| 1. |
- 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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| 2. |
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| 3. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 4. |
- Ding, Huaiyi, et al.
(author)
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Maximizing Integrated Optical and Electrical Properties of a Single ZnO Nanowire through Native Interfacial Doping
- 2014
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In: Advanced Materials. - : Wiley. - 0935-9648 .- 1521-4095. ; 26:19, s. 3035-3041
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Journal article (peer-reviewed)abstract
- A native interfacial doping layer introduced in core-shell type ZnO nanowires by a simple vapor phase re-growth procedure endows the produced nanowires with both excellent electrical and optical performances compared to conventional homogeneous ZnO nanowires. The unique Zn-rich interfacial structure in the core-shell nanowires plays a crucial role in the outstanding performances.
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| 5. |
- Chen, Guanghui, et al.
(author)
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Optimization of tunnel support parameters with consideration of seismic wave radiation pattern in the fault-slip burst
- 2017
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In: Journal of Mining and Safety Engineering. - : China University of Mining and Technology. - 1673-3363. ; 34:4, s. 715-722
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Journal article (peer-reviewed)abstract
- As the underground mining extends gradually towards depth, more and more seismic events induced by fault slip occur and cause great damages, which have become a severe potential threat to mining safety. In view of the plane strain problems, through the three dimensional discrete model established, comparison and analysis was carried out between the equivalent calculation of plane strain in 3D model and a 2D discrete model. The results have shown that the research model developed to simulate the propagation of seismic wave in 3D is feasible and applicable. The study of the effect of radiation pattern on seismic propagation revealed and tested the direction of P-and S-wave propagation, which presents high consistency to double couple model of the fault slip. On this basis, the comparison with the design scaling law formulas proposed by Kaiser and associates finds that the existing design scaling law does not totally satisfy the demand of practical engineering. Numerical calculation and analysis with the three dimensional discrete model can further optimize the support parameters, provide better service for system design of mining support, and ensure the safety and high efficiency in mining.
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| 6. |
- Jiang, Pengfei, et al.
(author)
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VLBI astrometry on the white dwarf pulsar AR Scorpii
- 2023
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In: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 520:2, s. 2942-2951
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Journal article (peer-reviewed)abstract
- AR Scorpii (AR Sco), the only-known radio-pulsing white dwarf binary, shows unusual pulsating emission at the radio, infrared, optical, and ultraviolet bands. To determine its astrometric parameters at the radio band independently, we conducted multi-epoch Very Long Baseline Interferometry (VLBI) phase-referencing observations with the European VLBI Network at 5 GHz and the Chinese VLBI Network plus the Warkworth 30-m telescope (New Zealand) at 8.6 GHz. By using the differential VLBI astrometry, we provide high-precision astrometric measurements on the parallax (pi = 8.52(-0.07)(+0.04) mas) and proper motion (mu(alpha) = 9.48(-0.07)(+0.04) mas yr(-1), mu(delta) = -51.32(-0.38)(+0.22) mas yr (-1)). The new VLBI results agree with the optical Gaia astrometry. Our kinematic analysis reveals that the Galactic space velocities of AR Sco are quite consistent with that of both intermediate polars and polars. Combined with the previous tightest VLBI constraint on the size, our parallax distance suggests that the radio emission of AR Sco should be located within the light cylinder of its white dwarf.
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| 8. |
- Ning, Yujie, et al.
(author)
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Comparative analysis of the gut microbiota composition between knee osteoarthritis and Kashin-Beck disease in Northwest China
- 2022
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In: Arthritis Research & Therapy. - : BioMed Central. - 1478-6362. ; 24:1
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Journal article (peer-reviewed)abstract
- Background: Osteoarthritis (OA) and Kashin-Beck disease (KBD) both are two severe osteochondral disorders. In this study, we aimed to compare the gut microbiota structure between OA and KBD patients.Methods: Fecal samples collected from OA and KBD patients were used to characterize the gut microbiota using 16S rDNA gene sequencing. To identify whether gut microbial changes at the species level are associated with the genes or functions of the gut bacteria between OA and KBD groups, metagenomic sequencing of fecal samples from OA and KBD subjects was performed.Results: The OA group was characterized by elevated Epsilonbacteraeota and Firmicutes levels. A total of 52 genera were identified to be significantly differentially abundant between the two groups. The genera Raoultella, Citrobacter, Flavonifractor, g__Lachnospiraceae_UCG-004, and Burkholderia-Caballeronia-Paraburkholderia were more abundant in the OA group. The KBD group was characterized by higher Prevotella_9, Lactobacillus, Coprococcus_2, Senegalimassilia, and Holdemanella. The metagenomic sequencing showed that the Subdoligranulum_sp._APC924/74, Streptococcus_parasanguinis, and Streptococcus_salivarius were significantly increased in abundance in the OA group compared to those in the KBD group, and the species Prevotella_copri, Prevotella_sp._CAG:386, and Prevotella_stercorea were significantly decreased in abundance in the OA group compared to those in the KBD group by using metagenomic sequencing.Conclusion: Our study provides a comprehensive landscape of the gut microbiota between OA and KBD patients and provides clues for better understanding the mechanisms underlying the pathogenesis of OA and KBD.
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| 9. |
- Ning, Yujie, et al.
(author)
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Genetic Variants and Protein Alterations of Selenium- and T-2 Toxin-Responsive Genes Are Associated With Chondrocytic Damage in Endemic Osteoarthropathy
- 2022
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In: Frontiers in Genetics. - : Frontiers Media S.A.. - 1664-8021. ; 12
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Journal article (peer-reviewed)abstract
- The mechanism of environmental factors in Kashin-Beck disease (KBD) remains unknown. We aimed to identify single nucleotide polymorphisms (SNPs) and protein alterations of selenium- and T-2 toxin-responsive genes to provide new evidence of chondrocytic damage in KBD. This study sampled the cubital venous blood of 258 subjects including 129 sex-matched KBD patients and 129 healthy controls for SNP detection. We applied an additive model, a dominant model, and a recessive model to identify significant SNPs. We then used the Comparative Toxicogenomics Database (CTD) to select selenium- and T-2 toxin-responsive genes with the candidate SNP loci. Finally, immunohistochemistry was applied to verify the protein expression of candidate genes in knee cartilage obtained from 15 subjects including 5 KBD, 5 osteoarthritis (OA), and 5 healthy controls. Forty-nine SNPs were genotyped in the current study. The C allele of rs6494629 was less frequent in KBD than in the controls (OR = 0.63, p = 0.011). Based on the CTD database, PPARG, ADAM12, IL6, SMAD3, and TIMP2 were identified to interact with selenium, sodium selenite, and T-2 toxin. KBD was found to be significantly associated with rs12629751 of PPARG (additive model: OR = 0.46, p = 0.012; dominant model: OR = 0.45, p = 0.049; recessive model: OR = 0.18, p = 0.018), rs1871054 of ADAM12 (dominant model: OR = 2.19, p = 0.022), rs1800796 of IL6 (dominant model: OR = 0.30, p = 0.003), rs6494629 of SMAD3 (additive model: OR = 0.65, p = 0.019; dominant model: OR = 0.52, p = 0.012), and rs4789936 of TIMP2 (recessive model: OR = 5.90, p = 0.024). Immunohistochemistry verified significantly upregulated PPARG, ADAM12, SMAD3, and TIMP2 in KBD compared with OA and normal controls (p < 0.05). Genetic polymorphisms of PPARG, ADAM12, SMAD3, and TIMP2 may contribute to the risk of KBD. These genes could promote the pathogenesis of KBD by disturbing ECM homeostasis.
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| 10. |
- Peng, Jianhui, et al.
(author)
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Achieving ultra-high electromagnetic wave absorption by anchoring Co0.33Ni0.33Mn0.33Fe2O4 nanoparticles on graphene sheets using microwave-assisted polyol method
- 2018
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In: Ceramics International. - : ELSEVIER SCI LTD. - 0272-8842 .- 1873-3956. ; 44:17, s. 21015-21026
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Journal article (peer-reviewed)abstract
- The Co0.33Ni0.33Mn0.33Fe2O4/graphene nanocomposite for electromagnetic wave absorption was successfully synthesized from metal chlorides solutions and graphite powder by a simple and rapid microwave-assisted polyol method via anchoring the Co0.33Ni0.33Mn0.33Fe2O4 nanoparticles on the layered graphene sheets. The Fe3+, Co2+, Ni2+ and Mn2+ ions in the solutions were attracted by graphene oxide obtained from graphite and converted to the precursors Fe(OH)(3), Co(OH)(2), Ni(OH)(2), and Mn(OH)(2) under slightly alkaline conditions. After the transformations of the precursors to Co-Ni-Mn ferrites and conversion of graphene oxide to graphene under microwave irradiation at 170 degrees C in just 25 min, the Co0.33Ni0.33Mn0.33Fe2O4/graphene nanocomposite was prepared. The composition and structure of the nanocomposite were characterized by X-ray diffraction (XRD), inductive coupled plasma emission spectroscopy (ICP), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy (RS), transmission electron microscopy (TEM), etc. It was found that with the filling ratio of only 20 wt% and the thickness of 2.3 mm, the nanocomposite showed an ultra-wide effective absorption bandwidth (less than -10 dB) of 8.48 GHz (from 9.52 to 18.00 GHz) with the minimum reflection loss of - 24.29 dB. Compared to pure graphene sheets, Co0.33Ni0.33Mn0.33Fe2O4 nano particles and the counterparts reported in literature, the nanocomposite exhibited much better electromagnetic wave absorption, mainly attributed to strong wave attenuation, as a result of synergistic effects of dielectric loss, conductive loss and magnetic loss, and to good impedance matching. In view of its thin thickness, light weight and outstanding electromagnetic wave absorption property, the nanocomposite could be used as a very promising electromagnetic wave absorber.
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