| 1. |
- Edwards, Robert A., et al.
(författare)
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Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
- 2019
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Ingår i: Nature Microbiology. - : Springer Science and Business Media LLC. - 2058-5276. ; 4:10, s. 1727-1736
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Tidskriftsartikel (refereegranskat)abstract
- Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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| 2. |
- Bagshaw, Dale, et al.
(författare)
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General Introduction
- 2007
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Ingår i: DRACON International: Empowering students to handle conflicts through school based programmes. - Malmö : MUEP (Malmö University Electronic Publishing). - 918881033X ; , s. 13-44
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Researchers from Australia, Malaysia and Sweden form part of DRACON International (DRAma for CONflict management) and share the basic view that drama can be an effective way for adolescents to learn to handle conflicts constructively. The main aims of the DRACON project have been: - to develop research methods in order to map students´ conflicts and strategies for handling conflicts and to study the effects of various drama exercises on individual, class and school levels; - to contribute to the development of a theory of conflict processes in different cultures in order to explain the effects of different types of interference´s in adolescents´ conflicts; - to develop and test integrated drama programmes giving adolescents in the three different cultures the opportunity of handling conflicts in a more constructive way. This book is the result of several years of collaborative teamwork between researchers from Australia, Malaysia and Sweden and aims at providing a starting-point for further development of drama and conflict management in educational settings.
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| 3. |
- Chyz̊y, K.T., et al.
(författare)
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LOFAR MSSS: Flattening low-frequency radio continuum spectra of nearby galaxies
- 2018
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 619
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Tidskriftsartikel (refereegranskat)abstract
- Aims. The shape of low-frequency radio continuum spectra of normal galaxies is not well understood, the key question being the role of physical processes such as thermal absorption in shaping them. In this work we take advantage of the LOFAR Multifrequency Snapshot Sky Survey (MSSS) to investigate such spectra for a large sample of nearby star-forming galaxies. Methods. Using the measured 150 MHz flux densities from the LOFAR MSSS survey and literature flux densities at various frequencies we have obtained integrated radio spectra for 106 galaxies characterised by different morphology and star formation rate. The spectra are explained through the use of a three-dimensional model of galaxy radio emission, and radiation transfer dependent on the galaxy viewing angle and absorption processes. Results. Our galaxies' spectra are generally flatter at lower compared to higher frequencies: the median spectral index αlow measured between ≈ 50 MHz and 1.5 GHz is -0.57 ± 0.01 while the high-frequency one αhigh, calculated between 1.3 GHz and 5 GHz, is -0.77 ± 0.03. As there is no tendency for the highly inclined galaxies to have more flattened low-frequency spectra, we argue that the observed flattening is not due to thermal absorption, contradicting the suggestion of Israel & Mahoney (1990, ApJ, 352, 30). According to our modelled radio maps for M 51-like galaxies, the free-free absorption effects can be seen only below 30 MHz and in the global spectra just below 20 MHz, while in the spectra of starburst galaxies, like M 82, the flattening due to absorption is instead visible up to higher frequencies of about 150 MHz. Starbursts are however scarce in the local Universe, in accordance with the weak spectral curvature seen in the galaxies of our sample. Locally, within galactic disks, the absorption effects are distinctly visible in M 51-like galaxies as spectral flattening around 100-200 MHz in the face-on objects, and as turnovers in the edge-on ones, while in M 82-like galaxies there are strong turnovers at frequencies above 700 MHz, regardless of viewing angle. Conclusions. Our modelling of galaxy spectra suggests that the weak spectral flattening observed in the nearby galaxies studied here results principally from synchrotron spectral curvature due to cosmic ray energy losses and propagation effects. We predict much stronger effects of thermal absorption in more distant galaxies with high star formation rates. Some influence exerted by the Milky Way's foreground on the spectra of all external galaxies is also expected at very low frequencies.
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| 4. |
- Esfahani, Mahdad Jafarzadeh, et al.
(författare)
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Validation of the sleep EEG headband ZMax
- 2023
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Ingår i: bioRxiv. - : Cold Spring Harbor Laboratory Press (CSHL). - 2692-8205.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Polysomnography (PSG) is the gold standard for recording sleep. However, the standard PSG systems are bulky, expensive, and often confined to lab environments. These systems are also time-consuming in electrode placement and sleep scoring. Such limitations render standard PSG systems less suitable for large-scale or longitudinal studies of sleep. Recent advances in electronics and artificial intelligence enabled ‘wearable’ PSG systems. Here, we present a study aimed at validating the performance of ZMax, a widely-used wearable PSG that includes frontal electroencephalography (EEG) and actigraphy but no submental electromyography (EMG). We analyzed 135 nights with simultaneous ZMax and standard PSG recordings amounting to over 900 hours from four different datasets, and evaluated the performance of the headband’s proprietary automatic sleep scoring (ZLab) alongside our open-source algorithm (DreamentoScorer) in comparison with human sleep scoring. ZLab and DreamentoScorer compared to human scorers with moderate and substantial agreement and Cohen’s kappa scores of 59.61% and 72.18%, respectively. We further analyzed the competence of these algorithms in determining sleep assessment metrics, as well as shedding more lights on the bandpower computation, and morphological analysis of sleep microstructural features between ZMax and standard PSG. Relative bandpower computed by ZMax implied an error of 5.5% (delta), 4.5% (theta), 1.6% (alpha), 0.5% (sigma), 0.8% (beta), and 0.2% (gamma), compared to standard PSG. In addition, the microstructural features detected in ZMax did not represent exactly the same characteristics as in standard PSG. Besides similarities and discrepancies between ZMax and standard PSG, we measured and discussed the technology acceptance rate, feasibility of data collection with ZMax, and highlighted essential factors for utilizing ZMax as a reliable tool for both monitoring and modulating sleep.
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| 5. |
- Forte, Castela, et al.
(författare)
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Deep Learning for Identification of Acute Illness and Facial Cues of Illness
- 2021
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Ingår i: Frontiers in Medicine. - : Frontiers Media SA. - 2296-858X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background: The inclusion of facial and bodily cues (clinical gestalt) in machine learning (ML) models improves the assessment of patients' health status, as shown in genetic syndromes and acute coronary syndrome. It is unknown if the inclusion of clinical gestalt improves ML-based classification of acutely ill patients. As in previous research in ML analysis of medical images, simulated or augmented data may be used to assess the usability of clinical gestalt.Objective: To assess whether a deep learning algorithm trained on a dataset of simulated and augmented facial photographs reflecting acutely ill patients can distinguish between healthy and LPS-infused, acutely ill individuals.Methods: Photographs from twenty-six volunteers whose facial features were manipulated to resemble a state of acute illness were used to extract features of illness and generate a synthetic dataset of acutely ill photographs, using a neural transfer convolutional neural network (NT-CNN) for data augmentation. Then, four distinct CNNs were trained on different parts of the facial photographs and concatenated into one final, stacked CNN which classified individuals as healthy or acutely ill. Finally, the stacked CNN was validated in an external dataset of volunteers injected with lipopolysaccharide (LPS).Results: In the external validation set, the four individual feature models distinguished acutely ill patients with sensitivities ranging from 10.5% (95% CI, 1.3-33.1% for the skin model) to 89.4% (66.9-98.7%, for the nose model). Specificity ranged from 42.1% (20.3-66.5%) for the nose model and 94.7% (73.9-99.9%) for skin. The stacked model combining all four facial features achieved an area under the receiver characteristic operating curve (AUROC) of 0.67 (0.62-0.71) and distinguished acutely ill patients with a sensitivity of 100% (82.35-100.00%) and specificity of 42.11% (20.25-66.50%).Conclusion: A deep learning algorithm trained on a synthetic, augmented dataset of facial photographs distinguished between healthy and simulated acutely ill individuals, demonstrating that synthetically generated data can be used to develop algorithms for health conditions in which large datasets are difficult to obtain. These results support the potential of facial feature analysis algorithms to support the diagnosis of acute illness.
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| 6. |
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| 7. |
- Geng, Xiaoyu, et al.
(författare)
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LEUNIG_HOMOLOG transcriptional co-repressor mediates aluminium sensitivity through PECTIN METHYLESTERASE46-modulated root cell wall pectin methylesterification in Arabidopsis
- 2017
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Ingår i: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 90:3, s. 491-504
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Tidskriftsartikel (refereegranskat)abstract
- A major factor determining aluminium (Al) sensitivity in higher plants is the binding of Al to root cell walls. The Al binding capacity of cell walls is closely linked to the extent of pectin methylesterification, as the presence of methyl groups attached to the pectin backbone reduces the net negative charge of this polymer and hence limits Al binding. Despite recent progress in understanding the molecular basis of Al resistance in a wide range of plants, it is not well understood how the methylation status of pectin is mediated in response to Al stress. Here we show in Arabidopsis that mutants lacking the gene LEUNIG_HOMOLOG (LUH), a member of the Groucho-like family of transcriptional co-repressor, are less sensitive to Al-mediated repression of root growth. This phenotype is correlated with increased levels of methylated pectin in the cell walls of luh roots as well as altered expression of cell wall-related genes. Among the LUH-repressed genes, PECTIN METHYLESTERASE46 (PME46) was identified as reducing Al binding to cell walls and hence alleviating Al-induced root growth inhibition by decreasing PME enzyme activity. seuss-like2 (slk2) mutants responded to Al in a similar way as luh mutants suggesting that a LUH-SLK2 complex represses the expression of PME46. The data are integrated into a model in which it is proposed that PME46 is a major inhibitor of pectin methylesterase activity within root cell walls.
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| 8. |
- Heald, G. H., et al.
(författare)
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The LOFAR Multifrequency Snapshot Sky Survey (MSSS) : I. Survey description and first results
- 2015
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 582, s. 1-22
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Tidskriftsartikel (refereegranskat)abstract
- We present the Multifrequency Snapshot Sky Survey (MSSS), the first northern-sky Low Frequency Array (LOFAR) imaging survey. In this introductory paper, we first describe in detail the motivation and design of the survey. Compared to previous radio surveys, MSSS is exceptional due to its intrinsic multifrequency nature providing information about the spectral properties of the detected sources over more than two octaves (from 30 to 160 MHz). The broadband frequency coverage, together with the fast survey speed generated by LOFAR’s multibeaming capabilities, make MSSS the first survey of the sort anticipated to be carried out with the forthcoming Square Kilometre Array (SKA). Two of the sixteen frequency bands included in the survey were chosen to exactly overlap the frequency coverage of large-area Very Large Array (VLA) and Giant Metrewave Radio Telescope (GMRT) surveys at 74 MHz and 151 MHz respectively. The survey performance is illustrated within the MSSS Verification Field (MVF), a region of 100 square degrees centered at (α,δ)J2000 = (15h,69°). The MSSS results from the MVF are compared with previous radio survey catalogs. We assess the flux and astrometric uncertainties in the catalog, as well as the completeness and reliability considering our source finding strategy. We determine the 90% completeness levels within the MVF to be 100 mJy at 135 MHz with 108″ resolution, and 550 mJy at 50 MHz with 166″ resolution. Images and catalogs for the full survey, expected to contain 150 000–200 000 sources, will be released to a public web server. We outline the plans for the ongoing production of the final survey products, and the ultimate public release of images and source catalogs.
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| 9. |
- Ishigaki, Kazuyoshi, et al.
(författare)
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Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis
- 2022
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Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 54:11, s. 1640-1651
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Tidskriftsartikel (refereegranskat)abstract
- Rheumatoid arthritis (RA) is a highly heritable complex disease with unknown etiology. Multi-ancestry genetic research of RA promises to improve power to detect genetic signals, fine-mapping resolution and performances of polygenic risk scores (PRS). Here, we present a large-scale genome-wide association study (GWAS) of RA, which includes 276,020 samples from five ancestral groups. We conducted a multi-ancestry meta-analysis and identified 124 loci (P < 5 × 10−8), of which 34 are novel. Candidate genes at the novel loci suggest essential roles of the immune system (for example, TNIP2 and TNFRSF11A) and joint tissues (for example, WISP1) in RA etiology. Multi-ancestry fine-mapping identified putatively causal variants with biological insights (for example, LEF1). Moreover, PRS based on multi-ancestry GWAS outperformed PRS based on single-ancestry GWAS and had comparable performance between populations of European and East Asian ancestries. Our study provides several insights into the etiology of RA and improves the genetic predictability of RA.
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| 10. |
- Jelic, V., et al.
(författare)
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Initial LOFAR observations of epoch of reionization windows II. Diffuse polarized emission in the ELAIS-N1 field
- 2014
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 568, s. A101-
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Tidskriftsartikel (refereegranskat)abstract
- Aims. This study aims to characterise the polarized foreground emission in the ELAIS-N1 field and to address its possible implications or extracting of the cosmological 21 cm signal from the LOw-Frequency ARray - Epoch of Reionization (LOFAR-EoR) data Methods. We used the high band antennas of LOFAR to image this region and RM-synthesis to unravel structures of polarized emission at high Galactic latitudes. Results. The brightness temperature of the detected Galactic emission is on average similar to 4 K in polarized intensity and covers the range from -10 to +13 rad m(-2) in Faraday depth, The total polarized intensity and polarization angle show a wide range of morphological features. We have also used the Westerbork Synthesis Radio Telescope (WSRT) at 350 MHz to image the same region. The LOFAR and WSRT images show a similar complex morphology at comparable brightness levels, but their spatial correlation is very low. The fractional polarization at 150 MHz, expressed as a percentage of the total intensity, amounts to approximate to 1.5%. There is no indication of diffuse emission in total intensity in the interferometric data. in line with results at higher frequencies Conclusions. The wide frequency range. high angular resolution, and high sensitivity make LOFAR an exquisite instrument for studying Galactic polarized emission at a resolution of similar to 1-2 rad m(-2) in Faraday depth. The different polarized patterns observed at 150 MHz and 350 MHz are consistent with different source distributions along the line of sight wring in a variety of Faraday thin regions of emission. The presence of polarized foregrounds is a serious complication for epoch of reionization experiments. To avoid the leakage of polarized emission into total intensity, which can depend on frequency, we need to calibrate the instrumental polarization across the field of view to a small fraction of 1%.
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