| 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. |
- Chong, Hui, et al.
(författare)
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Organo-ptii complexes for potent photodynamic inactivation of multi-drug resistant bacteria and the influence of configuration
- 2024
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Ingår i: Advanced Science. - : John Wiley & Sons. - 2198-3844. ; 11:14
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Tidskriftsartikel (refereegranskat)abstract
- PtII based organometallic photosensitizers (PSs) have emerged as novel potent photodynamic inactivation (PDI) reagents through their enhanced intersystem crossing (ISC) processes. Currently, few PtII PSs have been investigated as antibacterial materials, with relatively poor performances reported and with structure-activity relationships not well described. Herein, a pair of configurational isomers are reported of Bis-BODIPY (4,4-difluoro-boradizaindacene) embedded PtII PSs. The cis-isomer (cis-BBP) displayed enhanced 1O2 generation and better bacterial membrane anchoring capability as compared to the trans-isomer (trans-BBP). The effective PDI concentrations (efficiency > 99.9%) for cis-BBP in Acinetobacter baumannii (multi-drug resistant (MDR)) and Staphylococcus aureus are 400 nM (12 J cm−2) and 100 nM (18 J cm−2), respectively; corresponding concentrations and light doses for trans-BBP in the two bacteria are 2.50 µM (30 J cm−2) and 1.50 µM (18 J cm−2), respectively. The 50% and 90% minimum inhibitory concentration (MIC50 and MIC90) ratio of trans-BBP to cis-BBP is 22.22 and 24.02 in A. baumannii (MDR); 21.29 and 22.36 in methicillin resistant S. aureus (MRSA), respectively. Furthermore, cis-BBP displays superior in vivo antibacterial performance, with acceptable dark and photoinduced cytotoxicity. These results demonstrate cis-BBP is a robust light-assisted antibacterial reagent at sub-micromolecular concentrations. More importantly, configuration of PtII PSs should be an important issue to be considered in further PDI reagents design.
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| 3. |
- Cui, Manying, et al.
(författare)
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Regulation of Lithium-Ion Flux by Nanotopology Lithiophilic Boron-Oxygen Dipole in Solid Polymer Electrolytes for Lithium-Metal Batteries
- 2023
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Ingår i: Energy & Environmental Materials. - 2575-0356.
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Tidskriftsartikel (refereegranskat)abstract
- Inhomogeneous lithium-ion (Li+) deposition is one of the most crucial problems, which severely deteriorates the performance of solid-state lithium metal batteries (LMBs). Herein, we discovered that covalent organic framework (COF-1) with periodically arranged boron-oxygen dipole lithiophilic sites could directionally guide Li+ even deposition in asymmetric solid polymer electrolytes. This in situ prepared 3D cross-linked network Poly(ACMO-MBA) hybrid electrolyte simultaneously delivers outstanding ionic conductivity (1.02 × 10−3 S cm−1 at 30 °C) and excellent mechanical property (3.5 MPa). The defined nanosized channel in COF-1 selectively conducts Li+ increasing Li+ transference number to 0.67. Besides, The COF-1 layer and Poly(ACMO-MBA) also participate in forming a boron-rich and nitrogen-rich solid electrolyte interface to further improve the interfacial stability. The Li‖Li symmetric cell exhibits remarkable cyclic stability over 1000 h. The Li‖NCM523 full cell also delivers an outstanding lifespan over 400 cycles. Moreover, the Li‖LiFePO4 full cell stably cycles with a capacity retention of 85% after 500 cycles. the Li‖LiFePO4 pouch full exhibits excellent safety performance under pierced and cut conditions. This work thereby further broadens and complements the application of COF materials in polymer electrolyte for dendrite-free and high-energy-density solid-state LMBs.
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| 4. |
- Liu, Huan, et al.
(författare)
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The first human induced pluripotent stem cell line of Kashin–Beck disease reveals involvement of heparan sulfate proteoglycan biosynthesis and PPAR pathway
- 2022
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Ingår i: The FEBS Journal. - : John Wiley & Sons. - 1742-464X .- 1742-4658. ; 289:1, s. 279-293
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: Kashin-Beck disease (KBD) is an endemic osteochondropathy. Due to a lack of suitable animal or cellular disease models, the research progress on KBD has been limited. Our goal was to establish the first disease-specific human induced pluripotent stem cells (hiPSCs) cellular disease model of KBD, and to explore its etiology and pathogenesis exploiting transcriptome sequencing.METHODS: HiPSCs were reprogrammed from dermal fibroblasts of two KBD and one healthy control donors via integration-free vectors. Subsequently, hiPSCs were differentiated into chondrocytes through three-week culture. Gene expression profiles in KBD, normal primary chondrocytes and hiPSC-derived chondrocytes were defined by RNA sequencing. A Venn diagram was constructed to show the number of shared differentially expressed genes (DEGs) between KBD and normal. Gene oncology and Kyoto Encyclopedia of Genes and Genomes annotations were performed, and six DEGs were further validated in other individuals by real-time quantitative reverse transcription PCR (RT-qPCR).RESULTS: KBD cellular disease models were successfully established by generation of hiPSC lines. Seventeen consistent and significant DEGs present in all compared groups (KBD and normal) were identified. RT-qPCR validation gave consistent results with the sequencing data. Glycosaminoglycan biosynthesis-heparan sulfate/heparin, PPAR signaling pathway and cell adhesion molecules (CAMs) pathways were identified to be significantly altered in KBD.CONCLUSION: Differentiated chondrocytes deriving from KBD-origin hiPSCs provide the first cellular disease model for etiological studies of KBD. This study also provides new sights into the pathogenesis and etiology of KBD and is likely to inform the development of targeted therapeutics for its treatment.
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| 5. |
- Zhao, W., et al.
(författare)
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Reconstructing CNC platform for EDM machines towards smart manufacturing
- 2020
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Ingår i: Procedia CIRP. - : Elsevier B.V.. - 2212-8271. ; , s. 161-177
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Konferensbidrag (refereegranskat)abstract
- CNC (computer numerical control) systems play an ultimately important role for controlling EDM (electrical discharge machining) machine tools and their machining processes. Till now, existing CNC systems do not offer sufficient openness that supports researchers and engineers to expend its capabilities and functionalities in response to the increasing demands of smart manufacturing; on the other hand, transforming an EDM machine made by small and medium-sized machine tool builders, into a smart manufacturing system has never been an easy job. To address the issues and overcome the difficulties which block the way towards smart manufacturing, this paper proposes an open architecture CNC platform for EDM machine tools. This platform utilizes the state-of-the-art technologies in implementation of the hardware and software without compromising with the constraints of obsolete techniques. For demonstrating the unique capabilities, the generalized unit arc length increment (GUALI) interpolation method and the Digitizer/Player system architecture are adopted. To exhibit the feasibilities of the newly developed platform, three kinds of EDM machine tools are applied associated with advanced functionalities such as machining process adaptive control, applications of machine learning, 6-axis EDM of shrouded turbine blisks etc. In addition, a small-scale smart manufacturing unit for drilling film cooling holes of turbine blades is built up into real production by applying the new CNC system and related software applications. From the practitioner's viewpoint, openness and standardization are the keys that enable the people from academia and industry bringing in their domain knowledge to enrich the smart manufacturing ecosystem.
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| 6. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 7. |
- Fu, Xi, et al.
(författare)
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Classroom microbiome, functional pathways and sick-building syndrome (SBS) in urban and rural schools-Potential roles of indoor microbial amino acids and vitamin metabolites
- 2021
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Ingår i: Science of the Total Environment. - : Elsevier. - 0048-9697 .- 1879-1026. ; 795
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Tidskriftsartikel (refereegranskat)abstract
- Sick building symptoms (SBS) are defined as non-specific symptoms related to indoor exposures, including mucosal symptoms in eye, nose, throat, and skin, and general symptoms as headache and tiredness. Indoor microbial composition is associated with SBS symptoms, but the impact of microbial functional genes and potential metabolic products has not been characterized. We conducted a shotgun microbial metagenomic sequencing for vacuum dust collected in urban and rural schools in Shanxi province, China. SBS symptoms in students were surveyed, and microbial taxa and functional pathways related to the symptoms were identified using a multilevel linear regression model. SBS symptoms were common in students, and the prevalence of ocular and throat symptoms, headache, and tiredness was higher in urban than in rural areas (p < 0.05). A significant higher microbial alpha-diversity was found in rural areas than in urban areas (Chao1, p = 0.001; ACE, p = 0.002). Also, significant variation in microbial taxonomic and functional composition (beta-diversity) was observed between urban and rural areas (p < 0.005). Five potential risk Actinobacteria species were associated with SBS symptoms (p < 0.01); students in the classrooms with a higher abundance of an unclassified Geodermatophilaceae, Geodermatophilus, Fridmanniella luteola, Microlunatus phosphovorus and Mycetocola reported more nasal and throat symptoms and tiredness. Students with a higher abundance of an unclassified flavobacteriaceae reported fewer throat symptoms and tiredness. The abundance of microbial metabolic pathways related to the synthesis of B vitamins (biotin and folate), gamma-aminobutyric acid (GABA), short-chain fatty acids (SCFAs), and peptidoglycan and were protectively (negatively) associated with SBS symptoms (FDR < 0.05). The result is consistent with human microbiota studies, which reported that these microbial products are extensively involved in immunological processes and anti-inflammatory effects. This is the first study to report the functional potential of the indoor microbiome and the occurrence of SBS, providing new insights into the potential etiologic mechanisms in chronic inflammatory diseases.
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| 8. |
- Fu, Xi, et al.
(författare)
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Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China : association with asthma, rhinitis and rhinoconjunctivitis in high school students
- 2021
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Ingår i: Microbiome. - : Springer Nature. - 2049-2618. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundStudies in developed countries have reported that the prevalence of asthma and rhinitis is higher in urban areas than in rural areas, and this phenomenon is associated with urbanization and changing indoor microbiome exposure. Developing countries such as China have experienced rapid urbanization in past years, but no study has investigated microbiome exposure and urban-rural health effects in these countries.MethodsNine high schools from urban and rural areas were randomly selected in Shanxi Province, China, and classroom vacuum dust was collected for shotgun metagenomic sequencing. A self-administered questionnaire was collected from 1332 students for personal information and health data. Three-level logistic regression was performed between microbial richness/abundance/functional pathways and the occurrence of asthma and rhinitis symptoms.ResultsConsistent with developed countries, the prevalence of wheeze and rhinitis was higher in urban areas than in rural areas (p < 0.05). Metagenomic profiling revealed 8302 bacterial, 395 archaeal, 744 fungal, 524 protist and 1103 viral species in classroom dust. Actinobacteria (mean relative abundance 49.7%), Gammaproteobacteria (18.4%) and Alphaproteobacteria (10.0%) were the most abundant bacterial classes. The overall microbiome composition was significantly different between urban and rural schools (p = 0.001, Adonis). Species from Betaproteobactera, Gammaproteobacteria and Bacilli were enriched in urban schools, and species from Actinobacteria and Cyanobacteria were enriched in rural schools. Potential pathogens were present in higher abundance in urban schools than in rural schools (p < 0.05). Pseudoalteromonas, Neospora caninum and Microbacterium foliorum were positively associated with the occurrence of wheeze, rhinitis and rhinoconjunctivitis, and Brachybacterium was protectively (negatively) associated with rhinitis (p < 0.01). The abundance of human endocrine and metabolic disease pathways was positively associated with rhinitis (p = 0.008), and butyrate and propionate metabolic genes and pathways were significantly enriched in rural schools (p < 0.005), in line with previous findings that these short-chain fatty acids protect against inflammatory diseases in the human gut.ConclusionsWe conducted the first indoor microbiome survey in urban/rural environments with shotgun metagenomics, and the results revealed high-resolution microbial taxonomic and functional profiling and potential health effects.
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| 9. |
- Fu, Xi, et al.
(författare)
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Microbial Virulence Factors, Antimicrobial Resistance Genes, Metabolites, and Synthetic Chemicals in Cabins of Commercial Aircraft
- 2023
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Ingår i: Metabolites. - : MDPI. - 2218-1989 .- 2218-1989. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- Passengers are at a higher risk of respiratory infections and chronic diseases due to microbial exposure in airline cabins. However, the presence of virulence factors (VFs), antimicrobial resistance genes (ARGs), metabolites, and chemicals are yet to be studied. To address this gap, we collected dust samples from the cabins of two airlines, one with textile seats (TSC) and one with leather seats (LSC), and analyzed the exposure using shotgun metagenomics and LC/MS. Results showed that the abundances of 17 VFs and 11 risk chemicals were significantly higher in TSC than LSC (p < 0.01). The predominant VFs in TSC were related to adherence, biofilm formation, and immune modulation, mainly derived from facultative pathogens such as Haemophilus parainfluenzae and Streptococcus pneumoniae. The predominant risk chemicals in TSC included pesticides/herbicides (carbofuran, bromacil, and propazine) and detergents (triethanolamine, diethanolamine, and diethyl phthalate). The abundances of these VFs and detergents followed the trend of TSC > LSC > school classrooms (p < 0.01), potentially explaining the higher incidence of infectious and chronic inflammatory diseases in aircraft. The level of ARGs in aircraft was similar to that in school environments. This is the first multi-omic survey in commercial aircraft, highlighting that surface material choice is a potential intervention strategy for improving passenger health.
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| 10. |
- Ji, Qinglei, et al.
(författare)
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A Flexible 4D Printing Service Platform for Smart Manufacturing
- 2020
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Ingår i: Swedish Production Symposium.
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Konferensbidrag (refereegranskat)abstract
- With the extensive application of 3D printing (3DP) in smartmanufacturing, 4D printing (4DP), which enhances 3D printed objects with shapemorphing ability by using smart materials, has shown significant industrial potentialand attracted tremendous attention. One key concern of 4DP is how to effectivelyand quickly meet different production and application requirements considering thecomplexity of materials and diversity of stimulus methods. In order to provide ageneral research platform for 4DP researchers, a flexible 4DP service platform isproposed. Components and modules for building 4DP and test systems are modeledand virtualized to form the different resources. These resources are then integratedvirtually or physically to provide some basic functions such as a 3D displacementstage or a visual monitoring system. According to different 4DP requirements, thesefunctions are then encapsulated into services to serve different research. Theplatform enables a variety of 4DP applications in smart manufacturing environmentssuch as 4D printed magnetic medical robots, test platform for studying the 4DPresponse, etc. A case study on designing a ferromagnetic 4DP platform based on theservice platform is performed to prove the feasibility of the method.
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