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| 2. |
- 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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| 3. |
- Anney, Richard, et al.
(författare)
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A genome-wide scan for common alleles affecting risk for autism.
- 2010
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 19:20, s. 4072-4082
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Tidskriftsartikel (refereegranskat)abstract
- Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
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| 4. |
- Brucalassi, Anna, et al.
(författare)
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A high resolution multi-object spectrograph for the VLT : a pre-concept design
- 2022
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Ingår i: Ground-based and Airborne Instrumentation for Astronomy IX. - : SPIE. - 1996-756X .- 0277-786X. - 9781510653498 ; 12184
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Konferensbidrag (refereegranskat)abstract
- Following the idea originally proposed during the ESO-Workshop The Very Large Telescope in 2030, the concept of a high resolution spectrograph for the VLT has been further explored, both for the science and technological aspects. Such an instrument will fill a gap in capabilities amongst the landscape of future instrumentation planned for the next decade. Its key characteristic will be high spectral resolution (R = 60000-80000) with multi-object (50-100) capabilities and, possibly, a stability that would provide high radial velocity precision (∼10m/s). In this work, we describe the science cases and driving science requirements for the instrument. Furthermore we will present some design solutions and technical options considered to meet these requirements.
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| 5. |
- Fernández-Alvar, Emma, et al.
(författare)
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The Pristine survey XIII : uncovering the very metal-poor tail of the thin disc
- 2021
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 508:1, s. 1509-1525
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Tidskriftsartikel (refereegranskat)abstract
- We evaluate the rotational velocity of stars observed by the Pristine survey towards the Galactic anticentre spanning a wide range of metallicities from the extremely metal-poor regime ([Fe/H] < −3) to nearly solar metallicity. In the Galactic anticentre direction, the rotational velocity (Vφ) is similar to the tangential velocity in the galactic longitude direction (V). This allows us to estimate Vφ from Gaia early data release 3 (Gaia EDR3) proper motions for stars without radial velocity measurements. This substantially increases the sample of stars in the outer disc with estimated rotational velocities. Our stellar sample towards the anticentre is dominated by a kinematical thin disc with a mean rotation of ∼−220 km s−1. However, our analysis reveals the presence of more stellar substructures. The most intriguing is a well-populated extension of the kinematical thin disc down to [Fe/H] ∼ −2 . A scarcer fast-rotating population reaching the extremely metal-poor regime down to [Fe/H] ∼ −3.5 is also detected but without statistical significance to unambiguously state whether this is the extremely metal-poor extension of the thin disc or the high-rotating tail of hotter structures (like the thick disc or the halo). In addition, a more slowly rotating kinematical thick disc component is also required to explain the observed V distribution at [Fe/H] > −1.5 . Furthermore, we detect signatures of a ‘heated disc’, the so-called Splash, at metallicities higher than ∼−1.5. Finally, at [Fe/H] < −1.5 our anticentre sample is dominated by a kinematical halo with a net prograde motion.
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| 6. |
- Kielty, Collin L., et al.
(författare)
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The Pristine survey - XII. Gemini-GRACES chemo-dynamical study of newly discovered extremely metal-poor stars in the Galaxy
- 2021
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 506:1, s. 1438-1461
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Tidskriftsartikel (refereegranskat)abstract
- High-resolution optical spectra of 30 metal-poor stars selected from the Pristine survey are presented, based on observations taken with the Gemini Observatory GRACES spectrograph. Stellar parameters Teff and log g are determined using a Gaia DR2 colour–temperature calibration and surface gravity from the Stefan–Boltzmann equation. GRACES spectra are used to determine chemical abundances (or upper limits) for 20 elements (Li, O, Na, Mg, K, Ca, Ti, Sc, Cr, Mn, Fe, Ni, Cu, Zn, Y, Zr, Ba, La, Nd, Eu). These stars are confirmed to be metal-poor ([Fe/H] < −2.5), with higher precision than from earlier medium-resolution analyses. The chemistry for most targets is similar to other extremely metal-poor stars in the Galactic halo. Three stars near [Fe/H] = −3.0 have unusually low Ca and high Mg, suggestive of contributions from few SN II where alpha-element formation through hydrostatic nucleosynthesis was more efficient. Three new carbon-enhanced metal-poor (CEMP) stars are also identified (two CEMP-s and one potential CEMP-no star) when our chemical abundances are combined with carbon from previous medium-resolution analyses. The GRACES spectra also provide precision radial velocities (σRV ≤ 0.2 km s−1) for dynamical orbit calculations with the Gaia DR2 proper motions. Most of our targets are dynamically associated with the Galactic halo; however, five stars with [Fe/H] < −3 have planar-like orbits, including one retrograde star. Another five stars are dynamically consistent with the Gaia-Sequoia accretion event; three have typical halo [α/Fe] ratios for their metallicities, whereas two are [Mg/Fe]-deficient, and one is a new CEMP-s candidate. These results are discussed in terms of the formation and early chemical evolution of the Galaxy.
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| 7. |
- Kordopatis, Georges, et al.
(författare)
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Automatic line selection for abundance determinations in large stellar spectroscopic surveys
- 2023
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 674
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Tidskriftsartikel (refereegranskat)abstract
- Context. Over the past few years, new multiplex spectrographs have emerged to observe several millions of stars. The optimisation of these instruments (w.r.t. their resolution or wavelength range), their associated surveys (choice of instrumental set-up), and their parameterisation pipelines require methods that estimate which wavelengths (or pixels) contain useful information. Aims. We propose a method that establishes the usefulness of an atomic spectral line, whereby usefulness is defined by the purity of the line and its detectability. We demonstrate two applications of our code: a) optimising an instrument by comparing the number of detected useful lines at a given wavelength range and resolution; and b) optimising the line list for a given set-up, in the sense of creating a golden subsample of the least-blended lines that are detectable at a range of signal-to-noise ratio values. Methods. The method compares pre-computed normalised synthetic stellar spectra containing all of the elements and molecules with spectra solely containing the lines of specific elements. Then, the flux ratios between the full spectrum and the element spectrum are computed to estimate the line purities. The method automatically identifies: (i) the line's central wavelength, (ii) its detectability based on its depth and a given signal-to-noise threshold, and (iii) its usefulness based on the purity ratio defined above. Results. We applied this method to compare the three WEAVE high-resolution set-ups (blue: 404-465 nm, green: 473-545 nm, red: 595-685 nm) and find that the green+red set-up both allows us to measure more elements and contains more numerous useful lines. However, there is a disparity in terms of which elements are detected over each of the set-ups that we have characterised. We also studied the performances of high-resolution (R similar to 20 000) and low-resolution (R similar to 6000) spectra covering the entire optical wavelength range. Assuming a purity threshold of 60%, we find that the high-resolution set-up contains a much wealthier selection of lines, for any of the considered elements; whereas the low-resolution set-up displays a 'loss' of 50% to 90% of the lines (depending on the nucleosynthetic channel considered), even when the signal-to-noise ratio is increased. Conclusions. The method presented here provides a vital diagnostic of where to focus to get the most out of a spectrograph. It is easy to implement for future instruments that have not yet determined their final configuration, as well as for pipelines that require line masks.
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| 8. |
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| 9. |
- Martin, Nicolas F., et al.
(författare)
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The Pristine survey - XVI. The metallicity of 26 stellar streams around the Milky Way detected with the STREAMFINDER in Gaia EDR3
- 2022
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 516:4, s. 5331-5354
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Tidskriftsartikel (refereegranskat)abstract
- We use the photometric metallicities provided by the panoramic Pristine survey to study the veracity and derive the metallicities of the numerous stellar streams found by the application of the STREAMFINDER algorithm to the Gaia Early Data Release 3 data. All 26 streams present in Pristine show a clear metallicity distribution function, which provides an independent check of the reality of these structures, supporting the reliability of STREAMFINDER in finding streams and the power of Pristine to measure precise metallicities. We further present six candidate structures with coherent phase-space and metallicity signals that are very likely streams. The majority of studied streams are very metal-poor (14 structures with [Fe/H] < −2.0) and include three systems with [Fe/H] < −2.9 (C-11, C-19, and C-20). These streams could be the closest debris of low-luminosity dwarf galaxies or may have originated from globular clusters of significantly lower metallicity than any known current Milky Way globular cluster. Our study shows that the promise of the Gaia data for Galactic Archeology studies can be substantially strengthened by quality photometric metallicities, allowing us to peer back into the earliest epochs of the formation of our Galaxy and its stellar halo constituents.
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| 10. |
- Morrison, Kathleen D., et al.
(författare)
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Mapping past human land use using archaeological data : A new classification for global land use synthesis and data harmonization
- 2021
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 16:4
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Tidskriftsartikel (refereegranskat)abstract
- In the 12,000 years preceding the Industrial Revolution, human activities led to significant changes in land cover, plant and animal distributions, surface hydrology, and biochemical cycles. Earth system models suggest that this anthropogenic land cover change influenced regional and global climate. However, the representation of past land use in earth system models is currently oversimplified. As a result, there are large uncertainties in the current understanding of the past and current state of the earth system. In order to improve representation of the variety and scale of impacts that past land use had on the earth system, a global effort is underway to aggregate and synthesize archaeological and historical evidence of land use systems. Here we present a simple, hierarchical classification of land use systems designed to be used with archaeological and historical data at a global scale and a schema of codes that identify land use practices common to a range of systems, both implemented in a geospatial database. The classification scheme and database resulted from an extensive process of consultation with researchers worldwide. Our scheme is designed to deliver consistent, empirically robust data for the improvement of land use models, while simultaneously allowing for a comparative, detailed mapping of land use relevant to the needs of historical scholars. To illustrate the benefits of the classification scheme and methods for mapping historical land use, we apply it to Mesopotamia and Arabia at 6 kya (c. 4000 BCE). The scheme will be used to describe land use by the Past Global Changes (PAGES) LandCover6k working group, an international project comprised of archaeologists, historians, geographers, paleoecologists, and modelers. Beyond this, the scheme has a wide utility for creating a common language between research and policy communities, linking archaeologists with climate modelers, biodiversity conservation workers and initiatives.
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