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- 2019
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Tidskriftsartikel (refereegranskat)
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- Chen, C. T.J., et al.
(författare)
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The XMM-SERVS survey : New XMM-Newton point-source catalogue for the XMM-LSS field
- 2018
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Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 478:2, s. 2132-2163
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Tidskriftsartikel (refereegranskat)abstract
- We present an X-ray point-source catalogue from the XMM-Large Scale Structure (XMMLSS) survey region, one of the XMM-Spitzer Extragalactic Representative Volume Survey (XMM-SERVS) fields. We target the XMM-LSS region with 1.3 Ms of new XMM-Newton AO-15 observations, transforming the archival X-ray coverage in this region into a 5.3 deg2 contiguous field with uniform X-ray coverage totaling 2.7 Ms of flare-filtered exposure, with a 46 ks median PN exposure time. We provide an X-ray catalogue of 5242 sources detected in the soft (0.5-2 keV), hard (2-10 keV), and/or full (0.5-10 keV) bands with a 1 per cent expected spurious fraction determined from simulations. A total of 2381 new X-ray sources are detected compared to previous source catalogues in the same area. Our survey has flux limits of 1.7 × 10-15, 1.3 × 10-14, and 6.5 × 10-15 erg cm-2 s-1 over 90 per cent of its area in the soft, hard, and full bands, respectively, which is comparable to those of the XMM-COSMOS survey. We identify multiwavelength counterpart candidates for 99.9 per cent of the X-ray sources, of which 93 per cent are considered as reliable based on their matching likelihood ratios. The reliabilities of these high-likelihood-ratio counterparts are further confirmed to be ≈97 per cent reliable based on deep Chandra coverage over ≈5 per cent of the XMM-LSS region. Results of multiwavelength identifications are also included in the source catalogue, along with basic optical-to-infrared photometry and spectroscopic redshifts from publicly available surveys. We compute photometric redshifts for X-ray sources in 4.5 deg2 of our field where forced-aperture multiband photometry is available; > 70 per cent of the X-ray sources in this subfield have either spectroscopic or high-quality photometric redshifts.
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- 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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- Ellinghaus, David, et al.
(författare)
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Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
- 2013
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Ingår i: Gastroenterology. - : Elsevier BV. - 0016-5085 .- 1528-0012. ; 145:2, s. 339-347
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND & AIMS: Genome-wide association studies (GWAS) have identified 140 Crohn's disease (CD) susceptibility loci. For most loci, the variants that cause disease are not known and the genes affected by these variants have not been identified. We aimed to identify variants that cause CD through detailed sequencing, genetic association, expression, and functional studies.METHODS: We sequenced whole exomes of 42 unrelated subjects with CD and 5 healthy subjects (controls) and then filtered single nucleotide variants by incorporating association results from meta-analyses of CD GWAS and in silico mutation effect prediction algorithms. We then genotyped 9348 subjects with CD, 2868 subjects with ulcerative colitis, and 14,567 control subjects and associated variants analyzed in functional studies using materials from subjects and controls and in vitro model systems.RESULTS: We identified rare missense mutations in PR domain-containing 1 (PRDM1) and associated these with CD. These mutations increased proliferation of T cells and secretion of cytokines on activation and increased expression of the adhesion molecule L-selectin. A common CD risk allele, identified in GWAS, correlated with reduced expression of PRDM1 in ileal biopsy specimens and peripheral blood mononuclear cells (combined P = 1.6 x 10(-8)). We identified an association between CD and a common missense variant, Val248Ala, in nuclear domain 10 protein 52 (NDP52) (P = 4.83 x 10(-9)). We found that this variant impairs the regulatory functions of NDP52 to inhibit nuclear factor kappa B activation of genes that regulate inflammation and affect the stability of proteins in Toll-like receptor pathways.CONCLUSIONS: We have extended the results of GWAS and provide evidence that variants in PRDM1 and NDP52 determine susceptibility to CD. PRDM1 maps adjacent to a CD interval identified in GWAS and encodes a transcription factor expressed by T and B cells. NDP52 is an adaptor protein that functions in selective autophagy of intracellular bacteria and signaling molecules, supporting the role of autophagy in the pathogenesis of CD.
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- Luo, B., et al.
(författare)
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The Chandra Deep Field-South Survey : 7 Ms Source Catalogs
- 2017
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Ingår i: Astrophysical Journal, Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 228:1
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Tidskriftsartikel (refereegranskat)abstract
- We present X-ray source catalogs for the ≈7 Ms exposure of the Chandra Deep Field-South (CDF-S), which covers a total area of 484.2 arcmin2. Utilizing wavdetect for initial source detection and ACIS Extract for photometric extraction and significance assessment, we create a main source catalog containing 1008 sources that are detected in up to three X-ray bands: 0.5-7.0 keV, 0.5-2.0 keV, and 2-7 keV. A supplementary source catalog is also provided, including 47 lower-significance sources that have bright (Ks ≤ 23) near-infrared counterparts. We identify multiwavelength counterparts for 992 (98.4%) of the main-catalog sources, and we collect redshifts for 986 of these sources, including 653 spectroscopic redshifts and 333 photometric redshifts. Based on the X-ray and multiwavelength properties, we identify 711 active galactic nuclei (AGNs) from the main-catalog sources. Compared to the previous ≈4 Ms CDF-S catalogs, 291 of the main-catalog sources are new detections. We have achieved unprecedented X-ray sensitivity with average flux limits over the central ≈1 arcmin2 region of ≈1.9 ×10-17, 6.4 ×10-18, and 2.7 ×10-17 erg cm-2 s-1 in the three X-ray bands, respectively. We provide cumulative number-count measurements observing, for the first time, that normal galaxies start to dominate the X-ray source population at the faintest 0.5-2.0 keV flux levels. The highest X-ray source density reaches ≈50,500 deg-2, and 47% ± 4% of these sources are AGNs (≈23,900 deg-2).
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- Prusakov, Pavel, et al.
(författare)
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A global point prevalence survey of antimicrobial use in neonatal intensive care units : The no-more-antibiotics and resistance (NO-MAS-R) study
- 2021
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Ingår i: eClinicalMedicine. - : Elsevier. - 2589-5370. ; 32
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Tidskriftsartikel (refereegranskat)abstract
- Background: Global assessment of antimicrobial agents prescribed to infants in the neonatal intensive care unit (NICU) may inform antimicrobial stewardship efforts.Methods: We conducted a one-day global point prevalence study of all antimicrobials provided to NICU infants. Demographic, clinical, and microbiologic data were obtained including NICU level, census, birth weight, gestational/chronologic age, diagnoses, antimicrobial therapy (reason for use; length of therapy), antimicrobial stewardship program (ASP), and 30-day in-hospital mortality.Findings: On July 1, 2019, 26% of infants (580/2,265; range, 0-100%; median gestational age, 33 weeks; median birth weight, 1800 g) in 84 NICUs (51, high-income; 33, low-to-middle income) from 29 countries (14, high-income; 15, low-to-middle income) in five continents received >= 1 antimicrobial agent (92%, antibacterial; 19%, antifungal; 4%, antiviral). The most common reasons for antibiotic therapy were "rule-out" sepsis (32%) and "culture-negative" sepsis (16%) with ampicillin (40%), gentamicin (35%), amikacin (19%), vancomycin (15%), and meropenem (9%) used most frequently. For definitive treatment of presumed/confirmed infection, vancomycin (26%), amikacin (20%), and meropenem (16%) were the most prescribed agents. Length of therapy for culture-positive and "culture-negative" infections was 12 days (median; IQR, 8-14) and 7 days (median; IQR, 5-10), respectively. Mortality was 6% (42%, infection-related). An NICU ASP was associated with lower rate of antibiotic utilization (p = 0.02).Interpretation: Global NICU antibiotic use was frequent and prolonged regardless of culture results. NICU-specific ASPs were associated with lower antibiotic utilization rates, suggesting the need for their implementation worldwide.
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| 13. |
- Trizuljak, Jakub, et al.
(författare)
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Clinical features and survival of patients with indolent systemic mastocytosis defined by the updated WHO classification
- 2020
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Ingår i: Allergy. European Journal of Allergy and Clinical Immunology. - : Wiley. - 0105-4538 .- 1398-9995. ; 75:8, s. 1927-1938
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Tidskriftsartikel (refereegranskat)abstract
- Background: In indolent systemic mastocytosis (ISM), several risk factors of disease progression have been identified. Previous studies, performed with limited patient numbers, have also shown that the clinical course in ISM is stable and comparable to that of cutaneous mastocytosis (CM). The aim of this project was to compare the prognosis of patients with ISM with that of patients with CM.Methods: We employed a dataset of 1993 patients from the registry of the European Competence Network on Mastocytosis (ECNM) to compare outcomes of ISM and CM.Results: We found that overall survival (OS) is worse in ISM compared to CM. Moreover, in patients with typical ISM, bone marrow mastocytosis (BMM), and smoldering SM (SSM), 4.1% of disease progressions have been observed (4.9% of progressions in typical ISM group, 1.7% in BMM, and 9.4% in SSM). Progressions to advanced SM were observed in 2.9% of these patients. In contrast, six patients with CM (1.7%) converted to ISM and no definitive progression to advanced SM was found. No significant differences in OS and event-free survival (EFS) were found when comparing ISM, BMM, and SSM. Higher risk of both progression and death was significantly associated with male gender, worse performance status, and organomegaly.Conclusion: Our data confirm the clinical impact of the WHO classification that separates ISM from CM and from other SM variants.
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| 15. |
- van Rheenen, W, et al.
(författare)
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Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology
- 2021
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 53:12, s. 1636-
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Tidskriftsartikel (refereegranskat)abstract
- Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a lifetime risk of one in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry genome-wide association study (GWAS) including 29,612 patients with ALS and 122,656 controls, which identified 15 risk loci. When combined with 8,953 individuals with whole-genome sequencing (6,538 patients, 2,415 controls) and a large cortex-derived expression quantitative trait locus (eQTL) dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, short tandem repeats or regulatory effects. ALS-associated risk loci were shared with multiple traits within the neurodegenerative spectrum but with distinct enrichment patterns across brain regions and cell types. Of the environmental and lifestyle risk factors obtained from the literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. The combination of all ALS-associated signals reveals a role for perturbations in vesicle-mediated transport and autophagy and provides evidence for cell-autonomous disease initiation in glutamatergic neurons.
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- Vito, F., et al.
(författare)
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High-redshift AGN in the Chandra Deep Fields : The obscured fraction and space density of the sub-L* population
- 2018
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Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 473:2, s. 2378-2406
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the population of high-redshift (3≤z < 6) active galactic nuclei (AGN) selected in the two deepest X-ray surveys, the 7 Ms Chandra Deep Field-South and 2 Ms Chandra Deep Field-North. Their outstanding sensitivity and spectral characterization of faint sources allow us to focus on the sub-L* regime (logLX ≲ 44), poorly sampled by previous works using shallower data, and the obscured population. Taking fully into account the individual photometric-redshift probability distribution functions, the final sample consists of ≈102 X-ray-selected AGN at 3 ≤ z < 6. The fraction of AGN obscured by column densities logNH > 23 is ~0.6-0.8, once incompleteness effects are taken into account, with no strong dependence on redshift or luminosity. We derived the high-redshift AGN number counts down to F0.5-2 keV = 7 × 10-18 erg cm-2 s-1, extending previous results to fainter fluxes, especially at z > 4. We put the tightest constraints to date on the low-luminosity end of AGN luminosity function at high redshift. The space density, in particular, declines at z > 3 at all luminosities, with only a marginally steeper slope for low-luminosity AGN. By comparing the evolution of the AGN and galaxy densities, we suggest that such a decline at high luminosities is mainly driven by the underlying galaxy population, while at low luminosities there are hints of an intrinsic evolution of the parameters driving nuclear activity. Also, the black hole accretion rate density and star formation rate density, which are usually found to evolve similarly at z ≲ 3, appear to diverge at higher redshifts.
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| 18. |
- Vito, F., et al.
(författare)
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The deepest X-ray view of high-redshift galaxies : Constraints on low-rate black hole accretion
- 2016
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Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 463:1, s. 348-374
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Tidskriftsartikel (refereegranskat)abstract
- We exploit the 7 Ms Chandra observations in the Chandra Deep Field-South (CDF-S), the deepest X-ray survey to date, coupled with CANDELS/GOODS-S data, to measure the total X-ray emission arising from 2076 galaxies at 3.5 ≤ z < 6.5. This aim is achieved by stacking the Chandra data at the positions of optically selected galaxies, reaching effective exposure times of ≥109s.We detect significant (>3.7s) X-ray emission from massive galaxies at z ≈ 4. We also report the detection of massive galaxies at z ≈ 5 at a 99.7 per cent confidence level (2.7σ), the highest significance ever obtained for X-ray emission from galaxies at such high redshifts. No significant signal is detected from galaxies at even higher redshifts. The stacking results place constraints on theBHADassociated with the known high-redshift galaxy samples, as well as on the SFRD at high redshift, assuming a range of prescriptions for X-ray emission due to X- ray binaries.We find that the X-ray emission from our sample is likely dominated by processes related to star formation. Our results show that low-rate mass accretion on to SMBHs in individually X-ray-undetected galaxies is negligible, compared with the BHAD measured for samples of X-ray detected AGN, for cosmic SMBH mass assembly at high redshift. We also place, for the first time, constraints on the faint-end of the AGN X-ray luminosity function (logLX ~ 42) at z > 4, with evidence for fairly flat slopes. The implications of all of these findings are discussed in the context of the evolution of the AGN population at high redshift.
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