| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- de Vries, Paul S., et al.
(författare)
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Multiancestry Genome-Wide Association Study of Lipid Levels Incorporating Gene-Alcohol Interactions
- 2019
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Ingår i: American Journal of Epidemiology. - : Oxford University Press. - 0002-9262 .- 1476-6256. ; 188:6, s. 1033-1054
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Tidskriftsartikel (refereegranskat)abstract
- A person's lipid profile is influenced by genetic variants and alcohol consumption, but the contribution of interactions between these exposures has not been studied. We therefore incorporated gene-alcohol interactions into a multiancestry genome-wide association study of levels of high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. We included 45 studies in stage 1 (genome-wide discovery) and 66 studies in stage 2 (focused follow-up), for a total of 394,584 individuals from 5 ancestry groups. Analyses covered the period July 2014-November 2017. Genetic main effects and interaction effects were jointly assessed by means of a 2-degrees-of-freedom (df) test, and a 1-df test was used to assess the interaction effects alone. Variants at 495 loci were at least suggestively associated (P < 1 x 10(-6)) with lipid levels in stage 1 and were evaluated in stage 2, followed by combined analyses of stage 1 and stage 2. In the combined analysis of stages 1 and 2, a total of 147 independent loci were associated with lipid levels at P < 5 x 10(-8) using 2-df tests, of which 18 were novel. No genome-wide-significant associations were found testing the interaction effect alone. The novel loci included several genes (proprotein convertase subtilisin/kexin type 5 (PCSK5), vascular endothelial growth factor B (VEGFB), and apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1) complementation factor (A1CF)) that have a putative role in lipid metabolism on the basis of existing evidence from cellular and experimental models.
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| 3. |
- Di Baldassarre, Giuliano, et al.
(författare)
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An integrative research framework to unravel the interplay of natural hazards and vulnerabilities
- 2018
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Ingår i: Earth's Future. - : John Wiley & Sons. - 2328-4277. ; 6:3, s. 305-310
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Tidskriftsartikel (refereegranskat)abstract
- Climate change, globalization, urbanization, social isolation, and increased interconnectednessbetween physical, human, and technological systems pose major challenges to disaster risk reduction(DRR). Subsequently, economic losses caused by natural hazards are increasing in many regions of theworld, despite scientific progress, persistent policy action, and international cooperation. We argue thatthese dramatic figures call for novel scientific approaches and new types of data collection to integratethe two main approaches that still dominate the science underpinning DRR: the hazard paradigm and thevulnerability paradigm. Building from these two approaches, here we propose a research framework thatspecifies the scope of enquiry, concepts, and general relations among phenomena. We then discuss theessential steps to advance systematic empirical research and evidence-based DRR policy action.
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| 4. |
- Dima, Danai, et al.
(författare)
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Subcortical volumes across the lifespan : Data from 18,605 healthy individuals aged 3-90 years.
- 2022
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Ingår i: Human Brain Mapping. - : Wiley. - 1065-9471 .- 1097-0193. ; 43:1, s. 452-469
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Tidskriftsartikel (refereegranskat)abstract
- Age has a major effect on brain volume. However, the normative studies available are constrained by small sample sizes, restricted age coverage and significant methodological variability. These limitations introduce inconsistencies and may obscure or distort the lifespan trajectories of brain morphometry. In response, we capitalized on the resources of the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) Consortium to examine age-related trajectories inferred from cross-sectional measures of the ventricles, the basal ganglia (caudate, putamen, pallidum, and nucleus accumbens), the thalamus, hippocampus and amygdala using magnetic resonance imaging data obtained from 18,605 individuals aged 3-90 years. All subcortical structure volumes were at their maximum value early in life. The volume of the basal ganglia showed a monotonic negative association with age thereafter; there was no significant association between age and the volumes of the thalamus, amygdala and the hippocampus (with some degree of decline in thalamus) until the sixth decade of life after which they also showed a steep negative association with age. The lateral ventricles showed continuous enlargement throughout the lifespan. Age was positively associated with inter-individual variability in the hippocampus and amygdala and the lateral ventricles. These results were robust to potential confounders and could be used to examine the functional significance of deviations from typical age-related morphometric patterns.
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| 5. |
- Frangou, Sophia, et al.
(författare)
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Cortical thickness across the lifespan : Data from 17,075 healthy individuals aged 3-90 years
- 2022
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Ingår i: Human Brain Mapping. - : John Wiley & Sons. - 1065-9471 .- 1097-0193. ; 43:1, s. 431-451
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Tidskriftsartikel (refereegranskat)abstract
- Delineating the association of age and cortical thickness in healthy individuals is critical given the association of cortical thickness with cognition and behavior. Previous research has shown that robust estimates of the association between age and brain morphometry require large-scale studies. In response, we used cross-sectional data from 17,075 individuals aged 3-90 years from the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) Consortium to infer age-related changes in cortical thickness. We used fractional polynomial (FP) regression to quantify the association between age and cortical thickness, and we computed normalized growth centiles using the parametric Lambda, Mu, and Sigma method. Interindividual variability was estimated using meta-analysis and one-way analysis of variance. For most regions, their highest cortical thickness value was observed in childhood. Age and cortical thickness showed a negative association; the slope was steeper up to the third decade of life and more gradual thereafter; notable exceptions to this general pattern were entorhinal, temporopolar, and anterior cingulate cortices. Interindividual variability was largest in temporal and frontal regions across the lifespan. Age and its FP combinations explained up to 59% variance in cortical thickness. These results may form the basis of further investigation on normative deviation in cortical thickness and its significance for behavioral and cognitive outcomes.
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| 6. |
- Fuentes-Andino, Diana, 1984-, et al.
(författare)
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Event and model dependent rainfall adjustments to improve discharge predictions
- 2017
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Ingår i: Hydrological Sciences Journal. - : Informa UK Limited. - 0262-6667 .- 2150-3435. ; 62:2, s. 232-245
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Tidskriftsartikel (refereegranskat)abstract
- Most conceptual rainfall–runoff models use as input spatially averaged rainfall fields which are typically associated with significant errors that affect the model outcome. In this study, it was hypothesised that a simple spatially and temporally averaged event-dependent rainfall multiplier can account for errors in the rainfall input. The potentials and limitations of this lumped multiplier approach were explored by evaluating the effects of multipliers on the accuracy and precision of the predictive distributions. Parameter sets found to be behavioural across a range of different flood events were assumed to be a good representation of the catchment dynamics and were used to identify rainfall multipliers for each of the individual events. An effect of the parameter sets on identified multipliers was found; however, it was small compared to the differences between events. Accounting for event-dependent multipliers improved the reliability of the predictions. At the cost of a small decrease in precision, the distribution of identified multipliers for past events can be used to account for possible rainfall errors when predicting future events. By using behavioural parameter sets to identify rainfall multipliers, the method offers a simple and computationally efficient way to address rainfall errors in hydrological modelling.
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| 7. |
- Fuentes-Andino, Diana, 1984-
(författare)
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Flood Hazard Assessment in Data-Scarce Basins : Use of alternative data and modelling techniques
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Flooding is of great concern world-wide, causing damage to infrastructure, property and loss of life. Low-income countries, in particular, can be negatively affected by flood events due to their inherent vulnerabilities. Moreover, data to perform studies for flood risk management in low-income regions are often scarce or lacking sufficient quality.This thesis proposes new methodologies and explores the use of unconventional sources of information in flood hazard assessment in areas where the quantity or sufficient quality of traditional hydrometrical data are lacking. One method was developed to account for errors in spatially averaged rainfall, from a sparse rain-gauge network, used as input to a rainfall-runoff model. A spatially-averaged and event-dependent rainfall depth multiplier led to improvements of the hydrographs at calibration. And by using a distribution of the multiplier, identified from previous events in the catchment, improvement in predictions could also be obtained.A second method explored the possibility of reproducing an unmeasured extreme flood event using a combination of models, post-event data, precipitation and an uncertainty-analysis framework. This combination allowed the identification of likelihood-associated parameter sets from which the flood hazard map for the extreme event could be obtained.A third and fourth study made at the regional scale explored the value of catchment similarities, and the effects of climate on the hydrological response of catchments.Flood frequency curves were estimated for 36 basins, assumed ungauged, using regional information of short flow records, and local information about the frequency of the storm. In the second regional study, hydro-climatic information provided great value to constrain predictions of series of daily flow from a hydrological model.Previously described methods, used in combination with unconventional information within an uncertainty analysis, proven to be useful for flood hazard assessment at basins with data limitations. The explored data included: post-event measurements of an extreme flood event, hydro-climate regional information and local precipitation data. The methods presented in this thesis are expected to support development of hydrological studies underpinning flood-risk reduction in data-poor areas.
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| 8. |
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| 9. |
- Gutman, Boris A, et al.
(författare)
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A meta-analysis of deep brain structural shape and asymmetry abnormalities in 2,833 individuals with schizophrenia compared with 3,929 healthy volunteers via the ENIGMA Consortium
- 2022
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Ingår i: Human Brain Mapping. - : John Wiley & Sons. - 1065-9471 .- 1097-0193. ; 43:1, s. 352-372
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Tidskriftsartikel (refereegranskat)abstract
- Schizophrenia is associated with widespread alterations in subcortical brain structure. While analytic methods have enabled more detailed morphometric characterization, findings are often equivocal. In this meta-analysis, we employed the harmonized ENIGMA shape analysis protocols to collaboratively investigate subcortical brain structure shape differences between individuals with schizophrenia and healthy control participants. The study analyzed data from 2,833 individuals with schizophrenia and 3,929 healthy control participants contributed by 21 worldwide research groups participating in the ENIGMA Schizophrenia Working Group. Harmonized shape analysis protocols were applied to each site's data independently for bilateral hippocampus, amygdala, caudate, accumbens, putamen, pallidum, and thalamus obtained from T1-weighted structural MRI scans. Mass univariate meta-analyses revealed more-concave-than-convex shape differences in the hippocampus, amygdala, accumbens, and thalamus in individuals with schizophrenia compared with control participants, more-convex-than-concave shape differences in the putamen and pallidum, and both concave and convex shape differences in the caudate. Patterns of exaggerated asymmetry were observed across the hippocampus, amygdala, and thalamus in individuals with schizophrenia compared to control participants, while diminished asymmetry encompassed ventral striatum and ventral and dorsal thalamus. Our analyses also revealed that higher chlorpromazine dose equivalents and increased positive symptom levels were associated with patterns of contiguous convex shape differences across multiple subcortical structures. Findings from our shape meta-analysis suggest that common neurobiological mechanisms may contribute to gray matter reduction across multiple subcortical regions, thus enhancing our understanding of the nature of network disorganization in schizophrenia.
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| 10. |
- Petrov, Dmitry, et al.
(författare)
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Machine Learning for Large-Scale Quality Control of 3D Shape Models in Neuroimaging
- 2017
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Ingår i: Machine learning in medical imaging. MLMI (Workshop). - Cham : Springer International Publishing. ; 10541, s. 371-378
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Tidskriftsartikel (refereegranskat)abstract
- As very large studies of complex neuroimaging phenotypes become more common, human quality assessment of MRI-derived data remains one of the last major bottlenecks. Few attempts have so far been made to address this issue with machine learning. In this work, we optimize predictive models of quality for meshes representing deep brain structure shapes. We use standard vertex-wise and global shape features computed homologously across 19 cohorts and over 7500 human-rated subjects, training kernelized Support Vector Machine and Gradient Boosted Decision Trees classifiers to detect meshes of failing quality. Our models generalize across datasets and diseases, reducing human workload by 30-70%, or equivalently hundreds of human rater hours for datasets of comparable size, with recall rates approaching inter-rater reliability.
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