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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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| 4. |
- Wang, Shi Zhi, et al.
(författare)
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Historic dog Furs Unravel the Origin and Artificial Selection of Modern Nordic Lapphund and Elkhound dog Breeds
- 2024
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 41:7
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Tidskriftsartikel (refereegranskat)abstract
- The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3′UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds.
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| 5. |
- Dai, Deliang, et al.
(författare)
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High-Dimensional Mahalanobis Distances of Complex Random Vectors
- 2021
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Ingår i: Mathematics. - : MDPI. - 2227-7390. ; 9:16
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we investigate the asymptotic distributions of two types of Mahalanobis distance (MD): leave-one-out MD and classical MD with both Gaussian- and non-Gaussian-distributed complex random vectors, when the sample size n and the dimension of variables p increase under a fixed ratio c = p/n -> infinity. We investigate the distributional properties of complex MD when the random samples are independent, but not necessarily identically distributed. Some results regarding the F-matrix F = S2-1S1-the product of a sample covariance matrix S-1 (from the independent variable array (be(Z(i))(1xn)) with the inverse of another covariance matrix S-2 (from the independent variable array (Z(j not equal i))(pxn))-are used to develop the asymptotic distributions of MDs. We generalize the F-matrix results so that the independence between the two components S-1 and S-2 of the F-matrix is not required.
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| 6. |
- Dai, Deliang, et al.
(författare)
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Regularized estimation of Kronecker structured covariance matrix using modified Cholesky decomposition
- 2023
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Ingår i: Journal of Statistical Computation and Simulation. - : Taylor & Francis Group. - 0094-9655 .- 1563-5163.
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we study a Kronecker structured model for covariance matrices when data are matrix-valued. Using the modified Cholesky decomposition for Kronecker structured covariance matrix, we propose a regularized covariance estimator by imposing shrinkage and smoothing penalties on the Cholesky factors. A regularized flip-flop (RFF) algorithm is developed to produce a statistically efficient estimator for a large covariance matrix of matrix-valued data. Asymptotic properties are investigated and the performance of the estimator is evaluated by simulations. The results presented are applied to real data example.
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| 7. |
- Dai, Deliang, et al.
(författare)
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Regularized estimation of the Mahalanobis distance based on modified Cholesky decomposition
- 2022
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Ingår i: Communications in Statistics: Case Studies, Data Analysis and Applications. - : Taylor & Francis. - 2373-7484. ; 8:4, s. 559-573
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Tidskriftsartikel (refereegranskat)abstract
- Estimating inverse covariance matrix is an essential part of many statistical methods. This paper proposes a regularized estimator for the inverse covariance matrix. Modified Cholesky decomposition (MCD) is utilized to construct positive definite estimators. Instead of directly regularizing the inverse covariance matrix itself, we impose regularization on the Cholesky factor. The estimated inverse covariance matrix is used to build Mahalanobis distance (MD). The proposed method is evaluated by detecting outliers through simulations and empirical studies.
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| 8. |
- Dai, Liang, 1984-, et al.
(författare)
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Testing Exchangeability With Martingale for Change-Point Detection
- 2021
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Ingår i: International Journal of Ambient Computing and Intelligence (IJACI). - Hershey, PA : IGI Global. - 1941-6237 .- 1941-6245. ; 12:2, s. 1-20
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Tidskriftsartikel (refereegranskat)abstract
- This work proposes a new exchangeability test for a random sequence through a martingale-based approach. Its main contributions include 1) an additive martingale which is more amenable for designing exchangeability tests by exploiting the Hoeffding-Azuma lemma and 2) different betting functions for constructing the additive martingale. By choosing the underlying probability density function of p-values as a betting function, it can be shown that, when a change-point appears, a satisfying trade-off between the smoothness and expected one-step increment of the martingale sequence can be obtained. An online algorithm based on beta distribution parametrization for constructing this betting function is discussed in detail as well. © 2021, IGI Global.
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| 9. |
- Dai, Y. L., et al.
(författare)
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Asynchronous embryonic germ cell development leads to a heterogeneity of postnatal ovarian follicle activation and may influence the timing of puberty onset in mice
- 2022
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 20:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Ovarian follicles, which are the basic units of female reproduction, are composed of oocytes and surrounding somatic (pre) granulosa cells (GCs). A recent study revealed that signaling in somatic preGCs controlled the activation (initial recruitment) of follicles in the adult ovaries, but it is also known that there are two waves of follicle with age-related heterogeneity in their developmental dynamics in mammals. Although this heterogeneity was proposed to be crucial for female reproduction, our understanding of how it arises and its significance is still elusive. Results In the current study, by deleting the key secreted factor KIT ligand from preGCs and analyzing the follicle cell developmental dynamics, we revealed distinct patterns of activation and growth associated with the two waves of follicles in mouse ovary. Our results confirmed that activation of adult wave follicles is initiated by somatic preGCs and dependent on the KIT ligand. By contrast, activation of first wave follicles, which are awakened from germ cells before follicle formation, can occur in the absence of preGC-secreted KIT ligand in postnatal ovaries and appears to be oocyte-initiated. We also found that the asynchronous activity of phosphatidylinositol 3 kinases (PI3K) signaling and meiotic process in embryonic germ cells lead to the follicle heterogeneity in postnatal ovaries. In addition, we supplied evidence that the time sequence of embryonic germ cell development and its related first wave follicle growth are correlated to the time of puberty onset in females. Conclusion Taken together, our study provides evidence that asynchronous development of embryonic oocytes leads to the heterogeneity of postnatal ovarian follicle activation and development, and affects the timing of onset of puberty in females.
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| 10. |
- Diego, Jose M., et al.
(författare)
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JWST's PEARLS : Mothra, a new kaiju star at z=2.091 extremely magnified by MACS0416, and implications for dark matter models
- 2023
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 679
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Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of Mothra, an extremely magnified monster star, likely a binary system of two supergiant stars, in one of the strongly lensed galaxies behind the galaxy cluster MACS J0416.1-2403. Mothra is in a galaxy with spectroscopic redshift z = 2.091 in a portion of the galaxy that is parsecs away from the cluster caustic. The binary star is observed only on the side of the critical curve with negative parity but has been detectable for at least eight years, implying the presence of a small lensing perturber. Microlenses alone cannot explain the earlier observations of this object made with the Hubble Space Telescope. A larger perturber with a mass of at least 10(4 )M(circle dot) offers a more satisfactory explanation. Based on the lack of perturbation on other nearby sources in the same arc, the maximum mass of the perturber is 2.5 x 10(6) M-circle dot, making this the smallest substructure constrained by lensing at z > 0.3. The existence of this millilens is fully consistent with expectations from standard cold dark matter cosmology. On the other hand, the existence of such a small substructure in a cluster environment has implications for other dark matter models. In particular, warm dark matter models with particle masses below 8.7 keV are excluded by our observations. Similarly, axion dark matter models are consistent with the observations only if the axion mass is in the range 0.5 x 10(-22) eV < m(a )< 5 x 10(-22) eV.
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