| 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. |
- Purdum, Josiah N., et al.
(författare)
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Time-series and Phase-curve Photometry of the Episodically Active Asteroid (6478) Gault in a Quiescent State Using APO, GROWTH, P200, and ZTF
- 2021
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Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 911:2
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Tidskriftsartikel (refereegranskat)abstract
- We observed the episodically active asteroid (6478) Gault in 2020 with multiple telescopes in Asia and North America and found that it is no longer active after its recent outbursts at the end of 2018 and the start of 2019. The inactivity during this apparition allowed us to measure the absolute magnitude of Gault of H ( r ) = 14.63 +/- 0.02, G ( r ) = 0.21 +/- 0.02 from our secular phase-curve observations. In addition, we were able to constrain Gault's rotation period using time-series photometric lightcurves taken over 17 hr on multiple days in 2020 August, September, and October. The photometric lightcurves have a repeating less than or similar to 0.05 mag feature suggesting that (6478) Gault has a rotation period of similar to 2.5 hr and may have a semispherical or top-like shape, much like the near-Earth asteroids Ryugu and Bennu. The rotation period of similar to 2.5 hr is near the expected critical rotation period for an asteroid with the physical properties of (6478) Gault, suggesting that its activity observed over multiple epochs is due to surface mass shedding from its fast rotation spin-up by the Yarkovsky-O'Keefe-Radzievskii-Paddack effect.
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| 3. |
- Chen, Ping, et al.
(författare)
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A 12.4-day periodicity in a close binary system after a supernova
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625:7994, s. 253-258
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Tidskriftsartikel (refereegranskat)abstract
- Neutron stars and stellar-mass black holes are the remnants of massive star explosions1. Most massive stars reside in close binary systems2, and the interplay between the companion star and the newly formed compact object has been theoretically explored3, but signatures for binarity or evidence for the formation of a compact object during a supernova explosion are still lacking. Here we report a stripped-envelope supernova, SN 2022jli, which shows 12.4-day periodic undulations during the declining light curve. Narrow Hα emission is detected in late-time spectra with concordant periodic velocity shifts, probably arising from hydrogen gas stripped from a companion and accreted onto the compact remnant. A new Fermi-LAT γ-ray source is temporally and positionally consistent with SN 2022jli. The observed properties of SN 2022jli, including periodic undulations in the optical light curve, coherent Hα emission shifting and evidence for association with a γ-ray source, point to the explosion of a massive star in a binary system leaving behind a bound compact remnant. Mass accretion from the companion star onto the compact object powers the light curve of the supernova and generates the γ-ray emission.
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| 4. |
- Chen, Zhishan, et al.
(författare)
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Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
- 2024
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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| 5. |
- Das, Kaustav K., et al.
(författare)
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Probing the Low-mass End of Core-collapse Supernovae Using a Sample of Strongly-stripped Calcium-rich Type IIb Supernovae from the Zwicky Transient Facility
- 2023
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 959:1
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Tidskriftsartikel (refereegranskat)abstract
- The fate of stars in the zero-age main-sequence (ZAMS) range ≈8–12 M⊙ is unclear. They could evolve to form white dwarfs or explode as electron-capture supernovae (SNe) or iron core-collapse SNe (CCSNe). Even though the initial mass function indicates that this mass range should account for over 40% of all CCSN progenitors, few have been observationally confirmed, likely due to the faintness and rapid evolution of some of these transients. In this paper, we present a sample of nine Ca-rich/O-poor Type IIb SNe detected by the Zwicky Transient Facility with progenitors likely in this mass range. These sources have a [Ca ii] λλ7291, 7324/[O i] λλ6300, 6364 flux ratio of ≳2 in their nebular spectra. Comparing the measured [O i] luminosity (≲1039 erg s−1) and derived oxygen mass (≈0.01 M⊙) with theoretical models, we infer that the progenitor ZAMS mass for these explosions is less than 12 M⊙. The ejecta properties (Mej ≲ 1 M⊙ and Ekin ∼ 1050 erg) are also consistent. The low ejecta mass of these sources indicates a class of strongly-stripped SNe that is a transition between the regular stripped-envelope SNe and ultra-stripped SNe. The progenitor could be stripped by a main-sequence companion and result in the formation of a neutron star−main sequence binary. Such binaries have been suggested to be progenitors of neutron star−white dwarf systems that could merge within a Hubble time and be detectable with LISA.
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| 6. |
- De, Kishalay, et al.
(författare)
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The Zwicky Transient Facility Census of the Local Universe. I. Systematic Search for Calcium-rich Gap Transients Reveals Three Related Spectroscopic Subclasses
- 2020
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 905:1
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Tidskriftsartikel (refereegranskat)abstract
- Using the Zwicky Transient Facility alert stream, we are conducting a large spectroscopic campaign to construct a complete, volume-limited sample of transients brighter than 20 mag, and coincident within 100 '' of galaxies in the Census of the Local Universe catalog. We describe the experiment design and spectroscopic completeness from the first 16 months of operations, which have classified 754 supernovae. We present results from a systematic search for calcium-rich gap transients in the sample of 22 low-luminosity (peak absolute magnitude M > -17), hydrogen-poor events found in the experiment. We report the detection of eight new events, and constrain their volumetric rate to greater than or similar to 15% +/- 5% of the SN Ia rate. Combining this sample with 10 previously known events, we find a likely continuum of spectroscopic properties ranging from events with SN Ia-like features (Ca-Ia objects) to those with SN Ib/c-like features (Ca-Ib/c objects) at peak light. Within the Ca-Ib/c events, we find two populations distinguished by their red (g - r approximate to 1.5 mag) or green (g - r approximate to 0.5 mag) colors at the r-band peak, wherein redder events show strong line blanketing features and slower light curves (similar to Ca-Ia objects), weaker He lines, and lower [Ca II]/[O I] in the nebular phase. We find that all together the spectroscopic continuum, volumetric rates, and striking old environments are consistent with the explosive burning of He shells on low-mass white dwarfs. We suggest that Ca-Ia and red Ca-Ib/c objects arise from the double detonation of He shells, while green Ca-Ib/c objects are consistent with low-efficiency burning scenarios like detonations in low-density shells or deflagrations.
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| 7. |
- Feng, Zhiwei, et al.
(författare)
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On the scheduling of fault-tolerant time-sensitive networking with IEEE 802.1CB
- 2024
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Ingår i: IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. - : Institute of Electrical and Electronics Engineers (IEEE). - 0278-0070 .- 1937-4151. ; 43:6, s. 1715-1728
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Tidskriftsartikel (refereegranskat)abstract
- Time-sensitive networking (TSN) has become the most popular technique in modern safety-critical automotive and industrial automation networks by providing deterministic transmission policies. However, the data of TSN messages may be affected by transient faults. IEEE 802.1CB, a reliability standard in TSN, protects against such faults by providing disjoint redundant routes for each stream. However, the unique assumption may present a new challenge, i.e., an inadequate number of redundant routes that may negatively impact stream scheduling. This article presents an offline fault-tolerant TSN scheduling approach that considers such impacts for real-time streams (such as time-trigger (TT) and audio video bridging (AVB) streams). Specifically, we intend to calculate the minimum upper bound number of disjoint routes required for each stream to meet the reliability requirements, subsequently enhancing the network's schedulability. We also propose a service degradation function for AVB streams when the network is under heavy load caused by redundant transmissions of TT streams. This function will maintain schedulability and reliability for AVB streams. Experiments with small- and large-scale synthetic networks show the efficiency.
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| 8. |
- Hammerstein, Erica, et al.
(författare)
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The Final Season Reimagined : 30 Tidal Disruption Events from the ZTF-I Survey
- 2023
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 942:1
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Tidskriftsartikel (refereegranskat)abstract
- Tidal disruption events (TDEs) offer a unique way to study dormant black holes. While the number of observed TDEs has grown thanks to the emergence of wide-field surveys in the past few decades, questions regarding the nature of the observed optical, UV, and X-ray emission remain. We present a uniformly selected sample of 30 spectroscopically classified TDEs from the Zwicky Transient Facility Phase I survey operations with follow-up Swift UV and X-ray observations. Through our investigation into correlations between light-curve properties, we recover a shallow positive correlation between the peak bolometric luminosity and decay timescales. We introduce a new spectroscopic class of TDE, TDE-featureless, which are characterized by featureless optical spectra. The new TDE-featureless class shows larger peak bolometric luminosities, peak blackbody temperatures, and peak blackbody radii. We examine the differences between the X-ray bright and X-ray faint populations of TDEs in this sample, finding that X-ray bright TDEs show higher peak blackbody luminosities than the X-ray faint subsample. This sample of optically selected TDEs is the largest sample of TDEs from a single survey yet, and the systematic discovery, classification, and follow-up of this sample allows for robust characterization of TDE properties, an important stepping stone looking forward toward the Rubin era.
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| 9. |
- Labadie, Julia D., et al.
(författare)
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Genome-wide association study identifies tumor anatomical site-specific risk variants for colorectal cancer survival
- 2022
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Identification of new genetic markers may improve the prediction of colorectal cancer prognosis. Our objective was to examine genome-wide associations of germline genetic variants with disease-specific survival in an analysis of 16,964 cases of colorectal cancer. We analyzed genotype and colorectal cancer-specific survival data from a consortium of 15 studies. Approximately 7.5 million SNPs were examined under the log-additive model using Cox proportional hazards models, adjusting for clinical factors and principal components. Additionally, we ran secondary analyses stratifying by tumor site and disease stage. We used a genome-wide p-value threshold of 5 × 10–8 to assess statistical significance. No variants were statistically significantly associated with disease-specific survival in the full case analysis or in the stage-stratified analyses. Three SNPs were statistically significantly associated with disease-specific survival for cases with tumors located in the distal colon (rs698022, HR = 1.48, CI 1.30–1.69, p = 8.47 × 10–9) and the proximal colon (rs189655236, HR = 2.14, 95% CI 1.65–2.77, p = 9.19 × 10–9 and rs144717887, HR = 2.01, 95% CI 1.57–2.58, p = 3.14 × 10–8), whereas no associations were detected for rectal tumors. Findings from this large genome-wide association study highlight the potential for anatomical-site-stratified genome-wide studies to identify germline genetic risk variants associated with colorectal cancer-specific survival. Larger sample sizes and further replication efforts are needed to more fully interpret these findings.
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| 10. |
- Lunnan, Ragnhild, et al.
(författare)
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Four (Super)luminous Supernovae from the First Months of the ZTF Survey
- 2020
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 901:1
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Tidskriftsartikel (refereegranskat)abstract
- We present photometry and spectroscopy of four hydrogen-poor luminous supernovae discovered during the 2-month long science commissioning and early operations of the Zwicky Transient Facility (ZTF) survey. Three of these objects, SN 2018bym (ZTF18aapgrxo), SN 2018avk (ZTF18aaisyyp), and SN 2018bgv (ZTF18aavrmcg), resemble typical SLSN-I spectroscopically, while SN 2018don (ZTF18aajqcue) may be an object similar to SN 2007bi experiencing considerable host galaxy reddening, or an intrinsically long-lived, luminous, and red SN Ic. We analyze the light curves, spectra, and host galaxy properties of these four objects and put them in context of the population of SLSN-I. SN 2018bgv stands out as the fastest-rising SLSN-I observed to date, with a rest-frame g-band rise time of just 10 days from explosion to peak—if it is powered by magnetar spin-down, the implied ejecta mass is only 1 M ⊙. SN 2018don also displays unusual properties—in addition to its red colors and comparatively massive host galaxy, the light curve undergoes some of the strongest light-curve undulations postpeak seen in an SLSN-I, which we speculate may be due to interaction with circumstellar material. We discuss the promises and challenges of finding SLSNe in large-scale surveys like ZTF given the observed diversity in the population.
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