| 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. |
- Ma, Ting, et al.
(author)
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Parameter study of transient carbon deposition effect on the performance of a planar solid oxide fuel cell
- 2015
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In: Applied Energy. - : Elsevier BV. - 1872-9118 .- 0306-2619. ; 152, s. 217-228
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Journal article (peer-reviewed)abstract
- Carbon deposition has a serious effect on the performance of solid oxide fuel cells (SOFCs). An unsteady-state 2D model based on COMSOL software is used to study the carbon deposition process in a planar SOFC. The carbon deposition, catalyst activity, reaction rate and temperature fields are obtained to analyse the mechanism of carbon deposition in the SOFC at different operating time. The effects of the operating voltage, inlet H-2 molar fraction, operating pressure and operating temperature on the performance of the SOFC are investigated in detail. It is found that the biggest variation of the performances caused by carbon deposition occurs in the inlet domain of the anode support layer. The increase of operating voltage, inlet H-2 molar fraction, operating pressure and temperature accelerates the carbon deposition process. The predicted results could deepen our understanding of carbon deposition and its transient quantitative effects on the catalyst, structure and cell performance. (C) 2014 Elsevier Ltd. All rights reserved.
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| 4. |
- Kristanl, Matej, et al.
(author)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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In: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 5. |
- Li, Dong, et al.
(author)
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Ionic switch controls the DNA state in phage λ.
- 2015
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 43:13, s. 6348-6358
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Journal article (peer-reviewed)abstract
- We have recently found that DNA packaged in phage λ undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious λ particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated λ-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid by changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is 'switched on' at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37°C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. These results suggest a remarkable adaptation of phage λ to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses.
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| 6. |
- Lin, Yi-Tao, et al.
(author)
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Phylogenetic placement, morphology and gill-associated bacteria of a new genus and species of deep-sea mussel (Mytilidae: Bathymodiolinae) from the South China Sea
- 2022
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In: Deep Sea Research Part I. - Amsterdam : Elsevier. - 0967-0637 .- 1879-0119. ; 190, s. 103894-103894
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Journal article (peer-reviewed)abstract
- Mussels in the subfamily Bathymodiolinae are common inhabitants of deep-sea chemosynthetic habitats, but in many places their diversity remains unknown. Here we describe Nypamodiolus samadiae n. gen. et n. sp. (Mytilidae: Bathymodiolinae) based on samples collected from the Haima cold seep in the South China Sea. Phylogenetic analyses based on fragments of three mitochondrial (cox1, 16S rRNA and nad4) and three nuclear (18S rRNA, 28S rRNA and histone H3) genes show that this new species belongs to a new genus, Nypamodiolus, which includes three named species (Myrina longissima Thiele and Jaeckel, 1931, Myrina simpsoni Marshall, 1900, Idasola japonica Habe, 1976) and a few undescribed species. Nypamodiolus n. gen. is characterized by small-sized, modioliform to fan-shaped shells with the umbones in a non-terminal position, and by robust anterior and posterior byssal retractor muscles arranged in roughly one plane. Most closely related to Nypamodiolus samadiae n. sp. is an undescribed species from the northern Papua New Guinea, to which it has a Kimura-2-parameter genetic distance of 11.8% for cox1. Sequencing the V3–V4 region of the microbial 16S rRNA gene reveals two dominant gill-associated bacteria in the new species, including one sulfur-oxidizing Gammaproteobacteria (relative abundance: 43.8–58.8%) and one unclassified Spirochaetes (relative abundance: 23.9–28.1%). Morphologically, N. samadiae n. sp. is similar to N. simpsoni, while can be distinguished by a larger maximum shell size (45.0 mm vs. 40.0 mm), larger length/height ratio (2.6–2.9 vs. 2.1–2.4), broader posterior end, slightly curved dorsal margin, and more anterior umbones.
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| 7. |
- Ma, Ting, et al.
(author)
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Experimental and numerical study on heat transfer and pressure drop performance of Cross-Wavy primary surface channel
- 2016
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In: Energy Conversion and Management. - : Elsevier BV. - 0196-8904. ; 125, s. 80-90
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Journal article (peer-reviewed)abstract
- The Cross-Wavy primary surface heat exchanger is one of the most promising candidates for microturbine recuperators. In this paper, naphthalene sublimation experiments are performed for Cross-Wavy channels in a wind tunnel. The experimental results indicate that the entrance region has a small effect on the unit-averaged heat transfer coefficient of whole Cross-Wavy channels. Correlations of Nusselt number and friction factor in the Cross-Wavy channel are obtained. However, only the Cross-Wavy channel with a large equivalent diameter is tested because the actual Cross-Wavy channels are very complicated and small. Therefore, based on the similarity rules, five Cross-Wavy channels with similar structures but different equivalent diameters are further investigated by numerical simulations. The numerical results indicate that the Cross-Wavy channels with similar structures but different equivalent diameters have similar thermal-hydraulic performance in the studied Reynolds number range.
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| 8. |
- Qiu, Ting, et al.
(author)
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Structural white matter properties and cognitive resilience to tau pathology
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In: Alzheimer's and Dementia. - 1552-5260.
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Journal article (peer-reviewed)abstract
- INTRODUCTION: We assessed whether macro- and/or micro-structural white matter properties are associated with cognitive resilience to Alzheimer's disease pathology years prior to clinical onset. METHODS: We examined whether global efficiency, an indicator of communication efficiency in brain networks, and diffusion measurements within the limbic network and default mode network moderate the association between amyloid-β/tau pathology and cognitive decline. We also investigated whether demographic and health/risk factors are associated with white matter properties. RESULTS: Higher global efficiency of the limbic network, as well as free-water corrected diffusion measures within the tracts of both networks, attenuated the impact of tau pathology on memory decline. Education, age, sex, white matter hyperintensities, and vascular risk factors were associated with white matter properties of both networks. DISCUSSION: White matter can influence cognitive resilience against tau pathology, and promoting education and vascular health may enhance optimal white matter properties. Highlights: Aβ and tau were associated with longitudinal memory change over ∼7.5 years. White matter properties attenuated the impact of tau pathology on memory change. Health/risk factors were associated with white matter properties.
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| 9. |
- Yang, Xi-Xi, et al.
(author)
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Theoretical study of the mechanism of the manganese catalase KatB
- 2019
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In: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 0949-8257 .- 1432-1327. ; 24:1, s. 103-115
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Journal article (peer-reviewed)abstract
- The mechanism of the H2O2 disproportionation catalyzed by the manganese catalase (MnCat) KatB was studied using the hybrid density functional theory B3LYP and the quantum chemical cluster approach. Compared to the previous mechanistic study at the molecular level for the Thermus thermophilus MnCat (TTC), more modern methodology was used and larger models of increasing sizes were employed with the help of the high-resolution X-ray structure. In the reaction pathway suggested for KatB using the Large chemical model, the O-O homolysis of the first substrate H2O2 occurs through a -(1):(1) coordination mode and requires a barrier of 10.9kcal/mol. In the intermediate state of the bond cleavage, two hydroxides form as terminal ligands of the dimanganese cluster at the Mn-2(III,III) oxidation state. One of the two Mn(III)-OH- moieties and a second-sphere tyrosine stabilize the second substrate H2O2 in the second-sphere of the active site via hydrogen bonding interactions. The H2O2, unbound to the metals, is first oxidized into HO2 through a proton-coupled electron transfer (PCET) step with a barrier of 9.5kcal/mol. After the system switches to the triplet surface, the uncoordinated HO2 replaces the product water terminally bound to the Mn(II) and is then oxidized into O-2 spontaneously. Transition states with structural similarities to those obtained for TTC, where -(2)-OH-/O2- groups play important roles, were found to be higher in energy.
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| 10. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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