| 1. |
- 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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| 2. |
- Bailey, Matthew H., et al.
(författare)
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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.
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| 3. |
- Cao, Y., et al.
(författare)
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Enhanced corrosion protection by Al surface immobilization of in-situ grown layered double hydroxide films co-intercalated with inhibitors and low surface energy species
- 2020
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Ingår i: Corrosion Science. - : Elsevier Ltd. - 0010-938X .- 1879-0496. ; 164
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Tidskriftsartikel (refereegranskat)abstract
- In this work, a novel in-situ grown layered double hydroxide (LDH) film co-intercalated with inhibitors (vanadates) and low surface energy substance (laurates) was immobilized on Al substrates. A long-term monitoring of electrochemical impedance spectra (EIS) of the various samples in 3.5 wt.% NaCl solution demonstrated the synergetic protection of the intercalated two functional species. Meanwhile, the X-ray diffraction (XRD) result of the samples after immersion in NaCl solution for a long time presented the anion-exchange process between vanadates/laurates and chlorides. The synergetic effect of the two species loaded film significantly contributed to the enhanced long-term corrosion protection of aluminum.
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| 4. |
- Dong, Tianyun, et al.
(författare)
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The effect of ground clearance on the aerodynamics of a generic high-speed train
- 2020
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Ingår i: Journal of Fluids and Structures. - : Elsevier BV. - 1095-8622 .- 0889-9746. ; 95
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Tidskriftsartikel (refereegranskat)abstract
- The influence of ground clearance on the flow around a simplified high-speed train is investigated in this paper. Four clearance heights are studied using IDDES. After a grid independence study, the results of the simulations are validated against experimental data present in the literature. It is found that the drag decreases when reducing the clearance gap from the baseline height to a possibly critical height, while drag remains constant when the clearance is lower than this critical height. The negative lift (downforce) increases with the decreasing of the clearance gap. The flow is particularly influenced by the gap height at the underbody and wake regions, where a lower underbody velocity and a higher wake velocity are observed with lower clearance down to case h2. Therefore, the different topologies of the wake are presented and described. Particular attention is paid to the description of the wake flow and to the position and the formation of the flow mixing region. Specifically, with decreasing clearance, the mix of the tail downwash and underbody flows happen earlier, and the core of the counter-rotating vortices in the wake tends to develop with an increasing height trend. Overall, aerodynamic performance and flow structure descriptions show positive and negative effects when decreasing gap clearances, which should be taken into account for new design strategies.
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| 5. |
- Dong, Tianyun, et al.
(författare)
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The effect of reducing the underbody clearance on the aerodynamics of a high-speed train
- 2020
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Ingår i: Journal of Wind Engineering and Industrial Aerodynamics. - : Elsevier BV. - 0167-6105. ; 204
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Tidskriftsartikel (refereegranskat)abstract
- The effect of lowering the ground clearance, on train aerodynamics is investigated using IDDES. The high speed train geometry with its full underbody complexity is used in the investigation. The clearance is reduced by installing extra panels on the track. The numerical results are verified and validated by a grid independence study and experimental data. This work shows that, when lowered the clearance, the underbody velocity at the head car decreases, while the underbody velocity at the middle and tail car increases. The reduced clearance barely affects the time-averaged slipstream at 3 m away from the center of track. However, at a closer distance to the train body, the difference in velocity is observed to reach up to 50% between the two clearance configurations and the clearance has an opposite effect on the trackside and platform slipstream. Based on the analysis of ensemble-averaged slipstream, lowering the underbody clearance, the characteristic air speed at the trackside and platform height increases by 2.0% and 6.7%, respectively. The total drag is almost unaffected by the clearance, but the changed distribution of the drag indicates a larger drag depends on the bogie structure if longer grouped train is used. The total lift decreases 25.9% after the clearance is reduced. Specifically, 4.1% of the negative lift is increased at the head car, while the positive lift decreases 92.7% and 1.8% for the middle and tail car, respectively. Overall it is shown that reducing the underbody clearance barely affect the slipstream at standard positions, but affects more aerodynamic loads of the train.
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| 6. |
- Huang, Ke, et al.
(författare)
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Tailoring magnetic order via atomically stacking 3d/5d electrons to achieve high-performance spintronic devices
- 2020
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Ingår i: Applied Physics Reviews. - : AMER INST PHYSICS. - 1931-9401. ; 7:1
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Forskningsöversikt (refereegranskat)abstract
- The ability to tune magnetic orders, such as magnetic anisotropy and topological spin texture, is desired to achieve high-performance spintronic devices. A recent strategy has been to employ interfacial engineering techniques, such as the introduction of spin-correlated interfacial coupling, to tailor magnetic orders and achieve novel magnetic properties. We chose a unique polar-nonpolar LaMnO3/SrIrO3 superlattice because Mn (3d)/Ir (5d) oxides exhibit rich magnetic behaviors and strong spin-orbit coupling through the entanglement of their 3d and 5d electrons. Through magnetization and magnetotransport measurements, we found that the magnetic order is interface-dominated as the superlattice period is decreased. We were able to then effectively modify the magnetization, tilt of the ferromagnetic easy axis, and symmetry transition of the anisotropic magnetoresistance of the LaMnO3/SrIrO3 superlattice by introducing additional Mn (3d) and Ir (5d) interfaces. Further investigations using in-depth first-principles calculations and numerical simulations revealed that these magnetic behaviors could be understood by the 3d/5d electron correlation and Rashba spin-orbit coupling. The results reported here demonstrate a new route to synchronously engineer magnetic properties through the atomic stacking of different electrons, which would contribute to future applications in high-capacity storage devices and advanced computing.
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| 7. |
- Jin, Binghan, et al.
(författare)
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Abdominal Adiposity and Total Body Fat as Predictors of Cardiometabolic Health in Children and Adolescents With Obesity
- 2020
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Ingår i: Frontiers in Endocrinology. - : FRONTIERS MEDIA SA. - 1664-2392. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Objective:We aimed to assess the role of adipose tissue distribution in cardiometabolic risk (in particular insulin sensitivity) in a population of children and adolescents with obesity. Methods:In this cross-sectional study, participants were 479 children and adolescents with obesity (322 boys and 157 girls) aged 3 to 18 years attending the Children's Hospital at Zhejiang University School of Medicine (Hangzhou, China). Clinical assessments included anthropometry, body composition (DXA scans), carotid artery ultrasounds, and OGTT. Insulin sensitivity was assessed using the Matsuda index. Participants were stratified into groups by sex and pubertal stage. Key predictors were DXA-derived android-to-gynoid-fat ratio (A/G) and total body fat percentage (TBF%). Results:Irrespective of sex and pubertal stage, there was a strong association between increasing A/G (i.e., greater abdominal adiposity) and lower insulin sensitivity. In multivariable models, every 0.1 increase in A/G was associated with a reduction in insulin sensitivity in prepubertal boys [-29% (95% CI -36%, -20%);p< 0.0001], pubertal boys [-13% (95% CI -21%, -6%);p= 0.001], and pubertal girls [-16% (95% CI -24%, -6%);p= 0.002]. In contrast, TBF% was not associated with insulin sensitivity when A/G was adjusted for, irrespective of pubertal stage or sex. In addition, every 0.1 increase in A/G was associated with increased likelihood of dyslipidemia in prepubertal boys [adjusted odds ratio (aOR) 1.62 (95% CI 1.05, 2.49)], impaired glucose tolerance in pubertal boys [aOR 1.64 (95% CI 1.07, 2.51)] and pubertal girls [aOR 1.81 (95% CI 1.10, 2.98)], and odds of NAFLD in both prepubertal [aOR 2.57 (95% CI 1.56, 4.21)] and pubertal [aOR 1.69 (95% CI 1.18, 2.40)] boys. In contrast, higher TBF% was only associated with higher fasting insulin and ALT in pubertal boys, being also predictive of NAFLD in this group [aOR 1.15 per percentage point (95% CI 1.06, 1.26)], but was not associated with the likelihood of other cardiometabolic outcomes assessed in any group. Conclusions:A/G is a much stronger independent predictor of cardiometabolic risk factors in children and adolescents with obesity in China, particularly glucose metabolism.
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| 8. |
- Liang, Dong, et al.
(författare)
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Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum
- 2020
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Crop protection strategies that are effective but that reduce our reliance on chemical pesticides are urgently needed to meet the UN sustainable development goals for global food security. Mycoparasitic oomycetes such as Pythium oligandrum and Pythium periplocum, have potential for the biological control of plant diseases that threaten crops and have attracted much attention due to their abilities to antagonize plant pathogens and modulate plant immunity. Studies of the molecular and genetic determinants of mycoparasitism in these species have been less well developed than those of their fungal counterparts. Carbohydrate-active enzymes (CAZymes) from P. oligandrum and P. periplocum are predicted to be important components of mycoparasitism, being involved in the degradation of the cell wall of their oomycete and fungal prey species. To explore the evolution of CAZymes of these species we performed an in silico identification and comparison of the full CAZyme complement (CAZyome) of the two mycoparasitic Pythium species (P. oligandrum and P. periplocum), with seven other Pythium species, and four Phytophthora species. Twenty CAZy gene families involved in the degradation of cellulose, hemicellulose, glucan, and chitin were expanded in, or unique to, mycoparasitic Pythium species and several of these genes were expressed during mycoparasitic interactions with either oomycete or fungal prey, as revealed by RNA sequencing and quantitative qRT-PCR. Genes from three of the cellulose and chitin degrading CAZy families (namely AA9, GH5_14, and GH19) were expanded via tandem duplication and predominantly located in gene sparse regions of the genome, suggesting these enzymes are putative pathogenicity factors able to undergo rapid evolution. In addition, five of the CAZy gene families were likely to have been obtained from other microbes by horizontal gene transfer events. The mycoparasitic species are able to utilize complex carbohydrates present in fungal cell walls, namely chitin and N-acetylglucosamine for growth, in contrast to their phytopathogenic counterparts. Nonetheless, a preference for the utilization of simple sugars for growth appears to be a common trait within the oomycete lineage.
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| 9. |
- Zhang, Shao-jie, et al.
(författare)
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Genomic regions under selection in the feralization of the dingoes
- 2020
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Dingoes are wild canids living in Australia, originating from domestic dogs. They have lived isolated from both the wild and the domestic ancestor, making them a unique model for studying feralization. Here, we sequence the genomes of 10 dingoes and 2 New Guinea Singing Dogs. Phylogenetic and demographic analyses show that dingoes originate from dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia around 8300 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identifies 50 positively selected genes enriched in digestion and metabolism, indicating a diet change during feralization of dingoes. Thirteen of these genes have shifted allele frequencies compared to dogs but not compared to wolves. Functional assays show that an A-to-G mutation in ARHGEF7 decreases the endogenous expression, suggesting behavioral adaptations related to the transitions in environment. Our results indicate that the feralization of the dingo induced positive selection on genomic regions correlated to neurodevelopment, metabolism and reproduction, in adaptation to a wild environment.
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