| 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. |
- Li, Zhuwei, et al.
(författare)
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Atomically dispersed Ni active sites on covalent organic frameworks for heterogeneous metallaphotocatalytic C–N cross-coupling
- 2024
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Ingår i: Applied Catalysis B. - : Elsevier BV. - 0926-3373 .- 1873-3883. ; 345
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Tidskriftsartikel (refereegranskat)abstract
- Covalent organic frameworks (COFs) have been acknowledged as a potential platform for heterogeneous photoredox cross-coupling due to their excellent chemical stability, admirable controllability, and extremely prominent surface area. However, synthesizing COFs with bidentate ligand units and utilizing active sites remain a grand challenge. Herein, we report a promising new family of 2,6-pyridinedicarboxaldehyde-bis-(p-aminophenylimine)-based two-dimensional (2D) COFs (PP-COF) using an amine monomer and classic tri-aldehydes. On this basis, dispersed Ni single-atom sites were immobilized on three-types imine-based bi-coordinated 2D COFs (Ni SAS-PP-COF) as heterogeneous dual photoredox catalysts for photo/Ni dual-catalyzed C–N cross-coupling between aryl bromides and alkyl/sulfo amines. Under solar energy irradiation, PP-COF could absorb light to generate electrons and holes, then the photogenerated electrons are transferred to Ni sites to reduce divalent nickel to monovalent nickel. Monovalent nickel is necessary to drive the nickel catalytic cycle. Due to the increased charge separation and abundant active sites, the state-of-the-art Ni SAS-PP-COFs catalyst achieves excellent catalytic performance in comparison of pristine PP-COF. The heterogeneous Ni SAS-PP-COF catalytic system not only confirms the prospect of COFs as potential photoredox/transition-metal dual catalysts, but also provides in-depth insights into the synthesis of functional COFs toward practical metallaphotocatalytic application.
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| 3. |
- Foss-Skiftesvik, Jon, et al.
(författare)
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Multi-ancestry genome-wide association study of 4069 children with glioma identifies 9p21.3 risk locus
- 2023
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Ingår i: Neuro-Oncology. - : Oxford University Press. - 1522-8517 .- 1523-5866. ; 25:9, s. 1709-1720
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Although recent sequencing studies have revealed that 10% of childhood gliomas are caused by rare germline mutations, the role of common variants is undetermined and no genome-wide significant risk loci for pediatric central nervous system tumors have been identified to date.METHODS: Meta-analysis of 3 population-based genome-wide association studies comprising 4069 children with glioma and 8778 controls of multiple genetic ancestries. Replication was performed in a separate case-control cohort. Quantitative trait loci analyses and a transcriptome-wide association study were conducted to assess possible links with brain tissue expression across 18 628 genes.RESULTS: Common variants in CDKN2B-AS1 at 9p21.3 were significantly associated with astrocytoma, the most common subtype of glioma in children (rs573687, P-value of 6.974e-10, OR 1.273, 95% CI 1.179-1.374). The association was driven by low-grade astrocytoma (P-value of 3.815e-9) and exhibited unidirectional effects across all 6 genetic ancestries. For glioma overall, the association approached genome-wide significance (rs3731239, P-value of 5.411e-8), while no significant association was observed for high-grade tumors. Predicted decreased brain tissue expression of CDKN2B was significantly associated with astrocytoma (P-value of 8.090e-8).CONCLUSIONS: In this population-based genome-wide association study meta-analysis, we identify and replicate 9p21.3 (CDKN2B-AS1) as a risk locus for childhood astrocytoma, thereby establishing the first genome-wide significant evidence of common variant predisposition in pediatric neuro-oncology. We furthermore provide a functional basis for the association by showing a possible link to decreased brain tissue CDKN2B expression and substantiate that genetic susceptibility differs between low- and high-grade astrocytoma.
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| 4. |
- Jin, Shaobo, 1987-
(författare)
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Essays on Estimation Methods for Factor Models and Structural Equation Models
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis which consists of four papers is concerned with estimation methods in factor analysis and structural equation models. New estimation methods are proposed and investigated.In paper I an approximation of the penalized maximum likelihood (ML) is introduced to fit an exploratory factor analysis model. Approximated penalized ML continuously and efficiently shrinks the factor loadings towards zero. It naturally factorizes a covariance matrix or a correlation matrix. It is also applicable to an orthogonal or an oblique structure.Paper II, a simulation study, investigates the properties of approximated penalized ML with an orthogonal factor model. Different combinations of penalty terms and tuning parameter selection methods are examined. Differences in factorizing a covariance matrix and factorizing a correlation matrix are also explored. It is shown that the approximated penalized ML frequently improves the traditional estimation-rotation procedure.In Paper III we focus on pseudo ML for multi-group data. Data from different groups are pooled and normal theory is used to fit the model. It is shown that pseudo ML produces consistent estimators of factor loadings and that it is numerically easier than multi-group ML. In addition, normal theory is not applicable to estimate standard errors. A sandwich-type estimator of standard errors is derived.Paper IV examines properties of the recently proposed polychoric instrumental variable (PIV) estimators for ordinal data through a simulation study. PIV is compared with conventional estimation methods (unweighted least squares and diagonally weighted least squares). PIV produces accurate estimates of factor loadings and factor covariances in the correctly specified confirmatory factor analysis model and accurate estimates of loadings and coefficient matrices in the correctly specified structure equation model. If the model is misspecified, robustness of PIV depends on model complexity, underlying distribution, and instrumental variables.
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| 5. |
- Lanner, Fredrik, et al.
(författare)
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Hypoxia-Induced Arterial Differentiation Requires Adrenomedullin and Notch Signaling
- 2013
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Ingår i: Stem Cells and Development. - : Mary Ann Liebert Inc. - 1547-3287 .- 1557-8534. ; 22:9, s. 1360-1369
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Tidskriftsartikel (refereegranskat)abstract
- Hypoxia (low oxygen) and Notch signaling are 2 important regulators of vascular development, but how they interact in controlling the choice between arterial and venous fates for endothelial cells during vasculogenesis is less well understood. In this report, we show that hypoxia and Notch signaling intersect in promotion of arterial differentiation. Hypoxia upregulated expression of the Notch ligand Dll4 and increased Notch signaling in a process requiring the vasoactive hormone adrenomedullin. Notch signaling also upregulated Dll4 expression, leading to a positive feedback loop sustaining Dll4 expression and Notch signaling. In addition, hypoxia-mediated upregulation of the arterial marker genes Depp, connexin40 (Gja5), Cxcr4, and Hey1 required Notch signaling. In conclusion, the data reveal an intricate interaction between hypoxia and Notch signaling in the control of endothelial cell differentiation, including a hypoxia/adrenomedullin/Dll4 axis that initiates Notch signaling and a requirement for Notch signaling to effectuate hypoxia-mediated induction of the arterial differentiation program.
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| 6. |
- Li, Jiahui, et al.
(författare)
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Pseudocapacitive Heteroatom-Doped Carbon Cathode for Aluminum-Ion Batteries with Ultrahigh Reversible Stability
- 2024
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Ingår i: Energy & Environmental Materials. - : WILEY. - 2575-0356.
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Tidskriftsartikel (refereegranskat)abstract
- Aluminum (Al)-ion batteries have emerged as a potential alternative to conventional ion batteries that rely on less abundant and costly materials like lithium. Nonetheless, given the nascent stage of advancement in Al-ion batteries (AIBs), attaining electrode materials that can leverage both intercalation capacity and structural stability remains challenging. Herein, we demonstrate a C3N4-derived layered N,S heteroatom-doped carbon, obtained at different pyrolysis temperatures, as a cathode material for AIBs, encompassing the diffusion-controlled intercalation and surface-induced capacity with ultrahigh reversibility. The developed layered N,S-doped corbon (N,S-C) cathode, synthesized at 900 degrees C, delivers a specific capacity of 330 mAh g(-1) with a relatively high coulombic efficiency of similar to 85% after 500 cycles under a current density of 0.5 A g(-1). Owing to its reinforced adsorption capability and enlarged interlayer spacing by doping N and S heteroatoms, the N,S-C900 cathode demonstrates outstanding energy storage capacity with excellent rate performance (61 mAh g(-1) at 20 A g(-1)) and ultrahigh reversibility (90 mAh g(-1) at 5 A g(-1) after 10 000 cycles).
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| 7. |
- Qiu, Meikang, et al.
(författare)
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Three-phase time-aware energy minimization with DVFS and unrolling for Chip Multiprocessors
- 2012
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Ingår i: Journal of systems architecture. - : Elsevier BV. - 1383-7621 .- 1873-6165. ; 58:10, s. 439-445
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Tidskriftsartikel (refereegranskat)abstract
- Energy consumption has been one of the most critical issues in the Chip Multiprocessor (CMP). Using the Dynamic Voltage and Frequency Scaling (DVFS), a CMP system can achieve a balance between the performance and the energy-efficiency. In this paper, we propose a three-phase discrete DVFS algorithm for a CMP system dedicated to applications where the period of the applications' task graph is smaller than the deadline of tasks. In these applications, multiple task graphs are unrolled and then concatenated together to form a new task graph. The proposed DVFS algorithm is applied to the newly formed task graph to stretch tasks' execution time, lower operating frequencies of processors and achieve the system power efficiency. Experimental results show that the proposed algorithm reduces the energy dissipation by 25% on average, compared to previous DVFS approaches.
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