| 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. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 4. |
- Lozano, Rafael, et al.
(författare)
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Measuring progress from 1990 to 2017 and projecting attainment to 2030 of the health-related Sustainable Development Goals for 195 countries and territories: a systematic analysis for the Global Burden of Disease Study 2017
- 2018
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Ingår i: The Lancet. - : Elsevier. - 1474-547X .- 0140-6736. ; 392:10159, s. 2091-2138
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Tidskriftsartikel (refereegranskat)abstract
- Background: Efforts to establish the 2015 baseline and monitor early implementation of the UN Sustainable Development Goals (SDGs) highlight both great potential for and threats to improving health by 2030. To fully deliver on the SDG aim of “leaving no one behind”, it is increasingly important to examine the health-related SDGs beyond national-level estimates. As part of the Global Burden of Diseases, Injuries, and Risk Factors Study 2017 (GBD 2017), we measured progress on 41 of 52 health-related SDG indicators and estimated the health-related SDG index for 195 countries and territories for the period 1990–2017, projected indicators to 2030, and analysed global attainment. Methods: We measured progress on 41 health-related SDG indicators from 1990 to 2017, an increase of four indicators since GBD 2016 (new indicators were health worker density, sexual violence by non-intimate partners, population census status, and prevalence of physical and sexual violence [reported separately]). We also improved the measurement of several previously reported indicators. We constructed national-level estimates and, for a subset of health-related SDGs, examined indicator-level differences by sex and Socio-demographic Index (SDI) quintile. We also did subnational assessments of performance for selected countries. To construct the health-related SDG index, we transformed the value for each indicator on a scale of 0–100, with 0 as the 2·5th percentile and 100 as the 97·5th percentile of 1000 draws calculated from 1990 to 2030, and took the geometric mean of the scaled indicators by target. To generate projections through 2030, we used a forecasting framework that drew estimates from the broader GBD study and used weighted averages of indicator-specific and country-specific annualised rates of change from 1990 to 2017 to inform future estimates. We assessed attainment of indicators with defined targets in two ways: first, using mean values projected for 2030, and then using the probability of attainment in 2030 calculated from 1000 draws. We also did a global attainment analysis of the feasibility of attaining SDG targets on the basis of past trends. Using 2015 global averages of indicators with defined SDG targets, we calculated the global annualised rates of change required from 2015 to 2030 to meet these targets, and then identified in what percentiles the required global annualised rates of change fell in the distribution of country-level rates of change from 1990 to 2015. We took the mean of these global percentile values across indicators and applied the past rate of change at this mean global percentile to all health-related SDG indicators, irrespective of target definition, to estimate the equivalent 2030 global average value and percentage change from 2015 to 2030 for each indicator. Findings: The global median health-related SDG index in 2017 was 59·4 (IQR 35·4–67·3), ranging from a low of 11·6 (95% uncertainty interval 9·6–14·0) to a high of 84·9 (83·1–86·7). SDG index values in countries assessed at the subnational level varied substantially, particularly in China and India, although scores in Japan and the UK were more homogeneous. Indicators also varied by SDI quintile and sex, with males having worse outcomes than females for non-communicable disease (NCD) mortality, alcohol use, and smoking, among others. Most countries were projected to have a higher health-related SDG index in 2030 than in 2017, while country-level probabilities of attainment by 2030 varied widely by indicator. Under-5 mortality, neonatal mortality, maternal mortality ratio, and malaria indicators had the most countries with at least 95% probability of target attainment. Other indicators, including NCD mortality and suicide mortality, had no countries projected to meet corresponding SDG targets on the basis of projected mean values for 2030 but showed some probability of attainment by 2030. For some indicators, including child malnutrition, several infectious diseases, and most violence measures, the annualised rates of change required to meet SDG targets far exceeded the pace of progress achieved by any country in the recent past. We found that applying the mean global annualised rate of change to indicators without defined targets would equate to about 19% and 22% reductions in global smoking and alcohol consumption, respectively; a 47% decline in adolescent birth rates; and a more than 85% increase in health worker density per 1000 population by 2030. Interpretation: The GBD study offers a unique, robust platform for monitoring the health-related SDGs across demographic and geographic dimensions. Our findings underscore the importance of increased collection and analysis of disaggregated data and highlight where more deliberate design or targeting of interventions could accelerate progress in attaining the SDGs. Current projections show that many health-related SDG indicators, NCDs, NCD-related risks, and violence-related indicators will require a concerted shift away from what might have driven past gains—curative interventions in the case of NCDs—towards multisectoral, prevention-oriented policy action and investments to achieve SDG aims. Notably, several targets, if they are to be met by 2030, demand a pace of progress that no country has achieved in the recent past. The future is fundamentally uncertain, and no model can fully predict what breakthroughs or events might alter the course of the SDGs. What is clear is that our actions—or inaction—today will ultimately dictate how close the world, collectively, can get to leaving no one behind by 2030.
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| 5. |
- Yang, Jun, 1979, et al.
(författare)
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A parsec-scale faint jet in the nearby changing-look Seyfert galaxy Mrk 590
- 2021
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Ingår i: Monthly Notices of the Royal Astronomical Society: Letters. - : Oxford University Press (OUP). - 1745-3925 .- 1745-3933. ; 502:1, s. L61-L65
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Tidskriftsartikel (refereegranskat)abstract
- Broad Balmer emission lines in active galactic nuclei (AGN) may display dramatic changes in amplitude, even disappearance and re-appearance in some sources. As a nearby galaxy at a redshift of z = 0.0264, Mrk 590 suffered such a cycle of Seyfert type changes between 2006 and 2017. Over the last 50 yr, Mrk 590 also underwent a powerful continuum outburst and a slow fading from X-rays to radio wavelengths with a peak bolometric luminosity reaching about 10 per cent of the Eddington luminosity. To track its past accretion and ejection activity, we performed very long baseline interferometry (VLBI) observations with the European VLBI Network (EVN) at 1.6 GHz in 2015. The EVN observations reveal a faint (∼1.7 mJy) radio jet extending up to ∼2.8 mas (projected scale ∼1.4 pc) toward north, and probably resulting from the very intensive AGN activity. To date, such a parsec-scale jet is rarely seen in the known changing-look AGN. The finding of the faint jet provides further strong support for variable accretion as the origin of the type changes in Mrk 590.
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| 6. |
- Yang, Jun, 1979, et al.
(författare)
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Structural and spectral properties of Galactic plane variable radio sources
- 2022
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Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 511:1, s. 280-294
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Tidskriftsartikel (refereegranskat)abstract
- In the time domain, the radio sky in particular along the Galactic plane direction may vary significantly because of various energetic activities associated with stars, stellar, and supermassive black holes. Multi-epoch Very Large Array surveys of the Galactic plane at 5.0 GHz enabled the finding of a catalogue of 39 variable radio sources in the flux density range 1-70 mJy. To probe their radio structures and spectra, we observed 17 sources with the very-long-baseline interferometric (VLBI) imaging technique and collected additional multifrequency data from the literature. We detected all of the sources at 5 GHz with the Westerbork Synthesis Radio Telescope, but only G23.6644-0.0372 with the European VLBI Network (EVN). Together with its decadal variability and multifrequency radio spectrum, we interpret it as an extragalactic peaked-spectrum source with a size of less than or similar to 10 pc. The remaining sources were resolved out by the long baselines of the EVN because of either strong scatter broadening at the Galactic latitude < 1 degrees or intrinsically very extended structures on centi-arcsec scales. According to their spectral and structural properties, we find that the sample has a diverse nature. We notice two young H ii regions and spot a radio star and a candidate planetary nebula. The rest of the sources are very likely associated with radio active galactic nuclei (AGNs). Two of them also display arcsec-scale faint jet activity. The sample study indicates that AGNs are common place even among variable radio sources in the Galactic plane.
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| 7. |
- Yang, Xiaolong, et al.
(författare)
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Extended Catalog of Winged or X-shaped Radio Sources from the FIRST Survey
- 2019
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Ingår i: Astrophysical Journal, Supplement Series. - : American Astronomical Society. - 1538-4365 .- 0067-0049. ; 245:1
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Tidskriftsartikel (refereegranskat)abstract
- We present a catalog of 290 ?winged? or X-shaped radio galaxies (XRGs) extracted from the latest (2014 December 17) data release of the ?Very Large Array Faint Images of the Radio Sky at Twenty centimeter.? We have combined these radio images with their counterparts in the TIFR GMRT sky survey at 150 MHz, in an attempt to identify any low surface brightness radio emission present in these sources. This has enabled us to assemble a sample of 106 ?strong? XRG candidates and 184 ?probable? XRG candidates whose XRG designation needs to be verified by further observations. The present sample of 290 XRG candidates is almost twice as large as the number of XRGs currently known. Twenty-five of our 290 XRG candidates (9 ?strong? and 16 ?probable?) are identified as quasars. Double-peaked narrow emission lines are seen in the optical spectra of three of the XRG candidates (two ?strong? and one ?probable?). Nearly 90% of the sample is located in the FR II domain of the Owen?Ledlow diagram. A few of the strong XRG candidates have a rather flat radio spectrum (spectral index ? flatter than ?0.3) between 150 MHz and 1.4 GHz, or between 1.4 and 5 GHz. Since this is not expected for lobe-dominated extragalactic radio sources (like nearly all known XRGs), these sources are particularly suited for follow-up radio imaging and near-simultaneous measurement of the radio spectrum.
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| 8. |
- Yang, Xiaolong, et al.
(författare)
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Radio Activity of Supermassive Black Holes with Extremely High Accretion Rates
- 2020
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 904:2
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Tidskriftsartikel (refereegranskat)abstract
- Radio emission from the high- A nd super-Eddington accreting active galactic nuclei (AGNs) has various origins: A persistent jet, the magnetized corona, and the wind-like outflows. It is still unclear which is the leading mechanism responsible for the observed radio emission and how the radio emission is related to other characteristic parameters such as the Eddington ratio and black hole mass. In this paper, we present the 5 GHz Very Large Array (VLA) observational results of a sample of 25 extremely high Eddington accreting supermassive black holes (EESBHs, the Eddington ratio λ Edd close to or above 1) in narrow-line Seyfert 1 galaxies, among which 22 sources are detected. Most of the EESBHs show a compact radio structure from a few hundred parsecs to 1 kpc scale. We estimated the lowest star formation rate surface density required for producing the observed radio emission and found that it is higher than the largest value previously detected in circumnuclear starburst galaxies, implying that the radio emission is from the AGN activity. Along with a comparison sample, we find an overall inverse-λ Edd correlation ranging from sub-to super-Eddington ratios. The high-Eddington and mildly super-Eddington AGNs (-0.5 < log) have a radio-to-X-ray luminosity ratio L R/L X ∼ 10-5-10-4 and a steep radio spectrum, supporting that the radio emission is from transient ejecta (outflows) of corona; however, the jet contribution cannot be entirely ruled out. Our highly super-Eddington sources (log) have a flatter radio spectrum, along with its low radio luminosity: ; their radio emission is likely dominated by a magnetized corona, and a radiation-pressure-caused jet is also proposed in this paper.
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| 9. |
- Yang, Xiaolong, et al.
(författare)
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Radio Observations of Four Active Galactic Nuclei Hosting Intermediate-mass Black Hole Candidates: Studying the Outflow Activity and Evolution
- 2022
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 941:1
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Tidskriftsartikel (refereegranskat)abstract
- Observational searches for intermediate-mass black holes (IMBHs; 102-106 M ⊙) include relatively isolated dwarf galaxies. For those that host active galactic nuclei (AGNs), the IMBH nature may be discerned through the accretion-jet activity. We present radio observations of four AGN-hosting dwarf galaxies, which potentially harbor IMBHs. Very large array (VLA) observations indicate steep spectra (indices of −0.63 to −1.05) between 1.4 and 9 GHz. However, a comparison with the 9 GHz in-band spectral index shows a steepening for GH047 and GH158 (implying older/relic emission) and flattening for GH106 and GH163 (implying recent activity). Overlapping emission regions in the VLA 1.4 GHz and our very long baseline array (VLBA) 1.5 GHz observations, and possibly symmetric pc-scale extensions, are consistent with recent activity in the latter two. Using the compact VLBA radio luminosity, X-ray luminosity (probing the accretion activity), and the black hole masses, all AGNs are found to lie on the empirical fundamental plane relation. The four AGNs are radio-quiet with relatively higher Eddington ratios (0.04-0.32) and resemble X-ray binaries during spectral state transitions that entail an outflow ejection. Furthermore, the radio to X-ray luminosity ratio log R X of −3.9 to −5.6 in these four sources support the scenarios that include corona mass ejection from the accretion disk and wind activity. The growth to kpc-scales likely proceeds along a similar trajectory to young AGNs and peaked spectrum sources. These complex clues can thus aid in the detection and monitoring of IMBHs in the nearby universe.
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| 10. |
- Agudo, I., et al.
(författare)
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Panning for gold, but finding helium: Discovery of the ultra-stripped supernova SN 2019wxt from gravitational-wave follow-up observations
- 2023
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 675
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Tidskriftsartikel (refereegranskat)abstract
- We present the results from multi-wavelength observations of a transient discovered during an intensive follow-up campaign of S191213g, a gravitational wave (GW) event reported by the LIGO-Virgo Collaboration as a possible binary neutron star merger in a low latency search. This search yielded SN 2019wxt, a young transient in a galaxy whose sky position (in the 80% GW contour) and distance (∼150 Mpc) were plausibly compatible with the localisation uncertainty of the GW event. Initially, the transienta's tightly constrained age, its relatively faint peak magnitude (Mi ∼ -16.7 mag), and the r-band decline rate of ∼1 mag per 5 days appeared suggestive of a compact binary merger. However, SN 2019wxt spectroscopically resembled a type Ib supernova, and analysis of the optical-near-infrared evolution rapidly led to the conclusion that while it could not be associated with S191213g, it nevertheless represented an extreme outcome of stellar evolution. By modelling the light curve, we estimated an ejecta mass of only ∼0.1 M·, with 56Ni comprising ∼20% of this. We were broadly able to reproduce its spectral evolution with a composition dominated by helium and oxygen, with trace amounts of calcium. We considered various progenitor channels that could give rise to the observed properties of SN 2019wxt and concluded that an ultra-stripped origin in a binary system is the most likely explanation. Disentangling genuine electromagnetic counterparts to GW events from transients such as SN 2019wxt soon after discovery is challenging: in a bid to characterise this level of contamination, we estimated the rate of events with a volumetric rate density comparable to that of SN 2019wxt and found that around one such event per week can occur within the typical GW localisation area of O4 alerts out to a luminosity distance of 500 Mpc, beyond which it would become fainter than the typical depth of current electromagnetic follow-up campaigns.
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