| 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. |
- Liu, Yang, et al.
(författare)
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MiR-378a suppresses tenogenic differentiation and tendon repair by targeting at TGF-β2
- 2019
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Ingår i: Stem Cell Research and Therapy. - : Springer Science and Business Media LLC. - 1757-6512. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Tendons are a crucial component of the musculoskeletal system and responsible for transmission forces derived from muscle to bone. Patients with tendon injuries are often observed with decreased collagen production and matrix degeneration, and healing of tendon injuries remains a challenge as a result of limited understanding of tendon biology. Recent studies highlight the contribution of miR-378a on the regulation gene expression during tendon differentiation. Methods: We examined the tendon microstructure and tendon repair with using miR-378a knock-in transgenic mice, and the tendon-derived stem cells were also isolated from transgenic mice to study their tenogenic differentiation ability. Meanwhile, the expression levels of tenogenic markers were also examined in mouse tendon-derived stem cells transfected with miR-378a mimics during tenogenic differentiation. With using online prediction software and luciferase reporter assay, the binding target of miR-378a was also studied. Results: Our results indicated miR-378a impairs tenogenic differentiation and tendon repair by inhibition collagen and extracellular matrix production both in vitro and in vivo. We also demonstrated that miR-378a exert its inhibitory role during tenogenic differentiation through binding at TGFβ2 by luciferase reporter assay and western blot. Conclusions: Our investigation suggests that miR-378a could be considered as a new potential biomarker for tendon injury diagnosis or drug target for a possible therapeutic approach in future clinical practice.
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| 3. |
- Lu, Yingchang, et al.
(författare)
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Identification of Novel Loci and New Risk Variant in Known Loci for Colorectal Cancer Risk in East Asians
- 2020
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Ingår i: Cancer Epidemiology, Biomarkers and Prevention. - : American Association for Cancer Research. - 1055-9965 .- 1538-7755. ; 29:2, s. 477-486
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Tidskriftsartikel (refereegranskat)abstract
- Background: Risk variants identified so far for colorectal cancer explain only a small proportion of milial risk of this cancer, particularly in Asians.Methods: We performed a genome-wide association study (GWAS) of colorectal cancer in East Asians, cluding 23,572 colorectal cancer cases and 48,700 controls. To identify novel risk loci, we selected 60 omising risk variants for replication using data from 58,131 colorectal cancer cases and 67,347 controls European descent. To identify additional risk variants in known colorectal cancer loci, we performed nditional analyses in East Asians.Results: An indel variant, rs67052019 at 1p13.3, was found to be associated with colorectal cancer risk P = 3.9 x 10(-8) in Asians (OR per allele deletion = 1.13, 95% confidence interval = 1.08-1.18). This sociation was replicated in European descendants using a variant (rs2938616) in complete linkage sequilibrium with rs67052019 (P = 7.7 x 10(-3)). Of the remaining 59 variants, 12 showed an association P < 0.05 in the European-ancestry study, including rs11108175 and rs9634162 at P < 5 x 10(-8) and o variants with an association near the genome-wide significance level (rs60911071, P = 5.8 x 10(-8); 62558833, P = 7.5 x 10(-8)) in the combined analyses of Asian- and European-ancestry data. In addition, ing data from East Asians, we identified 13 new risk variants at 11 loci reported from previous GWAS.Conclusions: In this large GWAS, we identified three novel risk loci and two highly suggestive loci for lorectal cancer risk and provided evidence for potential roles of multiple genes and pathways in the iology of colorectal cancer. In addition, we showed that additional risk variants exist in many colorectal ncer risk loci identified previously.Impact: Our study provides novel data to improve the understanding of the genetic basis for colorectal ncer risk.
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| 4. |
- Qin, Jiajun, et al.
(författare)
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From optical pumping to electrical pumping: the threshold overestimation in metal halide perovskites
- 2023
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Ingår i: Materials Horizons. - : ROYAL SOC CHEMISTRY. - 2051-6347 .- 2051-6355. ; 10:4, s. 1446-1453
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Tidskriftsartikel (refereegranskat)abstract
- The threshold carrier density, conventionally evaluated from optical pumping, is a key reference parameter towards electrically pumped lasers with the widely acknowledged assumption that optically excited charge carriers relax to the band edge through an ultrafast process. However, the characteristically slow carrier cooling in perovskites challenges this assumption. Here, we investigate the optical pumping of state-of-the-art bromide- and iodine-based perovskites. We find that the threshold decreases by one order of magnitude with decreasing excitation energy from 3.10 eV to 2.48 eV for methylammonium lead bromide perovskite (MAPbBr(3)), indicating that the low-energy photon excitation facilitates faster cooling and hence enables efficient carrier accumulation for population inversion. Our results are then interpreted due to the coupling of phonon scattering in connection with the band structure of perovskites. This effect is further verified in the two-photon pumping process, where the carriers relax to the band edge with a smaller difference in phonon momentum that speeds up the carrier cooling process. Furthermore, by extrapolating the optical pumping threshold to the band edge excitation as an analog of the electrical carrier injection to the perovskite, we obtain a critical threshold carrier density of similar to 1.9 x 10(17) cm(-3), which is one order of magnitude lower than that estimated from the conventional approach. Our work thus highlights the feasibility of metal halide perovskites for electrically pumped lasers.
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| 5. |
- Shen, Tangyao, et al.
(författare)
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Giant magneto field effect in up-conversion amplified spontaneous emission via spatially extended states in organic-inorganic hybrid perovskites
- 2022
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Ingår i: Opto-Electronic Advances. - : Editorial Office of Opto-Electronic Advances. - 2096-4579. ; 5:2
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Tidskriftsartikel (refereegranskat)abstract
- Up-conversion lasing actions are normally difficult to realize in light-emitting materials due to small multi-photon absorption cross section and fast dephasing of excited states during multi-photon excitation. This paper reports an easily accessible up-conversion amplified spontaneous emission (ASE) in organic-inorganic hybrid perovskites (MAPbBr(3)) films by optically exciting broad gap states with sub-bandgap laser excitation. The broad absorption was optimized by adjusting the grain sizes in the MAPbBr3 films. At low sub-bandgap pumping intensities, directly exciting the gap states leads to 2-photon, 3-photon, and 4-photon up-conversion spontaneous emission, revealing a large optical cross section of multiphoton excitation occurring in such hybrid perovskite films. At moderate pumping intensity (1.19 mJ/cm(2)) of 700 nm laser excitation, a significant spectral narrowing phenomenon was observed with the full width at half maximum (FWHM) decreasing from 18 nm to 4 nm at the peak wavelength of 550 nm, simultaneously with a nonlinear increase on spectral peak intensity, showing an up-conversion ASE realized at low threshold pumping fluence. More interestingly, the up-conversion ASE demonstrated a giant magnetic field effect, leading to a magneto-ASE reaching 120%. In contrast, the upconversion photoluminescence (PL) showed a negligible magnetic field effect (< 1%). This observation provides an evidence to indicate that the light-emitting states responsible for up-conversion ASE are essentially formed as spatially extended states. The angular dependent spectrum results further verify the existence of spatially extended states which are polarized to develop coherent in-phase interaction. Clearly, using broad gap states with spatially extended light-emitting states presents a new approach to develop up-conversion ASE in organic-inorganic hybrid perovskites.
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| 6. |
- Shi, Jiajun, et al.
(författare)
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Automated Underwater Pipeline Damage Detection using Neural Nets
- 2019
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Konferensbidrag (refereegranskat)abstract
- Pipeline inspection is a very human intensive taskand automation could improve efficiencies significantly. We propose a system that could allow an autonomous underwater vehicle (AUV), to detect pipeline damage in a stream of images.Our classifiers were based on transfer learning from pre-trained convolutional neural networks (CNN). This allows us to achieve good results despite relatively few training examples of damage. We test the approach using data from an actual pipeline inspection.
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| 7. |
- Shi, Tingting, et al.
(författare)
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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees
- 2024
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Ingår i: Molecular Plant. - : Elsevier. - 1674-2052 .- 1752-9867. ; 17:5, s. 725-746
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.
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| 8. |
- Wen, Wanqing, et al.
(författare)
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Genome-wide association studies in East Asians identify new loci for waist-hip ratio and waist circumference
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Sixty genetic loci associated with abdominal obesity, measured by waist circumference (WC) and waist-hip ratio (WHR), have been previously identified, primarily from studies conducted in Europeanancestry populations. We conducted a meta-analysis of associations of abdominal obesity with approximately 2.5 million single nucleotide polymorphisms (SNPs) among 53,052 (for WC) and 48,312 (for WHR) individuals of Asian descent, and replicated 33 selected SNPs among 3,762 to 17,110 additional individuals. We identified four novel loci near the EFEMP1, ADAMTSL3, CNPY2, and GNAS genes that were associated with WC after adjustment for body mass index (BMI); two loci near the NID2 and HLA-DRB5 genes associated with WHR after adjustment for BMI, and three loci near the CEP120, TSC22D2, and SLC22A2 genes associated with WC without adjustment for BMI. Functional enrichment analyses revealed enrichment of corticotropin-releasing hormone signaling, GNRH signaling, and/or CDK5 signaling pathways for those newly-identified loci. Our study provides additional insight on genetic contribution to abdominal obesity.
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| 9. |
- Wu, Bingze, et al.
(författare)
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Significant electron-phonon coupling in nanographene confined in single-walled carbon nanotubes due to the large amplitude of radial breathinglike vibrations
- 2024
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 109:19
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Tidskriftsartikel (refereegranskat)abstract
- One-dimensional (1D) van der Waals heterostructures (vdWHs) exhibit many properties, but many of these are difficult to understand because of their complicated structures and host-guest couplings that remain challenging to understand. Here, we observe a significant electron-phonon coupling (EPC) in 1D armchair graphene nanoribbons (AGNRs) confined in single-walled carbon nanotubes (SWNTs) via resonance Raman spectroscopy combined with theoretical calculation. A strong coupling between radial breathinglike mode (RBLM) phonons and the host nanotubes occurs due to the large vibration amplitude of RBLMs of the guest AGNRs. This results in unique deformation potential interactions in the heterostructure, contributing to the observed EPC enhancement. The EPC could be further modulated and strengthened by high pressure through tuning the RBLM-nanotube interactions. In this paper, we discover a mechanism governing the EPC in vdWHs and pave the way for manipulating the host-guest EPC for further control of the physical properties and potential device applications.
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