| 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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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Stanaway, Jeffrey D., et al.
(författare)
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Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990-2017: A systematic analysis for the Global Burden of Disease Study 2017
- 2018
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Ingår i: The Lancet. - 1474-547X .- 0140-6736. ; 392:10159, s. 1923-1994
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Tidskriftsartikel (refereegranskat)abstract
- Background The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 comparative risk assessment (CRA) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk-outcome associations. With each annual GBD study, we update the GBD CRA to incorporate improved methods, new risks and risk-outcome pairs, and new data on risk exposure levels and risk- outcome associations. Methods We used the CRA framework developed for previous iterations of GBD to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. This study included 476 risk-outcome pairs that met the GBD study criteria for convincing or probable evidence of causation. We extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. Using the counterfactual scenario of theoretical minimum risk exposure level (TMREL), we estimated the portion of deaths and DALYs that could be attributed to a given risk. We explored the relationship between development and risk exposure by modelling the relationship between the Socio-demographic Index (SDI) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by SDI. Finally, we explored temporal changes in risk-attributable DALYs by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and DALY rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the TMREL for all risk factors included in GBD 2017.
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| 4. |
- Deng, Liying, et al.
(författare)
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KCl acts as a flux to assist the growth of sub-millimeter-scale metallic 2D non-layered molybdenum dioxide
- 2024
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Ingår i: Rare Metals. - 1001-0521 .- 1867-7185. ; In Press
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Tidskriftsartikel (refereegranskat)abstract
- Two-dimensional (2D) metal oxides (2DMOs), such as MoO2, have made impressive strides in recent years, and their applicability in a number of fields such as electronic devices, optoelectronic devices and lasers has been demonstrated. However, 2DMOs present challenges in their synthesis using conventional methods due to their non-van der Waals nature. We report that KCl acts as a flux to prepare large-area 2DMOs with sub-millimeter scale. We systematically investigate the effects of temperature, homogeneous time and cooling rate on the products in the flux method, demonstrating that in this reaction a saturated homogenous solution is obtained upon the melting of the salt and precursor. Afterward, the cooling rate was adjusted to regulate the thickness of the target crystals, leading to the precipitation of 2D non-layered material from the supersaturated solution; by applying this method, the highly crystalline non-layered 2D MoO2 flakes with so far the largest lateral size of up to sub-millimeter scale (~ 464 μm) were yielded. Electrical studies have revealed that the 2D MoO2 features metallic properties, with an excellent sheet resistance as low as 99 Ω·square−1 at room temperature, and exhibits a property of charge density wave in the measurement of resistivity as a function of temperature. Graphical abstract: TOC (Table of Content) (Figure presented.)
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| 5. |
- Ding, Shaozhen, et al.
(författare)
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novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model
- 2020
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:W1, s. W477-W487
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Tidskriftsartikel (refereegranskat)abstract
- To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/.
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| 6. |
- Han, Mengying, et al.
(författare)
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ChemHub: a knowledgebase of functional chemicals for synthetic biology studies
- 2021
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 37:22, s. 4275-4276
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Tidskriftsartikel (refereegranskat)abstract
- The field of synthetic biology lacks a comprehensive knowledgebase for selecting synthetic target molecules according to their functions, economic applications and known biosynthetic pathways. We implemented ChemHub, a knowledgebase containing >90 000 chemicals and their functions, along with related biosynthesis information for these chemicals that was manually extracted from >600 000 published studies by more than 100 people over the past 10 years.
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| 7. |
- Hsu, Li-Han, 1981, et al.
(författare)
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Design of Flip-Chip Interconnect Using Epoxy-Based Underfill Up to V-Band Frequencies With Excellent Reliability
- 2010
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Ingår i: IEEE Transactions on Microwave Theory and Techniques. - 0018-9480 .- 1557-9670. ; 58:8, s. 2244-2250
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- This study demonstrates a flip-chip interconnect with epoxy-based underfill (epsilon(r) = 3.5 and tan delta = 0.02 at 10 MHz) for packaging applications up to V-band frequencies. To achieve the best interconnect performance, both the matching designs on GaAs chip and Al2O3 substrate were adopted with the underfill effects taken into consideration. The optimized flip-chip interconnect showed excellent performance from dc to 67 GHz with return loss below -20 dB and insertion loss less than 0.6 dB. Furthermore, the dielectric loss induced by the underfill was extracted from measurement and compared with the simulation results. The reliability tests including 85 degrees C/85 % relative humidity test, thermal cycling test, and shear force test were performed. For the first time, the S-parameters measurement was performed to check the flip-chip reliability, and no performance decay was observed after 1000 thermal cycles. Moreover, the mechanical strength was improved about 12 times after the underfill was applied. The results show that the proposed flip-chip architecture has excellent reliability and can be applied for commercial applications.
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| 8. |
- Hu, M., et al.
(författare)
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Decision Tree-Based Maneuver Prediction for Driver Rear-End Risk-Avoidance Behaviors in Cut-In Scenarios
- 2017
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Ingår i: Journal of Advanced Transportation. - : Hindawi Limited. - 0197-6729 .- 2042-3195. ; 2017, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- Predicting driver rear-end risk-avoidance maneuvers in cut-in scenarios, especially dangerous precrash scenarios, benefits the customization of automatic driving, particularly automatic steering. This paper studies driver rear-end risk-avoidance behaviors in cut-in scenarios on a straight three-lane highway. Data from 24 participants in 1326 valid trials were collected using amotion-based driving simulator. An Eysenck Personality Questionnaire (revised for Chinese participants) was used to obtain the personality traits of the participants. Based on a statistical analysis, the candidate features used in the driver maneuver prediction were determined as a combination of objective risk indicators and driver characteristics. A decision tree-based model was constructed for maneuver prediction in cut-in scenarios. The prediction accuracy of the extracted classification rules was 79.2% for the training data set and 80.3% for the test data set. The most powerful predictive variables were extracted, and their effects on maneuver decisions were analyzed. The results show that driver characteristics strongly influence the prediction of maneuver decisions.
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| 9. |
- Liu, Xiuyu, et al.
(författare)
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Structure-function analysis of CYP719As involved in methylenedioxy bridge-formation in the biosynthesis of benzylisoquinoline alkaloids and its de novo production
- 2023
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Ingår i: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Benzylisoquinoline alkaloids (BIAs) are a type of secondary metabolite with clinical application value. (S)-stylopine is a special BIA which contains methylenedioxy bridge structures. CYP719As could catalyze the methylenedioxy bridge-formation on the A or D rings of protoberberine alkaloids, while displaying significant substrate regiospecificity. To explore the substrate preference of CYP719As, we cloned and identified five CyCYP719A candidates from Corydalis yanhusuo. Two CyCYP719As (CyCYP719A39 and CyCYP719A42) with high catalytic efficiency for the methylenedioxy bridge-formation on the D or A rings were characterized, respectively. The residues (Leu 294 for CyCYP719A42 and Asp 289 for CyCYP719A39) were identified as the key to controlling the regioselectivity of CYP719As affecting the methylenedioxy bridge-formation on the A or D rings by homology modeling and mutation analysis. Furthermore, for de novo production of BIAs, CyCYP719A39, CyCYP719A42, and their mutants were introduced into the (S)-scoulerine-producing yeast to produce 32 mg/L (S)-stylopine. These results lay a foundation for understanding the structure-function relationship of CYP719A-mediated methylenedioxy bridge-formation and provide yeast strains for the BIAs production by synthetic biology.
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| 10. |
- Nabiollahi, Nabi, 1983, et al.
(författare)
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FEM Simulation of Bimodal and Trimodal Thermally Conductive Adhesives
- 2009
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Ingår i: 2009 9th IEEE Conference on Nanotechnology, IEEE NANO 2009; Genoa; Italy; 26 July 2009 through 30 July 2009. - 9789810836948 ; , s. 422-425
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Konferensbidrag (refereegranskat)abstract
- A simulation with combination of a finite element analysis of Thermally Conductive Adhesive and contact resistance modeling has been presented. Using ANSYS and MATLAB software thermal conductivity and electrical resistivity of Conductive Adhesives with Ag filler and Epoxy matrix has been calculated. Thermally Conductive Adhesives are used as a thermal interface material to provide a better conduction and heat transfer between two surfaces. The results show that the conductivity dependency is relatively high for different filler shape and alignment. Discussed models are bimodal, Ag flakes and Ag spherical micro particles and trimodal with Multi-WallCNT nano particles.
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