| 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. |
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| 3. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 4. |
- Melgarejo, Jesus D., et al.
(författare)
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Association of Fatal and Nonfatal Cardiovascular Outcomes With 24-Hour Mean Arterial Pressure
- 2021
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Ingår i: Hypertension. - : Wolters Kluwer. - 0194-911X .- 1524-4563. ; 77:1, s. 39-48
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Tidskriftsartikel (refereegranskat)abstract
- Major adverse cardiovascular events are closely associated with 24-hour blood pressure (BP). We determined outcome-driven thresholds for 24-hour mean arterial pressure (MAP), a BP index estimated by oscillometric devices. We assessed the association of major adverse cardiovascular events with 24-hour MAP, systolic BP (SBP), and diastolic BP (DBP) in a population-based cohort (n=11 596). Statistics included multivariable Cox regression and the generalized R-2 statistic to test model fit. Baseline office and 24-hour MAP averaged 97.4 and 90.4 mm Hg. Over 13.6 years (median), 2034 major adverse cardiovascular events occurred. Twenty-four-hour MAP levels of <90 (normotension, n=6183), 90 to <92 (elevated MAP, n=909), 92 to <96 (stage-1 hypertension, n=1544), and >= 96 (stage-2 hypertension, n=2960) mm Hg yielded equivalent 10-year major adverse cardiovascular events risks as office MAP categorized using 2017 American thresholds for office SBP and DBP. Compared with 24-hour MAP normotension, hazard ratios were 0.96 (95% CI, 0.80-1.16), 1.32 (1.15-1.51), and 1.77 (1.59-1.97), for elevated and stage-1 and stage-2 hypertensive MAP. On top of 24-hour MAP, higher 24-hour SBP increased, whereas higher 24-hour DBP attenuated risk (P<0.001). Considering the 24-hour measurements, R-2 statistics were similar for SBP (1.34) and MAP (1.28), lower for DBP than for MAP (0.47), and reduced to null, if the base model included SBP and DBP; if the ambulatory BP indexes were dichotomized according to the 2017 American guideline and the proposed 92 mm Hg for MAP, the R-2 values were 0.71, 0.89, 0.32, and 0.10, respectively. In conclusion, the clinical application of 24-hour MAP thresholds in conjunction with SBP and DBP refines risk estimates.
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| 5. |
- Wu, Jingnan, 1994, et al.
(författare)
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Modulating the nanoscale morphology on carboxylate-pyrazine containing terpolymer toward 17.8% efficiency organic solar cells with enhanced thermal stability
- 2022
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Ingår i: Chemical Engineering Journal. - : Elsevier BV. - 1385-8947. ; 446
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Tidskriftsartikel (refereegranskat)abstract
- It had been commonly accepted in the organic photovoltaic (OPV) community that subtle variations in the molecular structure of active layer materials would cause profound impacts on their aggregating structure and blend morphology and therefore the performance of such polymer solar cells (PSCs). Herein, we employed an electron-deficient building block 3,6-dithiophenyl-2-carboxylate pyrazine (DTCPz) for constructing one series of promising donor terpolymers of PMZ1, PMZ2, and PMZ3, respectively, gaining their relatively lower-lying highest occupied molecular orbital (HOMO) energy levels, more closed π-π stacking and enhanced crystallinity in thin films, and lower miscibility with acceptor Y6, in comparison with their parent polymer counterpart (namely PM6). Reaching DTCPz moieties up to 20% (mol/mol%) in its terpolymer composition, the resulting polymer (PMZ2) achieved more favorable phase separation with improved exciton dissociation, and charge transport and extraction. As a result, an outstanding fill factor of 77.2% and a promising power conversion efficiency of 17.8 % was achieved. Moreover, the corresponding device shows better thermal stability over the PM6-based one. This work suggests a facile method for significantly improving the thin film morphology of the active-layer materials via fine-tuning the chemical structure of electron-deficient units on the backbone of the wide bandgap donor polymer, therefore achieving enhanced photovoltaic performance and thermal stability for practical applications.
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| 6. |
- Armstrong, Joel, et al.
(författare)
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Progressive Cactus is a multiple-genome aligner for the thousand-genome era
- 2020
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 587:7833, s. 246-251
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Tidskriftsartikel (refereegranskat)abstract
- New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies(1-3). For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database(4) increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies(5) are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes. This coming era and its unprecedented amount of data offer the opportunity to uncover many insights into genome evolution but also present challenges in how to adapt current analysis methods to meet the increased scale. Cactus(6), a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequences. Here we describe progressive extensions to Cactus to create Progressive Cactus, which enables the reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We describe results from an alignment of more than 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment created so far. The Progressive Cactus program can create reference-free alignments of hundreds of large vertebrate genomes efficiently, and is used for the alignment of more than 600 amniote genomes.
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| 7. |
- Chen, Yu, et al.
(författare)
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The thermodynamics of enhanced dope stability of cellulose solution in NaOH solution by urea
- 2023
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Ingår i: Carbohydrate Polymers. - : Elsevier BV. - 0144-8617 .- 1879-1344. ; 311, s. 120744-
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Tidskriftsartikel (refereegranskat)abstract
- The addition of urea in pre-cooled alkali aqueous solution is known to improve the dope stability of cellulose solution. However, its thermodynamic mechanism at a molecular level is not fully understood yet. By using molecular dynamics simulation of an aqueous NaOH/urea/cellulose system using an empirical force field, we found that urea was concentrated in the first solvation shell of the cellulose chain stabilized mainly by dispersion interaction. When adding a glucan chain into the solution, the total solvent entropy reduction is smaller if urea is present. Each urea molecule expelled an average of 2.3 water molecules away from the cellulose surface, releasing water entropy that over-compensates the entropy loss of urea and thus maximizing the total entropy. Scaling the Lennard-Jones parameter and atomistic partial charge of urea revealed that direct urea/cellulose interaction was also driven by dispersion energy. The mixing of urea solution and cellulose solution in the presence or absence of NaOH are both exothermic even after correcting for the contribution from dilution.
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| 8. |
- 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.
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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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| 9. |
- Despeisse, Mélanie, 1985, et al.
(författare)
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Battery Production Systems: State of the Art and Future Developments
- 2023
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Ingår i: IFIP Advances in Information and Communication Technology. - 1868-4238 .- 1868-422X. ; 692, s. 521-535
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Konferensbidrag (refereegranskat)abstract
- This paper discusses the state of the art in battery production research, focusing on high-importance topics to address industrial needs and sustainability goals in this rapidly growing field. We first present current research around three themes: human-centred production, smart production management, and sustainable manufacturing value chains. For each theme, key subtopics are explored to potentially transform battery value chains and shift to more sustainable production models. Such systemic transformations are supported by technological advances to enable superior manufacturing performance through: skills and competence development, improved production ergonomics and human factors, automation and human-robot collaboration, smart production planning and control, smart maintenance, data-driven solutions for production quality and its impact on battery performance (operational efficiency and durability), circular battery systems supported by service-based business models, more integrated and digitalized value chains, and increased industrial resilience. Each subtopic is discussed to suggest directions for further research to realise the full potential of digitalization for sustainable battery production.
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| 10. |
- Despeisse, Mélanie, 1985, et al.
(författare)
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Developing Data Models for Smart Environmental Performance Management in Production
- 2023
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Ingår i: IFIP Advances in Information and Communication Technology. - 1868-4238 .- 1868-422X. ; 692, s. 3-15
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Konferensbidrag (refereegranskat)abstract
- For manufacturing companies to prosper in the long term, they must demonstrate contribution to sustainable development by implementing greener practices using approaches such eco-efficiency and circular economy; i.e., creating social and economic value while minimising the environmental impact of production through efficient, closed-loop circulation of resources. In addition, industrial digitalization presents new opportunities to unlock new ways to measure complex systems’ performance and systematically improve towards circular economy and sustainability. This paper presents the results of a feasibility study aiming to develop a practical toolkit to implement environmental sustainability concepts at factory level. To achieve the project objective, we focused on data handling practices for environmental performance management, including process mapping, data inventory, data quality assessment, and gap analysis to identify existing strengths and define areas of improvement to boost the environmental performance of production systems.
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