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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- 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. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 5. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 6. |
- Song, Hong-Wei, et al.
(författare)
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Thermal fatigue on pistons induced by shaped high power laser : Part II: Design of spatial intensity distribution via numerical simulation
- 2008
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Ingår i: International Journal of Heat and Mass Transfer. - : Elsevier BV. - 0017-9310 .- 1879-2189. ; 51:3-4, s. 768-778
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Tidskriftsartikel (refereegranskat)abstract
- In the laser induced thermal fatigue simulation test on pistons, the high power laser was transformed from the incident Gaussian beam into a concentric multi-circular pattern with specific intensity ratio. The spatial intensity distribution of the shaped beam, which determines the temperature field in the piston, must be designed before a diffractive optical element (DOE) can be manufactured. In this paper, a reverse method based on finite element model (FEM) was proposed to design the intensity distribution in order to simulate the thermal loadings on pistons. Temperature fields were obtained by solving a transient three-dimensional heat conduction equation with convective boundary conditions at the surfaces of the piston workpiece. The numerical model then was validated by approaching the computational results to the experimental data. During the process, some important parameters including laser absorptivity, convective heat transfer coefficient, thermal conductivity and Biot number were also validated. Then, optimization procedure was processed to find favorable spatial intensity distribution for the shaped beam, with the aid of the validated FEM. The analysis shows that the reverse method incorporated with numerical simulation can reduce design cycle and design expense efficiently. This method can serve as a kind of virtual experimental vehicle as well, which makes the thermal fatigue simulation test more controllable and predictable.
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| 7. |
- Hu, Chang-Kang, et al.
(författare)
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Native Conditional iSWAP Operation with Superconducting Artificial Atoms
- 2023
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Ingår i: Physical Review Applied. - 2331-7019. ; 20:3
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Tidskriftsartikel (refereegranskat)abstract
- Controlling the flow of quantum information is a fundamental task for quantum computers, which is unfeasible to realize on classical devices. Coherent devices, which can process quantum states are thus required to route the quantum states that encode information. In this paper we demonstrate experimentally the smallest quantum transistor with a superconducting quantum processor, which is composed of a collector qubit, an emitter qubit, and a coupler (transistor gate). The interaction strength between the collector and emitter qubits is controlled by the frequency and state of the coupler, effectively implementing a quantum switch. Through the coupler-state-dependent Heisenberg (inherent) interaction between the qubits, a single-step (native) conditional iSWAP operation can be applied. To this end, we find that it is useful to take into consideration the higher-energy level for achieving a native and high-fidelity transistor operation. By reconstructing the quantum process tomography, we obtain an operation fidelity of 92.36% when the transistor gate is open (iSWAP implementation) and 95.23% in the case of closed gate (identity gate implementation). The architecture has strong potential in quantum information processing applications with superconducting qubits.
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| 8. |
- Hu, Chang-Kang, et al.
(författare)
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Optimal charging of a superconducting quantum battery
- 2022
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Ingår i: Quantum Science and Technology. - : IOP Publishing. - 2058-9565. ; 7:4
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Tidskriftsartikel (refereegranskat)abstract
- Quantum batteries are miniature energy storage devices and play a very important role in quantum thermodynamics. In recent years, quantum batteries have been extensively studied, but limited in theoretical level. Here we report the experimental realization of a quantum battery based on superconducting qutrit. Our model explores dark and bright states to achieve stable and powerful charging processes, respectively. Our scheme makes use of the quantum adiabatic brachistochrone, which allows us to speed up the battery ergotropy injection. Due to the inherent interaction of the system with its surrounding, the battery exhibits a self-discharge, which is shown to be described by a supercapacitor-like self-discharging mechanism. Our results paves the way for proposals of new superconducting circuits able to store extractable work for further usage.
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| 9. |
- Luo, Yang, et al.
(författare)
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Three-dimensional and temperature-dependent electronic structure of the heavy-fermion compound CePt2In7 studied by angle-resolved photoemission spectroscopy
- 2020
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Ingår i: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 101:11
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Tidskriftsartikel (refereegranskat)abstract
- The three-dimensional and temperature-dependent electronic structures of the heavy-fermion superconductor CePt2In7 are investigated. Angle-resolved photoemission spectroscopy using variable photon energy establishes the existence of quasi-two- and three-dimensional Fermi surface topologies. Temperature-dependent 4d-4f on-resonance photoemission spectroscopies data reveal that heavy quasiparticle bands begin to form at a temperature well above the characteristic (coherence) temperature T+. The emergence of low-lying crystal electric field excitation may be responsible for the "relocalization" or the precursor to the establishment of heavy electrons coherence in heavy-fermion compounds. These findings provide critical insight into understanding the hybridization in heavy-fermion systems.
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