| 1. |
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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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| 3. |
- Wang, Zhuoyan, et al.
(författare)
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Mechanistic Investigation into Dynamic Function of Third-Component Incorporated in Ternary Near-Infrared Nonfullerene Organic Solar Cells
- 2020
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Ingår i: Advanced Functional Materials. - : Wiley. - 1616-301X .- 1616-3028. ; 30:31
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Tidskriftsartikel (refereegranskat)abstract
- Organic solar cells (OSCs) consisting of an ultralow-bandgap nonfullerene acceptor (NFA) with an optical absorption edge that extends to the near-infrared (NIR) region are of vital interest to semitransparent and tandem devices. However, huge energy-loss related to inefficient charge dissociation hinders their further development. The critical issues of charge separation as exemplified in NIR-NFA OSCs based on the paradigm blend of PTB7–Th donor (D) and IEICO–4F acceptor (A) are revealed here. These studies corroborate efficient charge transfer between D and A, accompanied by geminate recombination of photo-excited charge carriers. Two key factors restricting charge separation are unveiled as the connection discontinuity of individual phases in the blend and long-lived interfacial charge-transfer states (CTS). By incorporation of a third-component of benchmark ITIC or PC71BM with various molar ratios, these two issues are well-resolved accordingly, yet in distinctly influencing mechanisms. ITIC molecules modulate film morphology to create more continuous paths for charge transportation, whereas PC71BM diminishes CTS and enhances electron transfer at the D/A interfaces. Consequently, the optimal untreated ternary OSCs comprising 0.3 wt% ITIC and 0.1 wt% PC71BM in the blend deliver higher JSC values of 21.9 and 25.4 mA cm-2, and hence increased PCE of 10.2% and 10.6%, respectively.
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| 4. |
- Bi, Zhenwang, et al.
(författare)
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Prevalence of the mcr-1 colistin resistance gene in extended-spectrum beta-lactamase-producing Escherichia coli from human faecal samples collected in 2012 in rural villages in Shandong Province, China
- 2017
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Ingår i: International Journal of Antimicrobial Agents. - : ELSEVIER SCIENCE BV. - 0924-8579 .- 1872-7913. ; 49:4, s. 493-497
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Tidskriftsartikel (refereegranskat)abstract
- Since its initial discovery in China in 2015, the plasmid-mediated colistin resistance gene mcr-1 has been reported in Escherichia coli isolated from clinical samples, animals and meat worldwide. In this study, 706 extended-spectrum beta-lactamase (ESBL)-producing E. coli from 411 persons were detected in a collection of faecal samples from 1000 rural residents in three counties in Shandong Province, China. These isolates were screened for mcr-1 and phenotypic colistin resistance. The gene was found in 3.5% of the isolates (from 4.9% of persons) from all three counties. All isolates with phenotypic colistin resistance carried mcr-1. These data indicate that commensal carriage of ESBL-producing E. coli with mcr-1 among persons in rural China was already present in 2012 and that mcr-1 was the most important colistin resistance mechanism. Interventions are necessary to minimise further dissemination of mcr-1, which would limit the future usefulness of colistin as a last-resort antibiotic. (C) 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.
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| 5. |
- Cao, Rihong, et al.
(författare)
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Failure mechanism of non-persistent jointed rock-like specimens under uniaxial loading : Laboratory testing
- 2020
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Ingår i: International Journal of Rock Mechanics And Mining Sciences. - : Elsevier. - 1365-1609 .- 1873-4545. ; 132
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Tidskriftsartikel (refereegranskat)abstract
- It is generally known that discontinuities have a remarkable influence on the mechanical behaviour of rock masses. To further understand the fracture mechanisms of jointed rock masses, substantial effort has been focused on the strength anisotropy and failure characteristics of rocks/rock-like specimens containing persistent joints with different geometric parameters. However, only a few laboratory tests have considered the failure mechanism of a rock mass with 3D joints, especially for non-persistent joints with different persistence levels. In the present work, experiments on cubic rock-like specimens containing non-persistent joints (in areal extent) subjected to uniaxial compression were conducted to further investigate the influence of the joint inclination (θ) and persistence (N) on the rock mechanical properties and failure characteristics. The strength of a 3D non-persistent jointed specimen is characterized by three stages as the joint inclination angle (θ) increases from 0° to 90°. The strength of jointed specimens decreases with increasing N for all θ values, with the highest strength obtained for N = 0.42 and the lowest strength recorded for N = 0.92. Based on CT scan results, four typical fracture modes were identified: splitting, splitting + sliding, sliding, and intact failure. Overall, as the joint inclination increases, the failure mode of the specimen transforms from splitting to sliding and then to the intact failure mode. However, with decreasing joint persistence, the failure modes of some specimens will change from sliding to mixed failure (splitting + sliding).
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| 6. |
- Cao, Ri-hong, et al.
(författare)
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Failure and Mechanical Behavior of Transversely Isotropic Rock under Compression-Shear Tests : Laboratory Testing and Numerical Simulation
- 2021
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Ingår i: Engineering Fracture Mechanics. - : Elsevier. - 0013-7944 .- 1873-7315. ; 241
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Tidskriftsartikel (refereegranskat)abstract
- The failure and mechanical behavior of transversely isotropic rock are significantly affected by the original bedding planes. Until now, few studies have been performed to investigate the influence of the geometrical and mechanical parameters of the bedding planes on the fracture characteristics of transversely isotropic rocks under planar shear fracture loading conditions. For this purpose, experimental and numerical compression-shear tests on double-notched specimens are conducted to investigate the fracturing characteristics of transversely isotropic rock under planar shear fracture loading. The experimental study that focuses on the influence of bedding plane inclination on fracture load, fracture pattern and AE evolution, and six inclination angles is conducted in this study. Based on the flat joint contact model (for the rock matrix) and smooth joint contact model (for the original bedding plane) in PFC2D (particle flow code), the microscale fracturing process of transversely isotropic rock with different inclinations is simulated and analyzed. The results show that the inclination has an important influence on the fracture load and fracture pattern, and the maximum and minimum fracture loads are obtained for specimens with inclination angles of 30° and 60°, respectively. Moreover, the strength and spacing of the original bedding planes also play an important role in fracture loads. Higher bedding plane strength and wider bedding plane spacing result in higher fracture loads. In addition, with a moderate inclination angle, transversely isotropic rock with higher bedding plane strength tends to form cracks that cut through the rock matrix. However, with the decrease in the bedding plane strength, more fractures form along the bedding planes.
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| 7. |
- de las Fuentes, Lisa, et al.
(författare)
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Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci
- 2021
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Ingår i: Molecular Psychiatry. - : Springer Nature. - 1359-4184 .- 1476-5578. ; 26:6, s. 2111-2125
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Tidskriftsartikel (refereegranskat)abstract
- Educational attainment is widely used as a surrogate for socioeconomic status (SES). Low SES is a risk factor for hypertension and high blood pressure (BP). To identify novel BP loci, we performed multi-ancestry meta-analyses accounting for gene-educational attainment interactions using two variables, “Some College” (yes/no) and “Graduated College” (yes/no). Interactions were evaluated using both a 1 degree of freedom (DF) interaction term and a 2DF joint test of genetic and interaction effects. Analyses were performed for systolic BP, diastolic BP, mean arterial pressure, and pulse pressure. We pursued genome-wide interrogation in Stage 1 studies (N = 117 438) and follow-up on promising variants in Stage 2 studies (N = 293 787) in five ancestry groups. Through combined meta-analyses of Stages 1 and 2, we identified 84 known and 18 novel BP loci at genome-wide significance level (P < 5 × 10-8). Two novel loci were identified based on the 1DF test of interaction with educational attainment, while the remaining 16 loci were identified through the 2DF joint test of genetic and interaction effects. Ten novel loci were identified in individuals of African ancestry. Several novel loci show strong biological plausibility since they involve physiologic systems implicated in BP regulation. They include genes involved in the central nervous system-adrenal signaling axis (ZDHHC17, CADPS, PIK3C2G), vascular structure and function (GNB3, CDON), and renal function (HAS2 and HAS2-AS1, SLIT3). Collectively, these findings suggest a role of educational attainment or SES in further dissection of the genetic architecture of BP.
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| 8. |
- de Vries, Paul S., et al.
(författare)
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Multiancestry Genome-Wide Association Study of Lipid Levels Incorporating Gene-Alcohol Interactions
- 2019
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Ingår i: American Journal of Epidemiology. - : Oxford University Press. - 0002-9262 .- 1476-6256. ; 188:6, s. 1033-1054
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Tidskriftsartikel (refereegranskat)abstract
- A person's lipid profile is influenced by genetic variants and alcohol consumption, but the contribution of interactions between these exposures has not been studied. We therefore incorporated gene-alcohol interactions into a multiancestry genome-wide association study of levels of high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. We included 45 studies in stage 1 (genome-wide discovery) and 66 studies in stage 2 (focused follow-up), for a total of 394,584 individuals from 5 ancestry groups. Analyses covered the period July 2014-November 2017. Genetic main effects and interaction effects were jointly assessed by means of a 2-degrees-of-freedom (df) test, and a 1-df test was used to assess the interaction effects alone. Variants at 495 loci were at least suggestively associated (P < 1 x 10(-6)) with lipid levels in stage 1 and were evaluated in stage 2, followed by combined analyses of stage 1 and stage 2. In the combined analysis of stages 1 and 2, a total of 147 independent loci were associated with lipid levels at P < 5 x 10(-8) using 2-df tests, of which 18 were novel. No genome-wide-significant associations were found testing the interaction effect alone. The novel loci included several genes (proprotein convertase subtilisin/kexin type 5 (PCSK5), vascular endothelial growth factor B (VEGFB), and apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1) complementation factor (A1CF)) that have a putative role in lipid metabolism on the basis of existing evidence from cellular and experimental models.
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| 9. |
- Deng, Tingzhi, et al.
(författare)
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Hippocampal Transcriptome-Wide Association Study Reveals Correlations Between Impaired Glutamatergic Synapse Pathway and Age-Related Hearing Loss in BXD-Recombinant Inbred Mice
- 2021
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Ingår i: Frontiers in Neuroscience. - : Frontiers Media S.A.. - 1662-4548 .- 1662-453X. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Age-related hearing loss (ARHL) is associated with cognitive dysfunction; however, the detailed underlying mechanisms remain unclear. The aim of this study is to investigate the potential underlying mechanism with a system genetics approach. A transcriptome-wide association study was performed on aged (12-32 months old) BXD mice strains. The hippocampus gene expression was obtained from 56 BXD strains, and the hearing acuity was assessed from 54 BXD strains. Further correlation analysis identified a total of 1,435 hearing-related genes in the hippocampus (p < 0.05). Pathway analysis of these genes indicated that the impaired glutamatergic synapse pathway is involved in ARHL (p = 0.0038). Further gene co-expression analysis showed that the expression level of glutamine synthetase (Gls), which is significantly correlated with ARHL (n = 26, r = -0.46, p = 0.0193), is a crucial regulator in glutamatergic synapse pathway and associated with learning and memory behavior. In this study, we present the first systematic evaluation of hippocampus gene expression pattern associated with ARHL, learning, and memory behavior. Our results provide novel potential molecular mechanisms involved in ARHL and cognitive dysfunction association.
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| 10. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 11. |
- Kristan, Matej, et al.
(författare)
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The Visual Object Tracking VOT2016 Challenge Results
- 2016
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Ingår i: COMPUTER VISION - ECCV 2016 WORKSHOPS, PT II. - Cham : SPRINGER INT PUBLISHING AG. - 9783319488813 - 9783319488806 ; , s. 777-823
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2016 aims at comparing short-term single-object visual trackers that do not apply pre-learned models of object appearance. Results of 70 trackers are presented, with a large number of trackers being published at major computer vision conferences and journals in the recent years. The number of tested state-of-the-art trackers makes the VOT 2016 the largest and most challenging benchmark on short-term tracking to date. For each participating tracker, a short description is provided in the Appendix. The VOT2016 goes beyond its predecessors by (i) introducing a new semi-automatic ground truth bounding box annotation methodology and (ii) extending the evaluation system with the no-reset experiment.
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| 12. |
- Wang, Di, et al.
(författare)
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Transmission of clones of carbapenem-resistant Escherichia coli between a hospital and an urban wastewater treatment plant*
- 2023
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Ingår i: Environmental Pollution. - : Elsevier. - 0269-7491 .- 1873-6424. ; 336
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Tidskriftsartikel (refereegranskat)abstract
- Carbapenem-resistant Enterobacterales (CRE) constitute an urgent threat to worldwide public health. The spread of CRE is facilitated by transmission via the environment. Wastewater treatment plants (WWTPs) are considered to be important sources of antibiotic resistance and hot spots of antibiotic-resistant bacteria (ARB) which can facilitate dissemination of antibiotic resistance genes. In this study, water samples were collected over one year from a WWTP in Jinan, Shandong province, China, from different functional sites in the wastewater treatment process. Carbapenem-resistant Escherichia coli (CREC) were isolated by selective cultivation and whole-genome sequenced to investigate the occurrence and characteristics of CREC in the WWTP. A total of 77 CREC isolates were included in the study and the detection rate of CREC in the WWTP water inlet was found to be 85%. An additional 10 CREC were isolated from a nearby teaching hospital during the sampling period and included for comparison to the environmental isolates. Susceptibility testing showed that all CREC were multidrug-resistant. 6 different carbapenem resistance genes (CRGs) were detected, including blaNDM-5 (n = 75), blaNDM-1 (n = 6), blaNDM-4 (n = 3), blaNDM-6 (n = 1), blaNDM-9 (n = 1), and blaKPC-2 (n = 4). 42 CREC isolates were whole-genome sequenced with Illumina short-read sequencing. 11 of these were also sequenced with Nanopore long-read sequencing. Plasmids carrying CRGs were found to belong to IncX3 (n = 35), IncFII (n = 12), IncFIA (n = 5), IncFIB (n = 2), IncC (n = 1), and IncP6 (n = 1). Clonal dissemination of CREC belonging to ST167, ST448, and ST746 was observed between different parts of the WWTP. Furthermore, isolates from the WWTP, including an isolate belonging to the high-risk ST167 strain, were found to be clonally related to CREC isolated at the hospital. The spread of CRGs is of considerable concern and strategies to prevent environmental dissemination of this contaminant urgently needs to be implemented.
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| 13. |
- Yao, Mingfei, et al.
(författare)
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Improved functionality of Ligilactobacillus salivarius Li01 in alleviating colonic inflammation by layer-by-layer microencapsulation
- 2021
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Ingår i: npj Biofilms and Microbiomes. - : Nature Research. - 2055-5008. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- The low viability during gastrointestinal transit and poor mucoadhesion considerably limits the effectiveness of Ligilactobacillus salivarius Li01 (Li01) in regulating gut microbiota and alleviating inflammatory bowel disease (IBD). In this study, a delivery system was designed through layer-by-layer (LbL) encapsulating a single Li01cell with chitosan and alginate. The layers were strengthened by cross-linking to form a firm and mucoadhesive shell (similar to 10 nm thickness) covering the bacterial cell. The LbL Li01 displayed improved viability under simulated gastrointestinal conditions and mucoadhesive function. Almost no cells could be detected among the free Li01 after 2 h incubation in digestive fluids, while for LbL Li01, the total reduction was around 3 log CFU/mL and the viable number of cells remained above 6 log CFU/mL. Besides, a 5-fold increase in the value of rupture length and a two-fold increase in the number of peaks were found in the (bacteria-mucin) adhesion curves of LbL Li01, compared to those of free Li01. Oral administration with LbL Li01 on colitis mice facilitated intestinal barrier recovery and restoration of the gut microbiota. The improved functionality of Li01 by LbL encapsulation could increase the potential for the probiotic to be used in clinical applications to treat IBD; this should be explored in future studies.
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| 14. |
- Yao, Wenjun, et al.
(författare)
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Solid-State Synthesis of Li4Ti5O12 Whiskers from TiO2-B
- 2016
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Ingår i: Materials research bulletin. - : Elsevier BV. - 0025-5408 .- 1873-4227. ; 75, s. 204-210
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Tidskriftsartikel (refereegranskat)abstract
- In this work, Li4Ti5O12 (LTO) was synthesized from the precursors of TiO2-B and anatase whiskers, respectively. The synthesized LTO whiskers from TiO2-B whiskers via a solid state reaction at 650 °C have a high degree of crystallinity with an average diameter of 300 nm. However, when anatase whiskers were used as the precursor, only particle morphology LTO was produced at 750 °C. The further analysis of the precursors, the intermediate products and the final products reveal that the crystal structure of the anatase hinders the diffusion of lithium, leading to a typical reaction-diffusion process. Under this condition, only particle morphology LTO can be produced. However, the crystal structure of the TiO2-B is easy for lithium diffusion and the process is performed in two separated steps (i.e. diffusion and reaction), which makes it possible to decrease the solid-state reaction temperature down to 650 °C and then maintain the morphologies of whiskers.
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