| 1. |
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| 2. |
- 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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| 3. |
- Zhang, Maomao, et al.
(author)
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Effect of pressure during graphitization on mechanical properties of graphene films
- 2019
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In: 2019 20th International Conference on Electronic Packaging Technology, ICEPT 2019.
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Conference paper (peer-reviewed)abstract
- Graphene films (GFs) can be used in the field of electronics cooling, owing to many outstanding properties. In the present paper, GFs samples were graphitized at different pressures to study their effect on the mechanical properties. The elastic modulus and hardness of GFs were measured by nanoindentation and the tensile strength of GFs were obtained by stretching GFs in a tensile tester. Meanwhile, GFs were characterized by X-ray diffraction(XRD), Scanning electron microscopy (SEM) and Raman spectroscopy. The results show that the modulus, hardness and tensile strength of GFs were strongly influenced by the defect and wrinkles among other things.
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| 4. |
- Boudreau, Mathieu, et al.
(author)
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Repeat it without me: Crowdsourcing the T1 mapping common ground via the ISMRM reproducibility challenge
- 2024
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In: MAGNETIC RESONANCE IN MEDICINE. - 0740-3194 .- 1522-2594. ; 92:3, s. 1115-1127
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Journal article (peer-reviewed)abstract
- Purpose T-1 mapping is a widely used quantitative MRI technique, but its tissue-specific values remain inconsistent across protocols, sites, and vendors. The ISMRM Reproducible Research and Quantitative MR study groups jointly launched a challenge to assess the reproducibility of a well-established inversion-recovery T-1 mapping technique, using acquisition details from a seminal T-1 mapping paper on a standardized phantom and in human brains. Methods The challenge used the acquisition protocol from Barral et al. (2010). Researchers collected T-1 mapping data on the ISMRM/NIST phantom and/or in human brains. Data submission, pipeline development, and analysis were conducted using open-source platforms. Intersubmission and intrasubmission comparisons were performed. Results Eighteen submissions (39 phantom and 56 human datasets) on scanners by three MRI vendors were collected at 3 T (except one, at 0.35 T). The mean coefficient of variation was 6.1% for intersubmission phantom measurements, and 2.9% for intrasubmission measurements. For humans, the intersubmission/intrasubmission coefficient of variation was 5.9/3.2% in the genu and 16/6.9% in the cortex. An interactive dashboard for data visualization was also eveloped: https://rrsg2020.dashboards.neurolibre.org. Conclusion The T-1 intersubmission variability was twice as high as the intrasubmission variability in both phantoms and human brains, indicating that the acquisition details in the original paper were insufficient to reproduce a quantitative MRI protocol. This study reports the inherent uncertainty in T-1 measures across independent research groups, bringing us one step closer to a practical clinical baseline of T-1 variations in vivo.
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| 5. |
- Deng, Huan, et al.
(author)
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Altered Expression of the Hedgehog Pathway Proteins BMP2, BMP4, SHH, and IHH Involved in Knee Cartilage Damage of Patients With Osteoarthritis and Kashin-Beck Disease
- 2022
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In: Cartilage. - : Sage Publications. - 1947-6035 .- 1947-6043. ; 13:1
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Journal article (peer-reviewed)abstract
- OBJECTIVE: To investigate the expression of Hedgehog (HH) signaling pathway proteins in knee articular cartilage from Kashin-Beck disease (KBD) and osteoarthritis (OA) patients.METHODS: Knee articular cartilage samples were collected from normal (N), OA, and KBD adults (aged 38-60 years) and divided into 3 groups with 6 subjects in each group. The localization of the HH pathway proteins bone morphogenetic protein 2 (BMP2), bone morphogenetic protein 4 (BMP4), Sonic hedgehog (SHH), and Indian hedgehog (IHH) was observed with the microscope after immunohistochemical (IHC) staining. Positive staining cell rates of each proteins were compared.RESULTS: The strongest stainings of all proteins were observed in the middle zones of all 3 groups. The positive staining rates of BMP4 and IHH were significantly lower in the OA and KBD groups than those in the N group in all 3 zones. The positive staining rates of BMP2 and SHH tend to be lower in the OA and KBD groups than those in the N group in the deep zone, while higher in the OA and KBD groups than those in the N group in superficial and middle zones.CONCLUSIONS: Altered expression of the HH pathway proteins BMP2, BMP4, SHH, and IHH was found in OA and KBD articular cartilage. There seemed to be a compensatory effect between SHH and IHH in cartilage damage. Further studies on the pathogenesis of OA and KBD may be carried out from these aspects in the future.
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| 6. |
- Franke, James A., et al.
(author)
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The GGCMI Phase 2 emulators : Global gridded crop model responses to changes in CO2, temperature, water, and nitrogen (version 1.0)
- 2020
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In: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 13:9, s. 3995-4018
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Journal article (peer-reviewed)abstract
- Statistical emulation allows combining advantageous features of statistical and process-based crop models for understanding the effects of future climate changes on crop yields. We describe here the development of emulators for nine process-based crop models and five crops using output from the Global Gridded Model Intercomparison Project (GGCMI) Phase 2. The GGCMI Phase 2 experiment is designed with the explicit goal of producing a structured training dataset for emulator development that samples across four dimensions relevant to crop yields: Atmospheric carbon dioxide (CO2) concentrations, temperature, water supply, and nitrogen inputs (CTWN). Simulations are run under two different adaptation assumptions: That growing seasons shorten in warmer climates, and that cultivar choice allows growing seasons to remain fixed. The dataset allows emulating the climatological-mean yield response of all models with a simple polynomial in mean growing-season values. Climatological-mean yields are a central metric in climate change impact analysis; we show here that they can be captured without relying on interannual variations. In general, emulation errors are negligible relative to differences across crop models or even across climate model scenarios; errors become significant only in some marginal lands where crops are not currently grown. We demonstrate that the resulting GGCMI emulators can reproduce yields under realistic future climate simulations, even though the GGCMI Phase 2 dataset is constructed with uniform CTWN offsets, suggesting that the effects of changes in temperature and precipitation distributions are small relative to those of changing means. The resulting emulators therefore capture relevant crop model responses in a lightweight, computationally tractable form, providing a tool that can facilitate model comparison, diagnosis of interacting factors affecting yields, and integrated assessment of climate impacts.
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| 7. |
- Ge, Linke, et al.
(author)
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Aqueous multivariate phototransformation kinetics of dissociated tetracycline : implications for the photochemical fate in surface waters
- 2018
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In: Environmental Science and Pollution Research. - : Springer Science and Business Media LLC. - 0944-1344 .- 1614-7499. ; 25:16, s. 15726-15732
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Journal article (peer-reviewed)abstract
- Antibiotics are ubiquitous pollutants in aquatic systems and can exist as different dissociated species depending on the water pH. New knowledge of their multivariate photochemical behavior (i.e., the photobehavior of different ionized forms) is needed to improve our understanding on the fate and possible remediation of these pharmaceuticals in surface and waste waters. In this study, the photochemical degradation of aqueous tetracycline (TC) and its dissociated forms (TCH20, TCH-, and TC2-) was investigated. Simulated sunlight experiments and matrix calculations indicated that the three dissociated species had dissimilar photolytic kinetics and photo-oxidation reactivities. TC2- photo-degraded the fastest due to apparent photolysis with a kinetic constant of 0.938 +/- 0.021 min(-1), followed by TCH- (0.020 +/- 0.005 min(-1)) and TCH20 (0.012 +/- 0.001 min(-1)), whereas Tar was found to be the most highly reactive toward center dot OH (105.78 +/- 3.40 M(-1 )s(-1)), and TC2- reacted the fastest with O-1(2) (344.96 +/- 45.07 M-1 s(-1)). Water with relatively high pH (e.g., similar to 8-9) favors the dissociated forms of TCH- and TC2- which are most susceptible to photochemical loss processes compared to neutral TC. The calculated corresponding environmental half-lives (t(1/2,E) ) in sunlit surface waters ranged from 0.05 h for pH = 9 in midsummer to 3.68 h for pH = 6 in midwinter at 45 degrees N latitude. The moms was dominated by apparent photolysis (especially in summer, 62-91%), followed by O-1(2) and center dot OH oxidation. Adjusting the pH to slightly alkaline conditions prior to UV or solar UV light treatment may be an effective way of enhancing the photochemical removal of TC from contaminated water.
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| 8. |
- Wang, Jianhao, et al.
(author)
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An Integrated Transcriptome Analysis Reveals IGFBP7 Upregulation in Vasculature in Traumatic Brain Injury
- 2021
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In: Frontiers in Genetics. - : Frontiers Media S.A.. - 1664-8021. ; 11
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Journal article (peer-reviewed)abstract
- Vasculature plays critical roles in the pathogenesis and neurological repair of traumatic brain injury (TBI). However, how vascular endothelial cells respond to TBI at the molecular level has not been systematically reviewed. Here, by integrating three transcriptome datasets including whole cortex of mouse brain, FACS-sorted mouse brain endothelial cells, and single cell sequencing of mouse brain hippocampus, we revealed the key molecular alteration of endothelial cells characterized by increased Myc targets and Epithelial-Mesenchymal Transition signatures. In addition, immunofluorescence staining of patients' samples confirmed that IGFBP7 was up-regulated in vasculature in response to TBI. TGF beta 1, mainly derived from microglia and endothelial cells, sufficiently induces IGFBP7 expression in cultured endothelial cells, and is significantly upregulated in response to TBI. Our results identified IGFBP7 as a potential biomarker of vasculature in response to TBI, and indicate that TGF beta signaling may contribute to the upregulation of IGFBP7 in the vasculature.
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| 9. |
- Wang, Longguang, et al.
(author)
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NTIRE 2023 Challenge on Stereo Image Super-Resolution : Methods and Results
- 2023
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In: IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops (CVPRW). - Vancover : Institute of Electrical and Electronics Engineers (IEEE). - 9798350302493 - 9798350302509 ; , s. 1346-1372
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Conference paper (other academic/artistic)abstract
- In this paper, we summarize the 2nd NTIRE challenge on stereo image super-resolution (SR) with a focus on new solutions and results. The task of the challenge is to super-resolve a low-resolution stereo image pair to a high-resolution one with a magnification factor of x4. Compared with single image SR, the major challenge of this challenge lies in how to exploit additional information in another viewpoint and how to maintain stereo consistency in the results. This challenge has 3 tracks, including one track on distortion (e.g., PSNR) and bicubic degradation, one track on perceptual quality (e.g., LPIPS) and bicubic degradation, as well as another track on real degradations. In total, 175, 93, and 103 participants were successfully registered for each track, respectively. In the test phase, 21, 17, and 12 teams successfully submitted results with PSNR (RGB) scores better than the baseline. This challenge establishes a new benchmark for stereo image SR.
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| 10. |
- Wang, Xinan, et al.
(author)
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Impact of individual level uncertainty of lung cancer polygenic risk score (PRS) on risk stratification
- 2024
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In: Genome Medicine. - : BioMed Central (BMC). - 1756-994X. ; 16:1
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Journal article (peer-reviewed)abstract
- Background: Although polygenic risk score (PRS) has emerged as a promising tool for predicting cancer risk from genome-wide association studies (GWAS), the individual-level accuracy of lung cancer PRS and the extent to which its impact on subsequent clinical applications remains largely unexplored.Methods: Lung cancer PRSs and confidence/credible interval (CI) were constructed using two statistical approaches for each individual: (1) the weighted sum of 16 GWAS-derived significant SNP loci and the CI through the bootstrapping method (PRS-16-CV) and (2) LDpred2 and the CI through posteriors sampling (PRS-Bayes), among 17,166 lung cancer cases and 12,894 controls with European ancestry from the International Lung Cancer Consortium. Individuals were classified into different genetic risk subgroups based on the relationship between their own PRS mean/PRS CI and the population level threshold.Results: Considerable variances in PRS point estimates at the individual level were observed for both methods, with an average standard deviation (s.d.) of 0.12 for PRS-16-CV and a much larger s.d. of 0.88 for PRS-Bayes. Using PRS-16-CV, only 25.0% of individuals with PRS point estimates in the lowest decile of PRS and 16.8% in the highest decile have their entire 95% CI fully contained in the lowest and highest decile, respectively, while PRS-Bayes was unable to find any eligible individuals. Only 19% of the individuals were concordantly identified as having high genetic risk (> 90th percentile) using the two PRS estimators. An increased relative risk of lung cancer comparing the highest PRS percentile to the lowest was observed when taking the CI into account (OR = 2.73, 95% CI: 2.12–3.50, P-value = 4.13 × 10−15) compared to using PRS-16-CV mean (OR = 2.23, 95% CI: 1.99–2.49, P-value = 5.70 × 10−46). Improved risk prediction performance with higher AUC was consistently observed in individuals identified by PRS-16-CV CI, and the best performance was achieved by incorporating age, gender, and detailed smoking pack-years (AUC: 0.73, 95% CI = 0.72–0.74). Conclusions: Lung cancer PRS estimates using different methods have modest correlations at the individual level, highlighting the importance of considering individual-level uncertainty when evaluating the practical utility of PRS.
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| 11. |
- Xiao, Xiang, et al.
(author)
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Chondroitin Sulfate and Hyaluronic Acid Perfusion for Interstitial Cystitis/Bladder Pain Syndrome : A Systematic Review and Meta-Analysis
- 2021
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In: Science Insights. - : Insights Publisher. - 2372-8191 .- 2329-5856. ; 39:4, s. 361-373
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Research review (peer-reviewed)abstract
- Currently, no suitable delivery methods are available for the drugs to interstitial cystitis/ bladder pain syndrome (IC/BPS). Herein we systematically evaluated the therapeutic effects of intravesical infusion of hyaluronic acid (HA) and chondroitin sulfate (CS) in patients with IC/BPS. This study includes randomized controlled trials (RCT) and self-controlled studies of IC/BPS patients treated with HA, CS, or both. English databases like PubMed, Cochrane Library, Embase, and Medline were searched until up to January 31, 2021. Information was extracted based on the inclusion and exclusion criteria, and then meta-analysis was performed. Sixteen studies including 491 patients were included and analyzed. The responsive rate of treatment was 91.24%. In 3 RCTs, the analogue scale (VAS) for pain on fix-effect model was [mean difference, MD -0.57 (95%CI, -1.55, -0.41)]. A significant improvement on random-effect model was [MD -2.78 (95%CI, -3.48, -2.07)] in 13 self-controlled studies. Outcomes on O’Leary-Sant Interstitial Cystitis Symptom Index, Problem Index, frequency, urgency, and bladder capacity were also significantly improved. Subgroup analysis showed significant difference between HA, CS, and the combination, and the perfusion of HA was more effective (Z = 29.97, P < 0.01). Also, different follow-up times after last treatment showed significant difference (Z = 7.69, P < 0.01). It can be beneficial for IC/BPS patients who have not responded to conventional treatments.
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| 12. |
- Yang, Xiaoyong, et al.
(author)
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An emerging Janus MoSeTe material for potential applications in optoelectronic devices
- 2019
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In: Journal of Materials Chemistry C. - : ROYAL SOC CHEMISTRY. - 2050-7526 .- 2050-7534. ; 7:39, s. 12312-12320
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Journal article (peer-reviewed)abstract
- Motivated by the extraordinary physical and chemical properties of Janus transition-metal dichalcogenides (TMDs) due to the change of the crystal field originating from their asymmetry structures, the electronic and optical properties of the MoSeTe monolayer in 2H and 1T phases are systematically studied by first-principles calculations, and a detailed comparison with the parental MoSe2 and MoTe2 monolayer is made. It is found that 2H-MoSeTe exhibits a direct bandgap of 1.859 eV and an indirect band gap of 0.391 eV in the 1T phase, resulting in a different way to interact with sunlight. Besides, the obtained results show that the SOC has little effects on the band gaps. The calculated optical properties show a significant red shift from the MoSe2 to MoSeTe to MoTe2 monolayer. However, a blue shift is observed from the in-plane to out-of-plane direction. Moreover, both electron-electron and electron-hole correlation effects are considered for obtaining the optical spectra of systems by G(0)W(0) and G(0)W(0) + BSE approaches. Besides, the absorption coefficient value reaches up to 1 x 10(6) cm(-1) in both phases, implying the high efficiency in the utilization of solar energy for the MoSeTe monolayer. Additionally, the 1T-MoSeTe monolayer is a good hot mirror material in that its maximum reflectivity could reach up to 51% in the infrared region. Additionally, the average optical absorbance of the Janus MoSeTe monolayer in the visible light region is calculated to be about 2% and the corresponding average transmittance is around 80%. More importantly, the difference in the optical response for the two side surfaces is considered in our work due to the intrinsic asymmetric structure of Janus MoSeTe. These results not only predict the great potential application of Janus MoSeTe in optoelectronics-electronic devices, but may enable the discovery of new optical science and the realization of various light emissions, detection, modulation and manipulation functions of specific frequencies.
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| 13. |
- Yang, Xiaoyong, et al.
(author)
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Interfacial aspect of ZnTe/In2Te3 heterostructures as an efficient catalyst for the hydrogen evolution reaction
- 2019
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In: Journal of Materials Chemistry A. - : Royal Society of Chemistry. - 2050-7488 .- 2050-7496. ; 7:48, s. 27441-27449
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Journal article (peer-reviewed)abstract
- In the class of two-dimensional (2D) materials, group III2-VI3 compounds have drawn intense attention due to its excellent surface properties. In this work, based on first-principles calculations, we have systematically investigated the structural, electronic, optical and photocatalytic properties of a ZnTe/In2Te3 heterostructure, along with its interfacial effects, to design an efficient photocatalyst. We have employed hydrogen adsorption free energy (Delta G(H*)) as a key parameter to demonstrate the enhancement in photocatalytic activity of ZnTe/In2Te3 compared to a pristine In2Te3 monolayer, which is further verified with the explicit water environment. The underlying mechanism is governed by the partial charge distributions of pristine In2Te3 and ZnTe/In2Te3 heterostructures. The presence of the ZnTe monolayer also altered the bandgap of the In2Te3 monolayer from an indirect gap of 1.238 eV to direct gaps of 0.298 eV and 0.181 eV in A- and B-type interfaces of the ZnTe/In2Te3 heterostructure, respectively. Calculated optical absorption spectra indicate that ZnTe/In2Te3 heterostructures possess better sunlight-harvesting capability compared to monolayer In2Te3 near the infrared and visible light regions, implying their potential as an excellent light-absorber. Our predictions provide new guidance for designing 2D III2-VI3 heterostructures and expand the applications of these materials in photovoltaics, photocatalysts, and other nanodevices in the future.
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| 14. |
- Yang, Xiaoyong, et al.
(author)
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Investigating the solution and diffusion properties of hydrogen in alpha-Uranium by first-principles calculations
- 2020
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In: Progress in nuclear energy (New series). - : PERGAMON-ELSEVIER SCIENCE LTD. - 0149-1970 .- 1878-4224. ; 122
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Journal article (peer-reviewed)abstract
- The stability, solution and diffusion properties of an interstitial hydrogen atom in uranium metal have been firstly investigated by first-principles calculations. In energy, the octahedral site is more favorable for hydrogen to occupy than tetrahedra site with neglectable anisotropic perturbation. Besides, the effects of temperature on solution energy are quantified, which demonstrate the solution energy decreases fast with temperature. The calculated density of states and electronic charge re-distribution are analyzed. It is found the conductivity of metal uranium remains well after hydrogen occupied the interstitial position with lower concentration. The minimum migration pathways of interstitial hydrogen in uranium lattice are characterized by the climbing image nudged elastic band (CINEB) method. The obtained energy barriers are 0.239 eV, 0.298 eV and 0.313 eV with respect to O <-> T, O <-> O and T <-> T pathways with feeble structural deterioration. We believe our results for hydrogen diffusion in such a complex f -electron system not only provide en evidence for uranium corrosion but also supports the future experiments on measuring the hydriding rate and their interpretations.
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| 15. |
- Yang, Xiaoyong, et al.
(author)
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Unveiling the energetic and structural properties of Pu doped zircon through electrochemical equilibrium diagram from DFT plus U calculations
- 2020
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In: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 539
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Journal article (peer-reviewed)abstract
- Zircon (ZrSiO4) mineral is a sustainable and promising material to store of radioactive waste that has received extensive attention by material, geochemical and environmental scientists. Although the incorporation of actinide elements in zircon lattices has been experimentally studied, bare fundamental work are carried out to systemically assess the structural and chemical stabilities of Pu doped zircon. The primary aim to unveil the Pu immobilization mechanism and assess the stability of PuxZr1-xSiO4 is carried out by calculating the formation energies, electron and hole affinities, and electronic levels of Pu doped zircon based on density functional theory. Our results reveal under mu = mu(O-poor) condition Pu-Si(4+), Pu-Zr(1+) and Pu-Zr(0) are respectively energetically favorable to form with increasing the electronic chemical potential. Besides, Pu-Zr(4+) is energetically favorable in an n-type environment under all these three conditions (i.e., mu = mu(O-poor), mu = mu(Pu/Zr), mu = mu(Pu/Si)). In addition, Pu doping will induce local structural distortion. Intriguingly however, self-repairing the symmetry of [ZrO8] polyhedra is first observed via the structural distortion in Pu-Zr(4+) configuration, which in turn could enhance the structural stability of PuxZr1-xSiO4. Ab initio molecular dynamic simulations demonstrate the configurations with negative formation energies are thermal stable at 500 K. The charge density difference and charge transfer are investigated to describe the chemical bonding nature. It is demonstrated Pu(5f)-O(2p) hybridization is more profound for interstitial Pu. Moreover, the bonding character of surrounding Zr atoms along [010] direction is almost identical to the pristine one, while it is distinctly changed towards [100] and [001] directions, showing remarkable anisotropy of PuxZr1-xSiO4. Oppositely, the ionicity in Pu-O bond is mainly featured when Zr or Si sites are substituted by Pu atoms which becomes stronger with increasing the hole doping process. (C) 2020 Elsevier B.V. All rights reserved.
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