| 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. |
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| 3. |
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| 4. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 5. |
- Cheung, Ho-Nam, et al.
(författare)
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Assessing the influence of sea surface temperature and arctic sea ice cover on the uncertainty in the boreal winter future climate projections
- 2022
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Ingår i: Climate Dynamics. - : Springer Science and Business Media LLC. - 0930-7575 .- 1432-0894. ; 59:1-2, s. 433-454
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the uncertainty (i.e., inter-model spread) in future projections of the boreal winter climate, based on the forced response of ten models from the CMIP5 following the RCP8.5 scenario. The uncertainty in the forced response of sea level pressure (SLP) is large in the North Pacific, the North Atlantic, and the Arctic. A major part of these uncertainties (31%) is marked by a pattern with a center in the northeastern Pacific and a dipole over the northeastern Atlantic that we label as the Pacific–Atlantic SLP uncertainty pattern (PA∆SLP). The PA∆SLP is associated with distinct global sea surface temperature (SST) and Arctic sea ice cover (SIC) perturbation patterns. To better understand the nature of the PA∆SLP, these SST and SIC perturbation patterns are prescribed in experiments with two atmospheric models (AGCMs): CAM4 and IFS. The AGCM responses suggest that the SST uncertainty contributes to the North Pacific SLP uncertainty in CMIP5 models, through tropical–midlatitude interactions and a forced Rossby wavetrain. The North Atlantic SLP uncertainty in CMIP5 models is better explained by the combined effect of SST and SIC uncertainties, partly related to a Rossby wavetrain from the Pacific and air-sea interaction over the North Atlantic. Major discrepancies between the CMIP5 and AGCM forced responses over northern high-latitudes and continental regions are indicative of uncertainties arising from the AGCMs. We analyze the possible dynamic mechanisms of these responses, and discuss the limitations of this work.
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| 6. |
- Gao, Xindi, et al.
(författare)
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Cryptococcal Hsf3 controls intramitochondrial ROS homeostasis by regulating the respiratory process
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Mitochondrial quality control prevents accumulation of intramitochondrial-derived reactive oxygen species (mtROS), thereby protecting cells against DNA damage, genome instability, and programmed cell death. However, underlying mechanisms are incompletely understood, particularly in fungal species. Here, we show that Cryptococcus neoformans heat shock factor 3 (CnHsf3) exhibits an atypical function in regulating mtROS independent of the unfolded protein response. CnHsf3 acts in nuclei and mitochondria, and nuclear- and mitochondrial-targeting signals are required for its organelle-specific functions. It represses the expression of genes involved in the tricarboxylic acid cycle while promoting expression of genes involved in electron transfer chain. In addition, CnHsf3 responds to multiple intramitochondrial stresses; this response is mediated by oxidation of the cysteine residue on its DNA binding domain, which enhances DNA binding. Our results reveal a function of HSF proteins in regulating mtROS homeostasis that is independent of the unfolded protein response.
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| 7. |
- Gao, X, et al.
(författare)
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Longitudinal patient-reported outcomes 1 year after thoracoscopic segmentectomy versus lobectomy for early-stage lung cancer: a multicentre, prospective cohort study protocol
- 2023
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Ingår i: BMJ open. - : BMJ. - 2044-6055. ; 13:1, s. e067841-
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Tidskriftsartikel (refereegranskat)abstract
- Segmentectomy and lobectomy are the main surgical procedures for early-stage lung cancer. However, few studies have analysed patient-reported outcomes after segmentectomy versus lobectomy. This study aims to compare patient-reported outcomes—such as symptoms, daily functioning and quality of life—between thoracoscopic segmentectomy and lobectomy for early-stage lung cancer during the 1 year after surgery.Methods and analysisOverall, 788 newly diagnosed patients with early-stage lung cancer (tumour size ≤2 cm), who are scheduled to undergo thoracoscopic segmentectomy or lobectomy, will be recruited in this multicentre, prospective cohort study. The patients will receive standardised care after surgery. The Perioperative Symptom Assessment for Lung Surgery—a validated lung cancer surgery-specific scale—will be used to assess the symptoms and functions at baseline, at discharge and monthly after discharge for 1 year. The European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core 30 and Lung Cancer module 29 will be used to assess the patients’ quality of life at the same time points. The primary outcome will be the shortness of breath scores during the first year after thoracoscopic segmentectomy and lobectomy and will be compared using mixed-effects models. The secondary outcomes will include other symptoms, indicators of daily functioning, quality of life scores and traditional clinical outcomes. These will be compared using mixed-effects models and the Student’s t-test, non-parametric test or Χ2test. Propensity score matching will be used to ensure an even distribution of known confounders between the groups.Ethics and disseminationThe Ethics Committee for Medical Research and New Medical Technology of Sichuan Cancer Hospital approved this study (approval number: SCCHEC-02-2022-002). All participants will be instructed to provide informed consent. The manuscript is based on protocol version 3.0. The study results will be presented at medical conferences and published in peer-reviewed journals.Trial registration numberChiCTR2200060753.
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| 8. |
- Tian, Shangjie, et al.
(författare)
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Magnetic topological insulator MnBi6 Te10 with a zero-field ferromagnetic state and gapped Dirac surface states
- 2020
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Ingår i: Physical Review B. - 2469-9950. ; 102:3
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Tidskriftsartikel (refereegranskat)abstract
- Magnetic topological insulators (TIs) with nontrivial topological electronic structure and broken time-reversal symmetry exhibit various exotic topological quantum phenomena. The realization of such exotic phenomena at high temperature is one of the central topics in this area. We reveal that MnBi6Te10 is a magnetic TI with an antiferromagnetic ground state below 10.8 K whose nontrivial topology is manifested by Dirac-like surface states. The ferromagnetic axion insulator state with Z4=2 emerges once spins are polarized at a field as low as 0.1 T, accompanied with saturated anomalous Hall resistivity up to 10 K. Such a ferromagnetic state is preserved even with an external field down to zero at 2 K. Theoretical calculations indicate that the few-layer ferromagnetic MnBi6Te10 is also topologically nontrivial with a nonzero Chern number. Angle-resolved photoemission spectroscopy experiments further reveal three types of Dirac surface states arising from different terminations on the cleavage surfaces, one of which has insulating behavior with an energy gap of ∼28 meV at the Dirac point. These outstanding features suggest that MnBi6Te10 is a promising system to realize various topological quantum effects at zero field and high temperature.
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| 9. |
- Wang, Heyong, 1989-, et al.
(författare)
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Impacts of the Lattice Strain on Perovskite Light-Emitting Diodes
- 2023
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Ingår i: Advanced Energy Materials. - : Wiley-V C H Verlag GMBH. - 1614-6832 .- 1614-6840. ; 13:33
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Tidskriftsartikel (refereegranskat)abstract
- The development of perovskite light-emitting diodes (PeLEDs) with both high efficiency and excellent stability remains challenging. Herein, a strong correlation between the lattice strain in perovskite films and the stability of resulting PeLEDs is revealed. Based on high-efficiency PeLEDs, the device lifetime is optimized by rationally tailoring the lattice strain in perovskite films. A PeLED with a high peak external quantum efficiency of 18.2% and a long lifetime of 151 h (T-70, under a current density of 20 mA cm(-2)) is realized with a minimized lattice strain in the perovskite film. In addition, an increase in the lattice strain is found during the long-time device stability test, indicating that the degradation of the local perovskite lattice structure could be one of the degradation mechanisms for long-term stable PeLEDs.
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| 10. |
- Wu, Zi Yi, et al.
(författare)
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Convective transport characteristics of condensing droplets in moist air flow
- 2023
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Ingår i: Physics of Fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 35:2
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Tidskriftsartikel (refereegranskat)abstract
- Condensation of convective moist air flow is a crucial physical process and is directly related to various industries. It is essential to understand the underlying growth mechanism of condensing droplets, while past studies have commonly considered convective transport with a negligible/simplified approach. In this work, a three-dimensional transient multiphysics coupling model was developed to investigate the transport characteristics of condensing droplets in convective moist air flow. This model typically interconnects heat transfer with vapor-liquid phase change, mass transport, and fluid flow. The results reveal that convective flow significantly dominates heat and mass transport during condensation. On the gas side, the incoming flow thins the diffusion layer at the windward part with a large concentration gradient. However, a low vapor-concentration zone behind the droplet is formed due to the resulting rear-side vortex, which presents an increased influence as the contact angle increases. By forcing molecular diffusion with convection transport, vapor transport from surroundings to the condensing interface is enhanced several times depending on the Reynolds number. Within the droplet, the flow shearing at the interface is principally responsible for the strong internal convection, while the Marangoni effect is negligible. The internal flow greatly affects the droplet temperature profile with a large gradient close to the base. Finally, convective flow contributes to over 3.3 times higher overall heat transfer coefficient than the quiescent environment. In addition, in interaction-governed growth, transport characteristics depend on not only the size and space distributions of droplets but also the interaction between droplets and convective flow.
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