| 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. |
- Ades, M., et al.
(author)
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Global Climate : in State of the climate in 2019
- 2020
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In: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 101:8, s. S17-S127
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Journal article (peer-reviewed)
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| 3. |
- Ades, M., et al.
(author)
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GLOBAL CLIMATE
- 2020
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In: BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY. - 0003-0007 .- 1520-0477. ; 101:8
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Journal article (peer-reviewed)
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| 4. |
- Li, Junhong, et al.
(author)
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Secretome from myoblasts statically loaded at low intensity promotes tenocyte proliferation via the IGF-1 receptor pathway
- 2023
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In: The FASEB Journal. - : John Wiley & Sons. - 0892-6638 .- 1530-6860. ; 37:10
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Journal article (peer-reviewed)abstract
- Exercise is widely recognized as beneficial for tendon healing. Recently, it has been described that muscle-derived molecules secreted in response to static exercise influence tendon healing. In this study, the optimal static loading intensity for tendon healing and the composition of secretome released by myoblasts in response to different intensities of static strain were investigated. In an in vitro coculture model, myoblasts were mechanically loaded using a Flexcell Tension System. Tenocytes were seeded on transwell inserts that allowed communication between the tenocytes and myoblasts without direct contact. Proliferation and migration assays, together with RNA sequencing, were used to determine potential cellular signaling pathways. The secretome from myoblasts exposed to 2% static loading increased the proliferation and migration of the cocultured tenocytes. RNA-seq analysis revealed that this loading condition upregulated the expression of numerous genes encoding secretory proteins, including insulin-like growth factor-1 (IGF-1). Confirmation of IGF-1 expression and secretion was carried out using qPCR and enzyme-linked immunosorbt assay (ELISA), revealing a statistically significant upregulation in response to 2% static loading in comparison to both control conditions and higher loading intensities of 5% and 10%. Addition of an inhibitor of the IGF-1 receptor (PQ401) to the tenocytes significantly reduced myoblast secretome-induced tenocyte proliferation. In conclusion, IGF-1 may be an important molecule in the statically loaded myoblast secretome, which is responsible for influencing tenocytes during exercise-induced healing.
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| 5. |
- Li, Xing Yu, et al.
(author)
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Ion Acceleration and Corresponding Bounce Echoes Induced by Electric Field Impulses: MMS Observations
- 2024
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In: Journal of Geophysical Research - Space Physics. - : American Geophysical Union (AGU). - 2169-9380 .- 2169-9402. ; 129:2
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Journal article (peer-reviewed)abstract
- Dayside magnetosphere interactions are essential for energy and momentum transport between the solar wind and the magnetosphere. In this study, we investigate a new phenomenon within this regime. Sudden enhancements of ion fluxes followed by repeating dropouts and recoveries were observed by Magnetospheric Multiscale on 5 November 2016, which is the very end of the recovery phase from a moderate geomagnetic storm. These repetitive flux variations display energy-dispersive characteristics with periods relevant to ion bounce motion, suggesting they are corresponding echoes. Alongside the flux variations, bipolar electric field impulses originating from external sources were detected. We traced the source region of the initial injection and found it is located near the spacecraft's position. To elucidate the underlying physics, a test-particle simulation is conducted. The results reveal that radial transport resulting from impulse-induced acceleration can give rise to these echoes. Observations demonstrate dayside magnetosphere interactions are more common than we previously considered, which warrants further research.
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| 6. |
- Zhou, Xin, et al.
(author)
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Secretome from in vitro mechanically loaded myoblasts induces tenocyte migration, transition to a fibroblastic phenotype and suppression of collagen production
- 2021
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In: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 22:23
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Journal article (peer-reviewed)abstract
- It is known that mechanical loading of muscles increases the strength of healing tendon tissue, but the mechanism involved remains elusive. We hypothesized that the secretome from myoblasts in co-culture with tenocytes affects tenocyte migration, cell phenotype, and collagen (Col) production and that the effect is dependent on different types of mechanical loading of myoblasts. To test this, we used an in vitro indirect transwell co-culture system. Myoblasts were mechanically loaded using the FlexCell® Tension system. Tenocyte cell migration, proliferation, apoptosis, collagen production, and several tenocyte markers were measured. The secretome from myoblasts decreased the Col I/III ratio and increased the expression of tenocyte specific markers as compared with tenocytes cultured alone. The secretome from statically loaded myoblasts significantly enhanced tenocyte migration and Col I/III ratio as compared with dynamic loading and controls. In addition, the secretome from statically loaded myoblasts induced tenocytes towards a myofibroblast-like phenotype. Taken together, these results demonstrate that the secretome from statically loaded myoblasts has a profound influence on tenocytes, affecting parameters that are related to the tendon healing process.
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| 7. |
- He, Mao Qiang, et al.
(author)
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Phylogenomics, divergence times and notes of orders in Basidiomycota
- 2024
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In: Fungal Diversity. - 1560-2745 .- 1878-9129. ; 126, s. 127-406
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Journal article (peer-reviewed)abstract
- Basidiomycota is one of the major phyla in the fungal tree of life. The outline of Basidiomycota provides essential taxonomic information for researchers and workers in mycology. In this study, we present a time-framed phylogenomic tree with 487 species of Basidiomycota from 127 families, 47 orders, 14 classes and four subphyla; we update the outline of Basidiomycota based on the phylogenomic relationships and the taxonomic studies since 2019; and we provide notes for each order and discuss the history, defining characteristics, evolution, justification of orders, problems, significance, and plates. Our phylogenomic analysis suggests that the subphyla diverged in a time range of 443–490 Myr (million years), classes in a time range of 312–412 Myr, and orders in a time range of 102–361 Myr. Families diverged in a time range of 50–289 Myr, 76–224 Myr, and 62–156 Myr in Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina, respectively. Based on the phylogenomic relationships and divergence times, we propose a new suborder Mycenineae in Agaricales to accommodate Mycenaceae. In the current outline of Basidiomycota, there are four subphyla, 20 classes, 77 orders, 297 families, and 2134 genera accepted. When building a robust taxonomy of Basidiomycota in the genomic era, the generation of molecular phylogenetic data has become relatively easier. Finding phenotypical characters, especially those that can be applied for identification and classification, however, has become increasingly challenging.
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| 8. |
- Li, Xing-Yu, et al.
(author)
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Comparative Study of Dayside Pulsating Auroras Induced by Ultralow-Frequency Waves
- 2023
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In: Universe. - : MDPI AG. - 2218-1997. ; 9:6
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Journal article (peer-reviewed)abstract
- Pulsating auroras are usually observed with ultralow-frequency (ULF) waves in the Pc 3-5 band (period 10-600 s). These auroras are thought to result from interactions between energetic electrons and chorus waves, but their relationship with ULF waves remains an open question. In this study, we investigated this question by conducting a comparative study on two ULF wave events with pulsating auroras observed near the magnetic footprints. Conjugate observations from the Magnetospheric Multiscale mission and the Chinese Yellow River Station were used. In both events, lower-band chorus waves were observed, which were suggested to be connected with the auroral pulsations by wavelet analysis. The intensity of these waves oscillates at the period of the ULF waves, but the physics laid behind them differs by events. During the event of 22 January 2019, compressional ULF waves changed the threshold for the whistler anisotropy instability periodically, affecting the emission of chorus waves. In the event on 10 January 2016, poloidal ULF waves modulated the chorus wave generation by regulating electron temperature anisotropy through drift resonance. ULF waves in these events may originate from perturbations in the solar wind. We highlight the role of ULF waves in the solar wind-magnetosphere-ionosphere coupling, which requires further study.
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| 9. |
- Li, Xing-Yu, et al.
(author)
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Off-Equatorial Minima Effects on ULF Wave-Ion Interaction in the Dayside Outer Magnetosphere
- 2021
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In: Geophysical Research Letters. - : American Geophysical Union (AGU). - 0094-8276 .- 1944-8007. ; 48:18
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Journal article (peer-reviewed)abstract
- The ultra-low frequency wave-particle drift-bounce resonance in the inner magnetosphere has been studied in detail, due to its important role in particle energization. However, it remains an open question how drift-bounce resonance manifests in the dayside outer magnetosphere, where particles' orbits show bifurcations because of off-equatorial magnetic field minima. In this study, we investigate this question, by analyzing Magnetospheric Multiscale observations of the January 20, 2017 event. A test-particle simulation is conducted to help us understand the observations. The observed pitch angle-time spectrograms show "pawtrack-like" structures. We find there are more than two resonant pitch angles at fixed energy, since off-equatorial minima change the relationship between the bounce (drift) frequency and pitch angle from unimodal function to trimodal function. These results reveal a new drift-bounce acceleration mechanism in the dayside outer magnetosphere, which potentially affects the efficiency of particle energization during geomagnetic activities like geomagnetic storms.
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| 10. |
- Li, Xing-Yu, et al.
(author)
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ULF Wave-Induced Ion Pitch Angle Evolution in the Dayside Outer Magnetosphere
- 2022
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In: Geophysical Research Letters. - : American Geophysical Union (AGU). - 0094-8276 .- 1944-8007. ; 49:8
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Journal article (peer-reviewed)abstract
- Drift-bounce resonance between ultralow frequency (ULF) waves and ions is essential for ion energization in the magnetosphere. Here, we present the first comprehensive study of drift-bounce resonance in the dayside outer magnetosphere, where off-equatorial magnetic field minima would strongly distort ions' bounce and drift motion. A generalized theory is proposed, in which the effects of off-equatorial minima, time-evolving fields and ion bounce motion are taken into account. In consequence of these effects, ion pitch angle distributions undergo dramatic changes. In the presence of off-equatorial minima, the time-of-flight effect of ion bounce motion forms latitude-dependent dispersions besides "paw-track shaped" structures, while evolving wave fields cause time-dependent phase shifts in "paw-tracks." All the predicted signatures have been confirmed by 5 years of Magnetospheric Multiscale spacecraft data and numerical simulations. These results allow us to better understand the interactions between ULF waves and thermal ion species in global magnetospheric dynamics.
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