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- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:2
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Tidskriftsartikel (refereegranskat)
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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. |
- Keeler, Bonnie L., et al.
(författare)
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Social-ecological and technological factors moderate the value of urban nature
- 2019
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Ingår i: Nature Sustainability. - : Springer Science and Business Media LLC. - 2398-9629. ; 2:1, s. 29-38
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Forskningsöversikt (refereegranskat)abstract
- Urban nature has the potential to improve air and water quality, mitigate flooding, enhance physical and mental health, and promote social and cultural well-being. However, the value of urban ecosystem services remains highly uncertain, especially across the diverse social, ecological and technological contexts represented in cities around the world. We review and synthesize research on the contextual factors that moderate the value and equitable distribution of ten of the most commonly cited urban ecosystem services. Our work helps to identify strategies to more efficiently, effectively and equitably implement nature-based solutions.
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| 6. |
- Baiser, Benjamin, et al.
(författare)
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Ecogeographical rules and the macroecology of food webs
- 2019
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Ingår i: Global Ecology and Biogeography. - : Wiley-Blackwell Publishing Inc.. - 1466-822X .- 1466-8238. ; 28:9, s. 1204-1218
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Tidskriftsartikel (refereegranskat)abstract
- AimHow do factors such as space, time, climate and other ecological drivers influence food web structure and dynamics? Collections of well‐studied food webs and replicate food webs from the same system that span biogeographical and ecological gradients now enable detailed, quantitative investigation of such questions and help integrate food web ecology and macroecology. Here, we integrate macroecology and food web ecology by focusing on how ecogeographical rules [the latitudinal diversity gradient (LDG), Bergmann's rule, the island rule and Rapoport's rule] are associated with the architecture of food webs.LocationGlobal.Time periodCurrent.Major taxa studiedAll taxa.MethodsWe discuss the implications of each ecogeographical rule for food webs, present predictions for how food web structure will vary with each rule, assess empirical support where available, and discuss how food webs may influence ecogeographical rules. Finally, we recommend systems and approaches for further advancing this research agenda.ResultsWe derived testable predictions for some ecogeographical rules (e.g. LDG, Rapoport's rule), while for others (e.g., Bergmann's and island rules) it is less clear how we would expect food webs to change over macroecological scales. Based on the LDG, we found weak support for both positive and negative relationships between food chain length and latitude and for increased generality and linkage density at higher latitudes. Based on Rapoport's rule, we found support for the prediction that species turnover in food webs is inversely related to latitude.Main conclusionsThe macroecology of food webs goes beyond traditional approaches to biodiversity at macroecological scales by focusing on trophic interactions among species. The collection of food web data for different types of ecosystems across biogeographical gradients is key to advance this research agenda. Further, considering food web interactions as a selection pressure that drives or disrupts ecogeographical rules has the potential to address both mechanisms of and deviations from these macroecological relationships. For these reasons, further integration of macroecology and food webs will help ecologists better understand the assembly, maintenance and change of ecosystems across space and time.
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| 7. |
- Donahue, Marie L., et al.
(författare)
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Using social media to understand drivers of urban park visitation in the Twin Cities, MN
- 2018
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Ingår i: Landscape and Urban Planning. - : Elsevier BV. - 0169-2046 .- 1872-6062. ; 175, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Green space and parks in urban environments provide a range of ecosystem services and public benefits. However, planners and park managers can lack tools and resources to gather local information on how parks are used and what makes them desirable places for recreation and a wide variety of uses. Traditional survey methods to monitor park use and user preferences can be costly, time consuming, and challenging to apply at scale. Here, we overcome this limitation by using geotagged social media data to assess patterns of visitation to urban and peti-urban green space across park systems in the metropolitan area of the Twin Cities, Minnesota, USA. We find that parks with nearby water features, more amenities, greater accessibility from the presence of trails, and that are located within neighborhoods with higher population density, are associated with higher rates of visitation. As cities grow and shifts in demographics occur, more responsive management of public green space will become increasingly important to ensure urban parks provide ecosystem services and meet users' needs. Using social media data to rapidly assess park use at a lower cost than traditional surveys has the potential to inform public green space management with targeted information on user behavior and values of urban residents.
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| 8. |
- Hamstead, Zoé A., et al.
(författare)
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Geolocated social media as a rapid indicator of park visitation and equitable park access
- 2018
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Ingår i: Computers, Environment and Urban Systems. - : Elsevier BV. - 0198-9715 .- 1873-7587. ; 72, s. 38-50
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Tidskriftsartikel (refereegranskat)abstract
- Understanding why some parks are used more regularly or intensely than others can inform ways in which urban parkland is developed and managed to meet the needs of a rapidly expanding urban population. Although geolocated social media (GSM) indicators have been used to examine park visitation rates, studies applying this approach are generally limited to flagship parks, national parks, or a small subset of urban parks. Here, we use geolocated Flickr and Twitter data to explore variation in use across New York City's 2143 diverse parks and model visitation based on spatially-explicit park characteristics and facilities, neighborhood-level accessibility features and neighborhood-level demographics. Findings indicate that social media activity in parks is positively correlated with proximity to public transportation and bike routes, as well as particular park characteristics such as water bodies, athletic facilities, and impervious surfaces, but negatively associated with green space and increased proportion of minority ethnicity and minority race in neighborhoods in which parks are located. Contrary to previous studies which describe park visitation as a form of nature-based recreation, our findings indicate that the kinds of green spaces present in many parks may not motivate visitation. From a social equity perspective, our findings may imply that parks in high-minority neighborhoods are not as accessible, do not accommodate as many visitors, and/or are of lower quality than those in low-minority neighborhoods. These implications are consistent with previous studies showing that minority populations disproportionately experience barriers to park access. In applying GSM data to questions of park access, we demonstrate a rapid, big data approach for providing information crucial for park management in a way that is less resource-intensive than field surveys.
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| 9. |
- Albouy, Camille, et al.
(författare)
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The marine fish food web is globally connected
- 2019
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Ingår i: Nature Ecology & Evolution. - : NATURE PUBLISHING GROUP. - 2397-334X. ; 3:8, s. 1153-
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Tidskriftsartikel (refereegranskat)abstract
- The productivity of marine ecosystems and the services they provide to humans are largely dependent on complex interactions between prey and predators. These are embedded in a diverse network of trophic interactions, resulting in a cascade of events following perturbations such as species extinction. The sheer scale of oceans, however, precludes the characterization of marine feeding networks through de novo sampling. This effort ought instead to rely on a combination of extensive data and inference. Here we investigate how the distribution of trophic interactions at the global scale shapes the marine fish food web structure. We hypothesize that the heterogeneous distribution of species ranges in biogeographic regions should concentrate interactions in the warmest areas and within species groups. We find that the inferred global metaweb of marine fish-that is, all possible potential feeding links between co-occurring species-is highly connected geographically with a low degree of spatial modularity. Metrics of network structure correlate with sea surface temperature and tend to peak towards the tropics. In contrast to open-water communities, coastal food webs have greater interaction redundancy, which may confer robustness to species extinction. Our results suggest that marine ecosystems are connected yet display some resistance to perturbations because of high robustness at most locations.
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