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- Lin, Ping-I, et al.
(författare)
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Comparing DNA methylation profiles across different tissues associated with the diagnosis of pediatric asthma
- 2020
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- DNA methylation (DNAm) profiles in central airway epithelial cells (AECs) may play a key role in pathological processes in asthma. The goal of the current study is to compare the diagnostic performance of DNAm markers across three tissues: AECs, nasal epithelial cells (NECs), and peripheral blood mononuclear cells (PBMCs). Additionally, we focused on the results using the machine learning algorithm in the context of multi-locus effects to evaluate the diagnostic performance of the optimal subset of CpG sites. We obtained 74 subjects with asthma and 41 controls from AECs, 15 subjects with asthma and 14 controls from NECs, 697 subjects with asthma and 97 controls from PBMCs. Epigenome-wide DNA methylation levels in AECs, NECs and PBMCs were measured using the Infinium Human Methylation 450K BeadChip. Overlap analysis across the three different sample sources at the locus and pathway levels were studied to investigate shared or unique pathophysiological processes of asthma across tissues. Using the top 100 asthma-associated methylation markers as classifiers from each dataset, we found that both AEC- and NEC-based DNAm signatures exerted a lower classification error than the PBMC-based DNAm markers (p-value = 0.0002). The area-under-the-curve (AUC) analysis based on out-of-bag errors using the random forest classification algorithm revealed that PBMC-, NEC-, and AEC-based methylation data yielded 31 loci (AUC: 0.87), 8 loci (AUC: 0.99), and 4 loci (AUC: 0.97) from each optimal subset of tissue-specific markers, respectively. We also discovered the locus-locus interaction of DNAm levels of the CDH6 gene and RAPGEF3 gene might interact with each other to jointly predict the risk of asthma - which suggests the pivotal role of cell-cell junction in the pathological changes of asthma. Both AECs and NECs might provide better diagnostic accuracy and efficacy levels than PBMCs. Further research is warranted to evaluate how these tissue-specific DNAm markers classify and predict asthma risk.
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- Baranowski, M, et al.
(författare)
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Contactless Electroreflectance, Photoluminescence and Time-Resolved Photoluminescence of GaInNAs Quantum Wells Obtained by the MBE Method with N-irradiation
- 2011
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Ingår i: Semiconductor Science and Technology. - : IOP Publishing. - 1361-6641 .- 0268-1242. ; 26:4, s. 045012-
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Tidskriftsartikel (refereegranskat)abstract
- The optical properties of GaInNAs quantum wells (QW) grown by molecular beam epitaxywith and without N-irradiation (i.e. grown by the classical method) were investigated by thecontactless electroreflectance (CER), temperature-dependent photoluminescence (PL) andtime-resolved PL (TRPL). From CER measurements it was concluded that one type ofnitrogen nearest-neighbor environment (In-rich environment) is dominant for GaInNAs QWsgrown with N-irradiation whereas various nitrogen environments are present for the referenceGaInNAs QW (i.e. the sample obtained by the classical method). PL and TRPL measurementsclearly show that the optical properties of GaInNAs QWs are affected mainly by the amount ofthe incorporated nitride atoms. It was observed that the PL decay time decreased from ∼200to ∼40 ps when the nitrogen concentration is increased from 0.8 to 2.2%. In addition, thepresence of As flux during N-irradiation reduces the amount of the incorporated nitrogen andsimultaneously improves the optical quality of GaInNAs QWs (i.e. it weakens the carrierlocalization at low temperatures and improves the quantum efficiency of PL).
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- 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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- Bornehag, Carl-Gustaf, 1957-, et al.
(författare)
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A Novel Approach to Chemical Mixture Risk Assessment—Linking Data from Population-Based Epidemiology and Experimental Animal Tests
- 2019
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Ingår i: Risk Analysis. - : John Wiley & Sons. - 0272-4332 .- 1539-6924. ; 39:10, s. 2259-2271
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Tidskriftsartikel (refereegranskat)abstract
- Humans are continuously exposed to chemicals with suspected or proven endocrine disrupting chemicals (EDCs). Risk management of EDCs presents a major unmet challenge because the available data for adverse health effects are generated by examining one compound at a time, whereas real-life exposures are to mixtures of chemicals. In this work, we integrate epidemiological and experimental evidence toward a whole mixture strategy for risk assessment. To illustrate, we conduct the following four steps in a case study: (1) identification of single EDCs (“bad actors”)—measured in prenatal blood/urine in the SELMA study—that are associated with a shorter anogenital distance (AGD) in baby boys; (2) definition and construction of a “typical” mixture consisting of the “bad actors” identified in Step 1; (3) experimentally testing this mixture in an in vivo animal model to estimate a dose–response relationship and determine a point of departure (i.e., reference dose [RfD]) associated with an adverse health outcome; and (4) use a statistical measure of “sufficient similarity” to compare the experimental RfD (from Step 3) to the exposure measured in the human population and generate a “similar mixture risk indicator” (SMRI). The objective of this exercise is to generate a proof of concept for the systematic integration of epidemiological and experimental evidence with mixture risk assessment strategies. Using a whole mixture approach, we could find a higher rate of pregnant women under risk (13%) when comparing with the data from more traditional models of additivity (3%), or a compound-by-compound strategy (1.6%).
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- Chen, Xiren, et al.
(författare)
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Bi-Induced Electron Concentration Enhancement Being Responsible for Photoluminescence Blueshift and Broadening in InAs Films
- 2019
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Ingår i: Physica Status Solidi (B): Basic Research. - : Wiley. - 1521-3951 .- 0370-1972. ; 256:5
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Tidskriftsartikel (refereegranskat)abstract
- Photoluminescence (PL) study is conducted on InAs films molecular beam epitaxially grown on GaAs substrates with different Bi flux levels. A PL peak blueshift accompanied by linewidth broadening is found with the increase of Bi/As flux ratio, in contrast to the common Bi isoelectronic incorporation or surfactant effect. It is, with detailed lineshape analysis and the evidence of PL peak splitting in a magnetic filed, attributed to the electron concentration enhancement induced by Bi flux. The electron concentration in InAs film is evaluated, which is about 5-fold enhanced as Bi/As flux ratio rises up from 0 to 1x10(-3). The temperature dependence of the PL spectrum indicates that the carrier redistribution augments while the carrier-phonon Frohlich scattering weakens in InAs films with high Bi/As flux ratios. These findings reveal a novel Bi effect of electron concentration enhancement, and contribute to the basic knowledge of Bi in III-V semiconductors.
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