| 1. |
|
|
| 2. |
- Bravo, L, et al.
(författare)
-
- 2021
-
swepub:Mat__t
|
|
| 3. |
- Tabiri, S, et al.
(författare)
-
- 2021
-
swepub:Mat__t
|
|
| 4. |
- Kanai, M, et al.
(författare)
-
- 2023
-
swepub:Mat__t
|
|
| 5. |
- Glasbey, JC, et al.
(författare)
-
- 2021
-
swepub:Mat__t
|
|
| 6. |
- Niemi, MEK, et al.
(författare)
-
- 2021
-
swepub:Mat__t
|
|
| 7. |
- Campbell, PJ, et al.
(författare)
-
Pan-cancer analysis of whole genomes
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
|
|
| 8. |
|
|
| 9. |
|
|
| 10. |
|
|
| 11. |
- Penston, M. V., et al.
(författare)
-
The extended narrow line region of NGC 4151. I. Emission line ratios and their implications
- 1990
-
Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 236:1, s. 53-6262
-
Tidskriftsartikel (refereegranskat)abstract
- The paper presents the first results from long-slit spectra of the Seyfert galaxy NGC 4151 which give average diagnostic ratios of weak lines in the extended narrow line region (ENLR) of that galaxy and the first direct density measurement in an ENLR. These data confirm that the ENLR is kinematically undisturbed gas in the disc of the galaxy which is illuminated by an ionizing continuum stronger by a factor of 13 than a power law interpolated between observed ultraviolet and X-ray fluxes. Explanations of this apparent excess include a hot thermal continuum, time variations and an anisotropic radiation field. The authors give reasons for favouring anisotropy which might be caused by shadowing by a thick accretion disc or by relativistic beaming. Shadowing by a molecular torus is unlikely, given the absence of an infrared signal from the reradiated flux absorbed by any torus. Anisotropy would have important implications for the bolometric luminosity and nature of active galactic nuclei
|
|
| 12. |
|
|
| 13. |
- Izadi, Z., et al.
(författare)
-
Association Between Tumor Necrosis Factor Inhibitors and the Risk of Hospitalization or Death Among Patients With Immune-Mediated Inflammatory Disease and COVID-19
- 2021
-
Ingår i: Jama Network Open. - : American Medical Association (AMA). - 2574-3805. ; 4:10
-
Tidskriftsartikel (refereegranskat)abstract
- IMPORTANCE Although tumor necrosis factor (TNF) inhibitors are widely prescribed globally because of their ability to ameliorate shared immune pathways across immune-mediated inflammatory diseases (IMIDs), the impact of COVID-19 among individuals with IMIDs who are receiving TNF inhibitors remains insufficiently understood. OBJECTIVE To examine the association between the receipt of TNF inhibitor monotherapy and the risk of COVID-19-associated hospitalization or death compared with other commonly prescribed immunomodulatory treatment regimens among adult patients with IMIDs. DESIGN, SETTING, AND PARTICIPANTS This cohort study was a pooled analysis of data from 3 international COVID-19 registries comprising individuals with rheumatic diseases, inflammatory bowel disease, and psoriasis from March 12, 2020, to February 1, 2021. Clinicians directly reported COVID-19 outcomes as well as demographic and clinical characteristics of individuals with IMIDs and confirmed or suspected COVID-19 using online data entry portals. Adults (age >= 18 years) with a diagnosis of inflammatory arthritis, inflammatory bowel disease, or psoriasis were included. EXPOSURES Treatment exposure categories included TNF inhibitor monotherapy (reference treatment), TNF inhibitors in combination with methotrexate therapy, TNF inhibitors in combination with azathioprine/6-mercaptopurine therapy, methotrexate monotherapy, azathioprine/6-mercaptopurine monotherapy, and Janus kinase (Jak) inhibitor monotherapy. MAIN OUTCOMES AND MEASURES The main outcome was COVID-19-associated hospitalization or death. Registry-level analyses and a pooled analysis of data across the 3 registries were conducted using multilevel multivariable logistic regression models, adjusting for demographic and clinical characteristics and accounting for country, calendar month, and registry-level correlations. RESULTS A total of 6077 patients from 74 countries were included in the analyses; of those, 3215 individuals (52.9%) were from Europe, 3563 individuals (58.6%) were female, and the mean (SD) age was 48.8 (16.5) years. The most common IMID diagnoses were rheumatoid arthritis (2146 patients [35.3%]) and Crohn disease (1537 patients [25.3%]). A total of 1297 patients (21.3%) were hospitalized, and 189 patients (3.1%) died. In the pooled analysis, compared with patients who received TNF inhibitor monotherapy, higher odds of hospitalization or death were observed among those who received a TNF inhibitor in combination with azathioprine/6-mercaptopurine therapy (odds ratio [OR], 1.74; 95% CI, 1.17-2.58; P = .006), azathioprine/6-mercaptopurine monotherapy (OR, 1.84; 95% CI, 1.30-2.61; P = .001), methotrexate monotherapy (OR, 2.00; 95% CI, 1.57-2.56; P < .001), and Jak inhibitor monotherapy (OR, 1.82; 95% CI, 1.21-2.73; P = .004) but not among those who received a TNF inhibitor in combination with methotrexate therapy (OR, 1.18; 95% CI, 0.85-1.63; P = .33). Similar findings were obtained in analyses that accounted for potential reporting bias and sensitivity analyses that excluded patients with a COVID-19 diagnosis based on symptoms alone. CONCLUSIONS AND RELEVANCE In this cohort study, TNF inhibitor monotherapy was associated with a lower risk of adverse COVID-19 outcomes compared with other commonly prescribed immunomodulatory treatment regimens among individuals with IMIDs.
|
|
| 14. |
- Tiegs, Scott D., et al.
(författare)
-
Global patterns and drivers of ecosystem functioning in rivers and riparian zones
- 2019
-
Ingår i: Science Advances. - Washington : American Association of Advancement in Science. - 2375-2548. ; 5:1
-
Tidskriftsartikel (refereegranskat)abstract
- River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.
|
|
| 15. |
- Costello, David M., et al.
(författare)
-
Global patterns and controls of nutrient immobilization on decomposing cellulose in riverine ecosystems
- 2022
-
Ingår i: Global Biogeochemical Cycles. - : John Wiley & Sons. - 0886-6236 .- 1944-9224. ; 36:3
-
Tidskriftsartikel (refereegranskat)abstract
- Microbes play a critical role in plant litter decomposition and influence the fate of carbon in rivers and riparian zones. When decomposing low-nutrient plant litter, microbes acquire nitrogen (N) and phosphorus (P) from the environment (i.e., nutrient immobilization), and this process is potentially sensitive to nutrient loading and changing climate. Nonetheless, environmental controls on immobilization are poorly understood because rates are also influenced by plant litter chemistry, which is coupled to the same environmental factors. Here we used a standardized, low-nutrient organic matter substrate (cotton strips) to quantify nutrient immobilization at 100 paired stream and riparian sites representing 11 biomes worldwide. Immobilization rates varied by three orders of magnitude, were greater in rivers than riparian zones, and were strongly correlated to decomposition rates. In rivers, P immobilization rates were controlled by surface water phosphate concentrations, but N immobilization rates were not related to inorganic N. The N:P of immobilized nutrients was tightly constrained to a molar ratio of 10:1 despite wide variation in surface water N:P. Immobilization rates were temperature-dependent in riparian zones but not related to temperature in rivers. However, in rivers nutrient supply ultimately controlled whether microbes could achieve the maximum expected decomposition rate at a given temperature. Collectively, we demonstrated that exogenous nutrient supply and immobilization are critical control points for decomposition of organic matter.
|
|
| 16. |
- Guimond, S. E., et al.
(författare)
-
Synthetic Heparan Sulfate Mimetic Pixatimod (PG545) Potently Inhibits SARS-CoV-2 by Disrupting the Spike-ACE2 Interaction
- 2022
-
Ingår i: ACS Central Science. - : American Chemical Society (ACS). - 2374-7943 .- 2374-7951. ; 8:5, s. 527-545
-
Tidskriftsartikel (refereegranskat)abstract
- Heparan sulfate (HS) is a cell surface polysaccharide recently identified as a coreceptor with the ACE2 protein for the S1 spike protein on SARS-CoV-2 virus, providing a tractable new therapeutic target. Clinically used heparins demonstrate an inhibitory activity but have an anticoagulant activity and are supply-limited, necessitating alternative solutions. Here, we show that synthetic HS mimetic pixatimod (PG545), a cancer drug candidate, binds and destabilizes the SARS-CoV-2 spike protein receptor binding domain and directly inhibits its binding to ACE2, consistent with molecular modeling identification of multiple molecular contacts and overlapping pixatimod and ACE2 binding sites. Assays with multiple clinical isolates of SARS-CoV-2 virus show that pixatimod potently inhibits the infection of monkey Vero E6 cells and physiologically relevant human bronchial epithelial cells at safe therapeutic concentrations. Pixatimod also retained broad potency against variants of concern (VOC) including B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron). Furthermore, in a K18-hACE2 mouse model, pixatimod significantly reduced SARS-CoV-2 viral titers in the upper respiratory tract and virus-induced weight loss. This demonstration of potent anti-SARS-CoV-2 activity tolerant to emerging mutations establishes proof-of-concept for targeting the HS-Spike protein-ACE2 axis with synthetic HS mimetics and provides a strong rationale for clinical investigation of pixatimod as a potential multimodal therapeutic for COVID-19.
|
|
| 17. |
- Caswell, J. L., et al.
(författare)
-
The 6-GHz methanol multibeam maser catalogue - I. Galactic Centre region, longitudes 345° to 6°
- 2010
-
Ingår i: MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY. - 0035-8711. ; 404:2, s. 1029-1060
-
Tidskriftsartikel (refereegranskat)abstract
- We have conducted a Galactic plane survey of methanol masers at 6668 MHz using a seven-beam receiver on the Parkes telescope. Here we present results from the first part, which provides sensitive unbiased coverage of a large region around the Galactic Centre. Details are given for 183 methanol maser sites in the longitude range 345° through the Galactic Centre to 6°. Within 6° of the Galactic Centre, we found 88 maser sites, of which more than half (48) are new discoveries. The masers are confined to a narrow Galactic latitude range, indicative of many sources at the Galactic Centre distance and beyond, and confined to a thin disc population; there is no high-latitude population that might be ascribed to the Galactic bulge. Within 2° of the Galactic Centre the maser velocities all lie between −60 and +77 km s−1, a range much smaller than the 540 km s−1 range observed in CO. Elsewhere, the maser with highest positive velocity (+107 km s−1) occurs, surprisingly, near longitude 355° and is probably attributable to the Galactic bar. The maser with the most negative velocity (−127 km s−1) is near longitude 346°, within the longitude–velocity locus of the near side of the ‘3-kpc arm’. It has the most extreme velocity of a clear population of masers associated with the near and far sides of the 3-kpc arm. Closer to the Galactic Centre the maser space density is generally low, except within 0.25 kpc of the Galactic Centre itself, the ‘Galactic Centre zone’, where it is 50 times higher, which is hinted at by the longitude distribution, and confirmed by the unusual velocities.
|
|
| 18. |
|
|
| 19. |
|
|
| 20. |
- Kehoe, Laura, et al.
(författare)
-
Make EU trade with Brazil sustainable
- 2019
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
|
|
| 21. |
- Meixner, Margaret, et al.
(författare)
-
Herschel and ALMA measurements of dust and molecules in supernova 1987A
- 2013
-
Ingår i: Proceedings of Science. - 1824-8039. ; Part F113823
-
Konferensbidrag (refereegranskat)abstract
- Dust production by supernovae is important in the dust life cycle of a galaxy. The explosion of SN 1987A was the nearest SN detected in the last 400 years, allowing us detailed studies of contemporary evolution of a supernova for the first time. In 2011, Matsuura et al. reported 0.4-0.7 M of dust in SN 1987A based on Herschel HERITAGE survey data, which is surprisingly large compared to prior measurements of supernovae. In this paper, we present our follow-up studies of this important discovery about SN 1987A using the Herschel Space Observatory and the Atacama Large Millimeter Array (ALMA). We highlight two important results, the detection of cold molecular gas and dust in the ejected material of SN 1987A. Our results suggest that SNe are significant producers of dust and molecules, as well as heavy elements, driving chemical evolution of galaxies.
|
|
| 22. |
- Falster, Daniel, et al.
(författare)
-
AusTraits, a curated plant trait database for the Australian flora
- 2021
-
Ingår i: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
-
Tidskriftsartikel (refereegranskat)abstract
- We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
|
|
| 23. |
- Green, J. A., et al.
(författare)
-
The 6-GHz multibeam maser survey-I. Techniques
- 2009
-
Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 392:2, s. 783-794
-
Tidskriftsartikel (refereegranskat)
|
|
| 24. |
|
|
| 25. |
- Danilovich, T., et al.
(författare)
-
ATOMIUM: halide molecules around the S-type AGB star W Aquilae
- 2021
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 655
-
Tidskriftsartikel (refereegranskat)abstract
- Context. S-type asymptotic giant branch (AGB) stars are thought to be intermediates in the evolution of oxygen- to carbon-rich AGB stars. The chemical compositions of their circumstellar envelopes are also intermediate but have not been studied in as much detail as their carbon- and oxygen-rich counterparts. W Aql is a nearby S-type star, with well-known circumstellar parameters, making it an ideal object for in-depth study of less common molecules. Aims. We aim to determine the abundances of AlCl and AlF from rotational lines, which have been observed for the first time towards an S-type AGB star. In combination with models based on PACS observations, we aim to update our chemical kinetics network based on these results. Methods. We analyse ALMA observations towards W Aql of AlCl in the ground and first two vibrationally excited states and AlF in the ground vibrational state. Using radiative transfer models, we determine the abundances and spatial abundance distributions of (AlCl)-Cl-35, (AlCl)-Cl-37, and AlF. We also model HCl and HF emission and compare these models to PACS spectra to constrain the abundances of these species. Results. AlCl is found in clumps very close to the star, with emission confined within 0 ''.1 of the star. AlF emission is more extended, with faint emission extending 0 ''.2 to 0 ''.6 from the continuum peak. We find peak abundances, relative to H-2, of 1.7 x 10(-7) for (AlCl)-Cl-35, 7 x 10(-8) for (AlCl)-Cl-37, and 1 x 10(-7) for AlF. From the PACS spectra, we find abundances of 9.7 x 10(-8) and <= 10(-8), relative to H-2, for HCl and HF, respectively. Conclusions. The AlF abundance exceeds the solar F abundance, indicating that fluorine synthesised in the AGB star has already been dredged up to the surface of the star and ejected into the circumstellar envelope. From our analysis of chemical reactions in the wind, we conclude that AlF may participate in the dust formation process, but we cannot fully explain the rapid depletion of AlCl seen in the wind.
|
|
