analyses of Fl and F2 fish revealed hepatocellular vacuolization, predominantly in males, following PFOS-exposure both alone and in combination with BPA. Hepatotoxicity by PFOS might explain the suppressed Vtg response seen in PFOS-exposed Fl and F2 males. PFOS-exposed fish also showed granulomas, mainly in the liver. Given previous reports of the immunosuppressive potential of PFOS, the granulomas could be a consequence of a PFOS-induced reduction of the immune response potential. In conclusion, the hypothesis that the presence of PFOS increases the endocrine potential of BPA could not be confirmed in zebrafish. Adverse effects on liver structure and survival were only seen at concentrations well above ecologically relevant concentrations; however, the decline in survival rates following PFOS-exposure seen over generations again documents the importance of long-term studies for the investigation of persistent environmental pollutants.
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| 9. |
- Ogunbode, Charles, et al.
(författare)
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Climate anxiety, wellbeing and pro-environmental action : Correlates of negative emotional responses to climate change in 32 countries
- 2022
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Ingår i: Journal of Environmental Psychology. - : Academic Press. - 0272-4944 .- 1522-9610. ; 84
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Tidskriftsartikel (refereegranskat)abstract
- This study explored the correlates of climate anxiety in a diverse range of national contexts. We analysed cross-sectional data gathered in 32 countries (N = 12,246). Our results show that climate anxiety is positively related to rate of exposure to information about climate change impacts, the amount of attention people pay to climate change information, and perceived descriptive norms about emotional responding to climate change. Climate anxiety was also positively linked to pro-environmental behaviours and inversely related to mental wellbeing. Notably, climate anxiety had a significant inverse association with mental wellbeing in 31 out of 32 countries, and with pro-environmental behaviour in 24 countries, it only predicted environmental activism in 12 countries. Our findings highlight contextual boundaries to engagement in environmental action as an antidote to climate anxiety, and the broad international significance of negative climate-related emotions as a plausible threat to wellbeing.
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