| 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. |
- Chen, Jie, et al.
(författare)
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Bidirectional Mendelian Randomisation Analysis Provides Evidence for the Causal Involvement of Dysregulation of CXCL9, CCL11 and CASP8 in the Pathogenesis of Ulcerative Colitis
- 2023
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Ingår i: Journal of Crohn's & Colitis. - : Oxford University Press. - 1873-9946 .- 1876-4479. ; 17:5, s. 777-785
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Tidskriftsartikel (refereegranskat)abstract
- Background and Aims Systemic inflammation is well recognised to be associated with ulcerative colitis [UC], but whether these effects are causal or consequential remains unclear. We aimed to define potential causal relationship of cytokine dysregulation with different tiers of evidence. Methods We first synthesised serum proteomic profiling data from two multicentred observational studies, in which a panel of systemic inflammatory proteins was analysed to examine their associations with UC risk. To further dissect observed associations, we then performed a bidirectional two-sample Mendelian randomisation [TSMR] analysis from both forward and reverse directions using five genome-wide association study [GWAS] summary level data for serum proteomic profiles and the largest GWAS of 28 738 European-ancestry individuals for UC risk. Results Pooled analysis of serum proteomic data identified 14 proteins to be associated with the risk of UC. Forward MR analysis using only cis-acting protein quantitative trait loci [cis-pQTLs] or trans-pQTLs further validated causal associations of two chemokines and the increased risk of UC: C-X-C motif chemokine ligand 9 [CXCL9] [OR 1.45, 95% CI 1.08, 1.95, p = 0.012] and C-C motif chemokine ligand 11 [CCL11] [OR 1.14, 95% CI 1.09, 1.18, p = 3.89 x 10(-10)]. Using both cis- and trans-acting pQTLs, an association of caspase-8 [CASP8] [OR 1.04, 95% CI 1.03, 1.05, p = 7.63 x 10(-19)] was additionally identified. Reverse MR did not find any influence of genetic predisposition to UC on any of these three inflammation proteins. Conclusion Pre-existing elevated levels of CXCL9, CCL11 and CASP8 may play a role in the pathogenesis of UC.
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| 3. |
- Li, Shaohan, et al.
(författare)
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Pushing the limit of thermal conductivity of MAX borides and MABs
- 2022
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Ingår i: Journal of Materials Science & Technology. - : Elsevier. - 1005-0302. ; 97, s. 79-88
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Tidskriftsartikel (refereegranskat)abstract
- The emergence of MAX borides as well as MAB phases attracted great attention because of the renewable developments of ternary ceramics and offering great opportunities in potential applications. However, the number of borides remains limited, and further fundamental descriptions and detailed investigations on various properties are still lacking. In this report, we employ an integrated computational scheme that combines density functional theory with the evolutional algorithm to search for the favorable structures of P- and S-glued ternary borides terminated by Nb metal. We discover that the structures of 212-type, as e.g. Nb2PB2 and Nb2SB2, belong to the P‾6m2 space group, while those of 211-type, as e.g. Nb2PB and Nb2SB, prefer to crystallize in the P63/mmc space group, and the corresponding carbides Nb2PC and Nb2SC are also considered for the sake of completeness and comparative analsys. The predicted Nb2PB2, Nb2PB, Nb2SB, Nb2PC and Nb2SC are energetically stable, as revealed by the negative formation energies and by the proposed reaction paths with respect to the most competing phases, as well as dynamically stable, as suggested by the non-imaginary phonon spectra. The thermal conductivities of the six materials show unusual behaviors, particularly for the acoustic and optical contributions, and are accompanied by a strong anisotropy. Most importantly, Nb2PB2 is found to be an excellent thermal conductor with a total thermal conductivity of ~65 W/(m K), while Nb2SC is found to be an ultra-low thermal conductor, with a total thermal conductivity of ~5 W/(m K). These values are clearly outside the currently reported range of thermal conductivities, which makes Nb2PB2 and Nb2SC extremely interesting for fundamental research as well as prospective applications with the aid of artificial tunings on the almost independent MB block and the A layer. The discovery of these novel materials is expected to contribute substantially to the rapid development of ternary ceramics and to accelerate attempts in the applicability of MAX phases for heat conduction.
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| 4. |
- Sun, Yuhao, et al.
(författare)
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The Contribution of Genetic Risk and Lifestyle Factors in the Development of Adult-Onset Inflammatory Bowel Disease : A Prospective Cohort Study
- 2023
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Ingår i: American Journal of Gastroenterology. - : Lippincott Williams & Wilkins. - 0002-9270 .- 1572-0241. ; 118:3, s. 511-522
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: The joint associations across genetic risk, modifiable lifestyle factors, and inflammatory bowel disease (IBD) remains unclear.METHODS: Genetic susceptibility to Crohn's disease (CD) and ulcerative colitis (UC) was estimated by polygenic risk scores and further categorized into high, intermediate, and low genetic risk categories. Weighted healthy lifestyle scores were constructed based on 5 common lifestyle factors and categorized into favorable (4 or 5 healthy lifestyle factors), intermediate (3 healthy lifestyle factors), and unfavorable (0-2 healthy lifestyle factors) groups. Cox proportional hazards regression model was used to estimate the hazard ratios (HR) and 95% confidence interval (CI) for their associations.RESULTS: During the 12-year follow-up, 707 cases with CD and 1576 cases with UC were diagnosed in the UK Biobank cohort. Genetic risk and unhealthy lifestyle categories were monotonically associated with CD and UC risk with no multiplicative interaction between them. The HR of CD and UC were 2.24 (95% CI 1.75-2.86) and 2.15 (95% CI 1.82-2.53) for those with a high genetic risk, respectively. The HR of CD and UC for individuals with an unfavorable lifestyle were 1.94 (95% CI 1.61-2.33) and 1.98 (95% CI 1.73-2.27), respectively. The HR of individuals with a high genetic risk but a favorable lifestyle (2.33, 95% CI 1.58-3.44 for CD, and 2.05, 95% CI 1.58-2.66 for UC) were reduced nearly by half, compared with those with a high genetic risk but an unfavorable lifestyle (4.40, 95% CI 2.91-6.66 for CD and 4.44, 95% CI 3.34-5.91 for UC).DISCUSSION: Genetic and lifestyle factors were independently associated with susceptibility to incident CD and UC. Adherence to a favorable lifestyle was associated with a nearly 50% lower risk of CD and UC among participants at a high genetic risk.
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| 5. |
- Yuan, Shuai, et al.
(författare)
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Sleep duration and daytime napping in relation to incident inflammatory bowel disease : a prospective cohort study
- 2023
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Ingår i: Alimentary Pharmacology and Therapeutics. - : John Wiley & Sons. - 0269-2813 .- 1365-2036. ; 57:5, s. 475-485
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Sleep dysregulation has been linked to gastrointestinal dysfunction and inflammation.AIMS: To explore the associations between sleep duration, daytime napping and inflammatory bowel disease (IBD), Crohn's disease (CD) and ulcerative colitis (UC).METHODS: Exposure information was obtained from the baseline questionnaire. Sleep duration was coded as continuous and categorical (≤5, 6, 7, 8, ≥9 h/day) variables. Daytime napping was defined as yes (sometimes/usually) and no (never/rarely). Incident IBD cases were defined from primary care and hospital inpatient records. Polygenic risk scores (PRS) for the outcomes were constructed and categorised into low, intermediate and high risk. Hazard ratio (HR) and confidence interval (CI) were estimated using Cox proportional hazard regression.RESULTS: The analysis included 2604 incident IBD cases (806 CD and 1798 UC) with a median follow-up of 12.0 years. Comparing sleep duration ≤5 with 7 h/day, the HR of IBD, CD and UC was 1.36 (95% CI, 1.17-1.59), 1.53 (95% CI, 1.17-2.00) and 1.29 (95% CI, 1.07-1.56), respectively. Comparing participants with and without daytime napping, the HR of IBD, CD and UC was 1.13 (95% CI, 1.05-1.23), 1.25 (95% CI, 1.08-1.44) and 1.09 (95% CI, 0.90-1.20), respectively. No interaction of sleep duration and daytime napping with PRS was detected. However, the associations appeared stronger in individuals with high rather than low PRS.CONCLUSIONS: This study reveals positive associations between short sleep duration and daytime napping and IBD risk.
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| 6. |
- Chen, Zhibin, et al.
(författare)
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Summary of the 3rd International Workshop on Gas-Dynamic Trap based Fusion Neutron Source (GDT-FNS)
- 2022
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:6
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Tidskriftsartikel (refereegranskat)abstract
- The 3rd International Workshop on Gas-Dynamic Trap-based Fusion Neutron Source (GDT-FNS) was held through the hybrid mode on 13-14 September 2021 in Hefei, China, jointly organized by the Hefei Institutes of Physical Science (HFIPS), Chinese Academy of Sciences (CAS), and the Budker Institute of Nuclear Physics (BINP), Russian Academy of Sciences (RAS). It followed the 1st GDT-FNS Workshop held in November 2018 in Hefei, China, and the 2nd taking place in November 2019 in Novosibirsk, Russian Federation. With the financial support from CAS and China Association for Science and Technology (CAST), this workshop was attended by more than 80 participants representing 20 institutes and universities from seven countries, with oral presentations broadcast via the Zoom conferencing system. Twenty-two presentations were made with topics covering design and key technologies, simulation and experiments, steady-state operation, status of the ALIANCE project, multi applications of neutron sources, and other concepts (Tokamaks, Mirrors, FRC, Plasma Focus, etc). The workshop consensus was made including the establishment of the ALIANCE International Working Group. The next GDT-FNS workshop is planned to be held in May 2022 in Novosibirsk.
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| 7. |
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| 8. |
- Garemark, Jonas, et al.
(författare)
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Top-Down Approach Making Anisotropic Cellulose Aerogels as Universal Substrates for Multifunctionalization
- 2020
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Ingår i: ACS Nano. - : AMER CHEMICAL SOC. - 1936-0851 .- 1936-086X. ; 14:6, s. 7111-7120
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Tidskriftsartikel (refereegranskat)abstract
- Highly porous, strong aerogels with anisotropic structural properties are of great interest for multifunctional materials for applications including insulators in buildings, filters for oil cleanup, electrical storage devices, etc. Contemporary aerogels are mostly extracted from fossil resources and synthesized from bottom-up techniques, often requiring additional strategies to obtain high anisotropy. In this work, a universal approach to prepare porous, strong, anisotropic aerogels is presented through exploiting the natural hierarchical and anisotropic structure of wood. The preparation comprises nanoscale removal of lignin, followed by dissolution-regeneration of nanofibers, leading to enhanced cell wall porosity with nanofibrillated networks occupying the pore space in the cellular wood structure. The aerogels retain structural anisotropy of natural wood, exhibit specific surface areas up to 247 m(2)/g, and show high compression strength at 95% porosity. This is a record specific area value for wood aerogels/foams and even higher than most cellulose-based aerogels for its assigned strength. The aerogel can serve as a platform for multifunctional composites including scaffolds for catalysis, gas separation, or liquid purification due to its porous matrix or as binder-free electrodes in electronics. To demonstrate the multifunctionality, the aerogels are successfully decorated with metal nanoparticles (Ag) and metal oxide nanoparticles (TiO2) by in situ synthesis, coated by the conductive polymer (PEDOT:PSS), and carbonized to yield conductive aerogels. This approach is found to be a universal way to prepare highly porous anisotropic aerogels.
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| 9. |
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| 10. |
- Jiang, Fangyuan, et al.
(författare)
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Association between antibiotic use during early life and early-onset colorectal cancer risk overall and according to polygenic risk and FUT2 genotypes
- 2023
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Ingår i: International Journal of Cancer. - : John Wiley & Sons. - 0020-7136 .- 1097-0215. ; 153:9, s. 1602-1611
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Tidskriftsartikel (refereegranskat)abstract
- Early-onset colorectal cancer (EOCRC) has been increasing worldwide. Potential risk factors may have occurred in childhood or adolescence. We investigated the associations between early-life factors and EOCRC risk, with a particular focus on long-term or recurrent antibiotic use (LRAU) and its interaction with genetic factors. Data on the UK Biobank participants recruited between 2006 and 2010 and followed up to February 2022 were used. We used logistic regression to estimate adjusted odds ratios (ORs) and 95% confidence intervals (95% CIs) of the associations between LRAU during early life and EOCRC risk overall and by polygenic risk score (constructed by 127 CRC-related genetic variants) and Fucosyltransferase 2 (FUT2), a gut microbiota regulatory gene. We also assessed the associations for early-onset colorectal adenomas, as precursor lesion of CRC, to examine the effect of LRAU during early-life and genetic factors on colorectal carcinogenesis. A total of 113 256 participants were included in the analysis, with 165 EOCRC cases and 719 EOCRA cases. LRAU was nominally associated with increased risk of early-onset CRC (OR = 1.48, 95% CI = 1.01-2.17, P = .046) and adenomas (OR = 1.40, 95% CI = 1.17-1.68, P < .001). When stratified by genetic polymorphisms of FUT2, LRAU appeared to confer a comparatively greater risk for early-onset adenomas among participants with rs281377 TT genotype (OR = 1.10, 95% CI = 0.79-1.52, P = .587, for CC genotype; OR = 1.75, 95% CI = 1.16-2.64, P = .008, for TT genotype; Pinteraction = .089). Our study suggested that LRAU during early life is associated with increased risk of early-onset CRC and adenomas, and the association for adenomas is predominant among individuals with rs281377 TT/CT genotype. Further studies investigating how LRAU contributes together with genetic factors to modify EOCRC risk, particularly concerning the microbiome-related pathway underlying colorectal carcinogenesis, are warranted.
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