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- 2017
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In: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:2
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Journal article (peer-reviewed)
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| 4. |
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- 2019
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Journal article (peer-reviewed)
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| 5. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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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| 6. |
- Clark, Andrew G., et al.
(author)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 7. |
- Birney, Ewan, et al.
(author)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Journal article (peer-reviewed)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 8. |
- Menkveld, Albert J., et al.
(author)
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Nonstandard Errors
- 2024
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In: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
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Journal article (peer-reviewed)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
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| 9. |
- Nandi, A., et al.
(author)
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Accretion flow dynamics during 1999 outburst of XTE J1859+226—modeling of broadband spectra and constraining the source mass
- 2018
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In: Astrophysics and Space Science. - : Springer Netherlands. - 0004-640X .- 1572-946X. ; 363:5
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Journal article (peer-reviewed)abstract
- We examine the dynamical behavior of accretion flow around XTE J1859+226 during the 1999 outburst by analyzing the entire outburst data (∼166 days) from RXTE Satellite. Towards this, we study the hysteresis behavior in the hardness intensity diagram (HID) based on the broadband (3–150 keV) spectral modeling, spectral signature of jet ejection and the evolution of Quasi-periodic Oscillation (QPO) frequencies using the two-component advective flow model around a black hole. We compute the flow parameters, namely Keplerian accretion rate (m˙ d), sub-Keplerian accretion rate (m˙ h), shock location (rs) and black hole mass (Mbh) from the spectral modeling and study their evolution along the q-diagram. Subsequently, the kinetic jet power is computed as Ljetobs∼3–6×1037ergs−1 during one of the observed radio flares which indicates that jet power corresponds to 8–16% mass outflow rate from the disc. This estimate of mass outflow rate is in close agreement with the change in total accretion rate (∼14%) required for spectral modeling before and during the flare. Finally, we provide a mass estimate of the source XTE J1859+226 based on the spectral modeling that lies in the range of 5.2–7.9 M⊙ with 90% confidence.
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| 10. |
- Qiu, Ren, 1993, et al.
(author)
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Effects of gas flow on detailed microstructure inhomogeneities in LPCVD TiAlN nanolamella coatings
- 2020
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In: Materialia. - : Elsevier BV. - 2589-1529. ; 9
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Journal article (peer-reviewed)abstract
- Depositing homogeneous TiAlN coatings with a high Al content on cutting tool inserts is a challenging task. In this work, high-Al cubic Ti1-xAlxN coatings (average x = 0.8) with periodic Ti(Al)N (x = 0.5) and Al(Ti)N (x = 0.9) nanolamellae structure were synthesized by low pressure chemical vapour deposition (LPCVD) with different gas flow velocities, and the detailed microstructure was investigated by electron microscopy and simulations. Using a high gas flow rate, the columnar TiAlN grains with regular periodic nanolamella structures disappeared, the coating became enriched in Ti and hexagonal AlN (h-AlN) formed in the coating. The high Ti content is suggested to be caused by the high gas flow rate that increases the mass transport of the reactants. However, this does not influence the Al-deposition much as it is mainly limited by the surface kinetics due to the relatively low deposition temperature. Density functional theory (DFT) modelling and electron microscopy showed that h-AlN tends to form on the Ti(Al)N phase with a specific crystallographic orientation relationship. The Ti enrichment due to high gas flow rate promotes the formation of h-AlN, which therefore deteriorates the nanolamella structure and causes the disappearance of the columnar TiAlN grains. Thus, by designing the CVD process conditions to avoid too high gas flow rates, homogenous TiAlN coatings with high Al content and nanolamella structures can be deposited, which should yield superior cutting performance.
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