| 1. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
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.
|
|
| 2. |
- Kim, Jae-Young, et al.
(författare)
-
Event Horizon Telescope imaging of the archetypal blazar 3C 279 at an extreme 20 microarcsecond resolution
- 2020
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 640
-
Tidskriftsartikel (refereegranskat)abstract
- 3C 279 is an archetypal blazar with a prominent radio jet that show broadband flux density variability across the entire electromagnetic spectrum. We use an ultra-high angular resolution technique - global Very Long Baseline Interferometry (VLBI) at 1.3mm (230 GHz) - to resolve the innermost jet of 3C 279 in order to study its fine-scale morphology close to the jet base where highly variable-ray emission is thought to originate, according to various models. The source was observed during four days in April 2017 with the Event Horizon Telescope at 230 GHz, including the phased Atacama Large Millimeter/submillimeter Array, at an angular resolution of ∼20 μas (at a redshift of z = 0:536 this corresponds to ∼0:13 pc ∼ 1700 Schwarzschild radii with a black hole mass MBH = 8 × 108 M⊙). Imaging and model-fitting techniques were applied to the data to parameterize the fine-scale source structure and its variation.We find a multicomponent inner jet morphology with the northernmost component elongated perpendicular to the direction of the jet, as imaged at longer wavelengths. The elongated nuclear structure is consistent on all four observing days and across diffierent imaging methods and model-fitting techniques, and therefore appears robust. Owing to its compactness and brightness, we associate the northern nuclear structure as the VLBI "core". This morphology can be interpreted as either a broad resolved jet base or a spatially bent jet.We also find significant day-to-day variations in the closure phases, which appear most pronounced on the triangles with the longest baselines. Our analysis shows that this variation is related to a systematic change of the source structure. Two inner jet components move non-radially at apparent speeds of ∼15 c and ∼20 c (∼1:3 and ∼1:7 μas day-1, respectively), which more strongly supports the scenario of traveling shocks or instabilities in a bent, possibly rotating jet. The observed apparent speeds are also coincident with the 3C 279 large-scale jet kinematics observed at longer (cm) wavelengths, suggesting no significant jet acceleration between the 1.3mm core and the outer jet. The intrinsic brightness temperature of the jet components are ≤1010 K, a magnitude or more lower than typical values seen at ≥7mm wavelengths. The low brightness temperature and morphological complexity suggest that the core region of 3C 279 becomes optically thin at short (mm) wavelengths.
|
|
| 3. |
|
|
| 4. |
- Abolfathi, Bela, et al.
(författare)
-
The LSST DESC DC2 Simulated Sky Survey
- 2021
-
Ingår i: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 253:31
-
Tidskriftsartikel (refereegranskat)abstract
- We describe the simulated sky survey underlying the second data challenge (DC2) carried out in preparation for analysis of the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) by the LSST Dark Energy Science Collaboration (LSST DESC). Significant connections across multiple science domains will be a hallmark of LSST; the DC2 program represents a unique modeling effort that stresses this interconnectivity in a way that has not been attempted before. This effort encompasses a full end-to-end approach: starting from a large N-body simulation, through setting up LSST-like observations including realistic cadences, through image simulations, and finally processing with Rubin's LSST Science Pipelines. This last step ensures that we generate data products resembling those to be delivered by the Rubin Observatory as closely as is currently possible. The simulated DC2 sky survey covers six optical bands in a wide-fast-deep area of approximately 300 deg2, as well as a deep drilling field of approximately 1 deg2. We simulate 5 yr of the planned 10 yr survey. The DC2 sky survey has multiple purposes. First, the LSST DESC working groups can use the data set to develop a range of DESC analysis pipelines to prepare for the advent of actual data. Second, it serves as a realistic test bed for the image processing software under development for LSST by the Rubin Observatory. In particular, simulated data provide a controlled way to investigate certain image-level systematic effects. Finally, the DC2 sky survey enables the exploration of new scientific ideas in both static and time domain cosmology.
|
|
| 5. |
- Afshari, Kevin, et al.
(författare)
-
Risk factors for developing Anorectal dysfunction after Anterior Resection
- 2021
-
Ingår i: International Journal of Colorectal Disease. - : Springer Nature. - 0179-1958 .- 1432-1262. ; 36:12, s. 2697-2705
-
Tidskriftsartikel (refereegranskat)abstract
- Anterior resection (AR) may result in defecatory dysfunction and the cause is multifactorial. The aim was to explore if dysfunction could be related to the part of the colon used for anastomosis (sigmoid or descending) and to identify other possible risk factors for bowel dysfunction after AR.This is a retrospective study based on prospectively registered data from a regional registry at the surgical department in Västmanland 1996–2019. Bowel function was registered at 1 year after AR or after stoma reversal. In total, 470 stage I–III rectal cancer patients had AR whereof 412 were included in this study.Clustering was seen in 57%, incontinence 29%, urgency 22%, and evacuatory dysfunction 16%. The part of the colon used for anastomosis, level of vascular tie, and gender were not significantly associated with defecatory dysfunction. The higher the anastomotic level, the lower the risk of incontinence (OR 0.75; CI 0.63–0.90; p < 0.001) and clustering (OR 0.78; CI 0.67–0.90; p < 0.001). Compared with patients without a loop-ileostomy, an increased risk of clustering (OR 1.89; 1.08–3.31; p = 0.03), incontinence (OR 2.48; 1.29–4.77; p < 0.01), and urgency (OR 4.61; CI 2.02–10.60; p < 0.001) was seen after loop-ileostomy closure. Preoperative radiotherapy had a negative impact on continence and clustering seen mainly in the unadjusted analysis.The part of the colon used for anastomosis was not a significantly associated functional outcome after anterior resection. Low anastomotic level and having had a diverting ileostomy were independent risk factors associated with negative functional outcomes.
|
|
| 6. |
- Ahearn, Thomas U., et al.
(författare)
-
Common variants in breast cancer risk loci predispose to distinct tumor subtypes
- 2022
-
Ingår i: Breast Cancer Research. - : Springer Nature. - 1465-5411 .- 1465-542X. ; 24:1
-
Tidskriftsartikel (refereegranskat)abstract
- BackgroundGenome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear.MethodsAmong 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes.ResultsEighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions.ConclusionThis report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.
|
|
| 7. |
- Akiyama, Kazunori, et al.
(författare)
-
First Sagittarius A* Event Horizon Telescope Results. II. EHT and Multiwavelength Observations, Data Processing, and Calibration
- 2022
-
Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 930:2
-
Tidskriftsartikel (refereegranskat)abstract
- We present Event Horizon Telescope (EHT) 1.3 mm measurements of the radio source located at the position of the supermassive black hole Sagittarius A* (Sgr A*), collected during the 2017 April 5-11 campaign. The observations were carried out with eight facilities at six locations across the globe. Novel calibration methods are employed to account for Sgr A*'s flux variability. The majority of the 1.3 mm emission arises from horizon scales, where intrinsic structural source variability is detected on timescales of minutes to hours. The effects of interstellar scattering on the image and its variability are found to be subdominant to intrinsic source structure. The calibrated visibility amplitudes, particularly the locations of the visibility minima, are broadly consistent with a blurred ring with a diameter of similar to 50 mu as, as determined in later works in this series. Contemporaneous multiwavelength monitoring of Sgr A* was performed at 22, 43, and 86 GHz and at near-infrared and X-ray wavelengths. Several X-ray flares from Sgr A* are detected by Chandra, one at low significance jointly with Swift on 2017 April 7 and the other at higher significance jointly with NuSTAR on 2017 April 11. The brighter April 11 flare is not observed simultaneously by the EHT but is followed by a significant increase in millimeter flux variability immediately after the X-ray outburst, indicating a likely connection in the emission physics near the event horizon. We compare Sgr A*'s broadband flux during the EHT campaign to its historical spectral energy distribution and find that both the quiescent emission and flare emission are consistent with its long-term behavior.
|
|
| 8. |
- Cashman, Kevin D., et al.
(författare)
-
Individual participant data (IPD)-level meta-analysis of randomised controlled trials with vitamin D-fortified foods to estimate Dietary Reference Values for vitamin D
- 2021
-
Ingår i: European Journal of Nutrition. - : Springer Berlin/Heidelberg. - 1436-6207 .- 1436-6215. ; 60:2, s. 939-959
-
Tidskriftsartikel (refereegranskat)abstract
- Context and purpose: Individual participant data-level meta-regression (IPD) analysis is superior to meta-regression based on aggregate data in determining Dietary Reference Values (DRV) for vitamin D. Using data from randomized controlled trials (RCTs) with vitamin D3-fortified foods, we undertook an IPD analysis of the response of winter serum 25-hydroxyvitamin (25(OH)D) to total vitamin D intake among children and adults and derived DRV for vitamin D.Methods: IPD analysis using data from 1429 participants (ages 2–89 years) in 11 RCTs with vitamin D-fortified foods identified via a systematic review and predefined eligibility criteria. Outcome measures were vitamin D DRV estimates across a range of serum 25(OH)D thresholds using unadjusted and adjusted models.Results: Our IPD-derived estimates of vitamin D intakes required to maintain 97.5% of winter 25(OH)D concentrations ≥ 25 and ≥ 30 nmol/L are 6 and 12 µg/day, respectively (unadjusted model). The intake estimates to maintain 90%, 95% and 97.5% of concentrations ≥ 50 nmol/L are 33.4, 57.5 and 92.3 µg/day, respectively (unadjusted) and 17.0, 28.1 and 43.6 µg/day, respectively (adjusted for mean values for baseline serum 25(OH)D, age and BMI).Conclusions: IPD-derived vitamin D intakes required to maintain 90%, 95% and 97.5% of winter 25(OH)D concentrations ≥ 50 nmol/L are much higher than those derived from standard meta-regression based on aggregate data, due to the inability of the latter to capture between person-variability. Our IPD provides further evidence that using food-based approaches to achieve an intake of 12 µg/day could prevent vitamin D deficiency (i.e., serum 25(OH)D < 30 nmol/L) in the general population.
|
|
| 9. |
- Chilcote, Jeffrey, et al.
(författare)
-
SCExAO/CHARIS Direct Imaging of A Low-mass Companion At A Saturn-like Separation from an Accelerating Young A7 Star
- 2021
-
Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 162:6
-
Tidskriftsartikel (refereegranskat)abstract
- We present the SCExAO direct imaging discovery and characterization of a low-mass companion to the nearby young A7IV star, HD 91312. SCExAO/CHARIS JHK (1.1–2.4 μm) spectra and SCExAO/HiCIAO H-band imaging identify the companion over a two year baseline in a highly inclined orbit with a maximum projected separation of 8 au. The companion, HD 91312 B, induces an 8.8σ astrometric acceleration on the star as seen with the Gaia & Hipparcos satellites and a long-term radial-velocity trend as previously identified by Borgniet et al. HD 91312 B's spectrum is consistent with that of an early-to-mid M dwarf. Hipparcos and Gaia absolute astrometry, radial-velocity data, and SCExAO/CHARIS astrometry constrain its dynamical mass to be 0.337-0.044+0.042 M⊙, consistent with - but far more precise than - masses derived from spectroscopy, and favors a nearly edge-on orbit with a semimajor axis of ∼9.7 au. This work is an example of precisely characterizing properties of low-mass companions at solar system-like scales from a combination of direct imaging, astrometry, and radial-velocity methods.
|
|
| 10. |
- Currie, Thayne, et al.
(författare)
-
SCExAO/CHARIS Direct Imaging Discovery of a 20 au Separation, Low-mass Ratio Brown Dwarf Companion to an Accelerating Sun-like Star
- 2020
-
Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 904:2
-
Tidskriftsartikel (refereegranskat)abstract
- We present the direct imaging discovery of a substellar companion to the nearby Sun-like star, HD 33632 Aa, at a projected separation of similar to 20 au, obtained with SCExAO/CHARIS integral field spectroscopy complemented by Keck/NIRC2 thermal infrared imaging. The companion, HD 33632 Ab, induces a 10.5 sigma astrometric acceleration on the star as detected with the Gaia and Hipparcos satellites. SCExAO/CHARIS JHK (1.1-2.4 mu m) spectra and Keck/NIRC2 L-p (3.78 mu m) photometry are best matched by a field L/T transition object: an older, higher-gravity, and less dusty counterpart to HR 8799 cde. Combining our astrometry with Gaia/Hipparcos data and archival Lick Observatory radial velocities, we measure a dynamical mass of 46.4 8 M-J and an eccentricity of e < 0.46 at 95% confidence. HD 33632 Ab's mass and mass ratio (4.0% 0.7%) are comparable to the low-mass brown dwarf GJ 758 B and intermediate between the more massive brown dwarf HD 19467 B and the (near-)planet-mass companions to HR 2562 and GJ 504. Using Gaia to select for direct imaging observations with the newest extreme adaptive optics systems can reveal substellar or even planet-mass companions on solar system-like scales at an increased frequency compared to blind surveys.
|
|
