| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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. |
- Sampson, Joshua N., et al.
(author)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Journal article (peer-reviewed)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 3. |
- Wang, Zhaoming, et al.
(author)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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| 4. |
- Jacobs, Kevin B, et al.
(author)
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Detectable clonal mosaicism and its relationship to aging and cancer.
- 2012
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In: Nature Genetics. - New York : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 44:6, s. 651-658
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Journal article (peer-reviewed)abstract
- In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.
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| 5. |
- Wang, Meiyang, et al.
(author)
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Promoted photocatalytic degradation and detoxication performance for norfloxacin on Z-scheme phosphate-doped BiVO4/graphene quantum dots/P-doped g-C3N4
- 2021
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In: Separation and Purification Technology. - : Elsevier BV. - 1383-5866. ; 274
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Journal article (peer-reviewed)abstract
- A novel kind of Z-scheme ternary heterojunctions phosphate-doped BiVO4/graphene quantum dots/P-doped g-C3N4 (BVP/GQDs/PCN) were fabricated for the visible light degradation of norfloxacin (NOR), a typical antibiotic. Compared with binary type-II heterojunction phosphate-doped BiVO4/PCN (BVP/PCN), Z-scheme BVP/GQDs/PCN exhibited promoted interfacial charge transfer efficiency and broadened visible light response range, endowing them with excellent photodegradation activity and mineralization ability in NOR degradation. A high NOR degradation rate of 86.3% with a removal rate of total organic carbon (TOC) of 55.8% can be achieved over BVP/GQDs/PCN for 120 min visible light irradiation, which is an excellent performance compared with ever reported similar photocatalysts. In particular, because of the enhanced redox ability of photogenerated charges and the generation of multiple active species (eg. [rad]OH and [rad]O2−) over Z-scheme photocatalytic system, the accumulation of highly toxic degradation intermediates was greatly inhibited, and a better detoxication performance was obtained compared to PCN and BVP/PCN. This work may shed light on the inhibition of highly toxic degradation intermediates of antibiotics by regulating the charge transfer mechanism, photocatalytic active species, and the degradation pathway of antibiotics.
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| 6. |
- Zhang, Yangfan, et al.
(author)
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Interfacial defective Ti3+ on Ti/TiO2 as visible-light responsive sites with promoted charge transfer and photocatalytic performance
- 2022
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In: Journal of Materials Science and Technology. - : Elsevier BV. - 1005-0302. ; 106, s. 139-146
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Journal article (peer-reviewed)abstract
- Defect sites on oxide semiconductors play a crucial role in promoting photocatalytiperformance and modulating the bandgap structure of photocatalysts. However, the role of interfacial coordinatively unsaturated defect sites between metal and oxide in photocatalysis is still under debate. So, we designed an experiment to probe the role of interfacial coordinatively unsaturated defect sites. In this work, a series of Ti/TiO2 photocatalysts with varying concentrations of interfacial Ti3+ sites were prepared through an epitaxial growth method under hydrothermal conditions. Through experimental and computational investigations, the roles of interfacial defect sites were discussed in detail. On the one hand, the interfacial coordinatively unsaturated Ti3+ sites could act as visible-light-responsive sites in photocatalytic reactions due to the overlap and hybridization of multiple electronic orbitals. On the other hand, the Ti/TiO2 interface exhibited a certain degree of metallic character near the Fermi level because of the partial delocalization and redistribution of electrons, facilitating the charge migration and separation across the metal-oxide interface. Consequently, the obtained Ti/TiO2 catalysts showed notably enhanced charge transfer efficiency and visible light photocatalytic activity compared to their pristine counterparts. This work may provide a new perspective to interfacial defect engineering in classic metal/oxide heterojunction photocatalysts and figure a more precise direction to synthesize higher effective photocatalysts for environmental governance.
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| 7. |
- Amundadottir, Laufey, et al.
(author)
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Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer.
- 2009
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 41, s. 986-990
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Journal article (peer-reviewed)abstract
- We conducted a two-stage genome-wide association study of pancreatic cancer, a cancer with one of the lowest survival rates worldwide. We genotyped 558,542 SNPs in 1,896 individuals with pancreatic cancer and 1,939 controls drawn from 12 prospective cohorts plus one hospital-based case-control study. We conducted a combined analysis of these groups plus an additional 2,457 affected individuals and 2,654 controls from eight case-control studies, adjusting for study, sex, ancestry and five principal components. We identified an association between a locus on 9q34 and pancreatic cancer marked by the SNP rs505922 (combined P = 5.37 x 10(-8); multiplicative per-allele odds ratio 1.20; 95% confidence interval 1.12-1.28). This SNP maps to the first intron of the ABO blood group gene. Our results are consistent with earlier epidemiologic evidence suggesting that people with blood group O may have a lower risk of pancreatic cancer than those with groups A or B.
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| 8. |
- Andhikaputra, Gerry, et al.
(author)
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The impact of temperature and precipitation on all-infectious-, bacterial-, and viral-diarrheal disease in Taiwan
- 2023
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In: Science of the Total Environment. - : Elsevier BV. - 1879-1026 .- 0048-9697. ; 862
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Journal article (peer-reviewed)abstract
- BACKGROUND: The ongoing climate change will elevate the incidence of diarrheal in 2030-2050 in Asia, including Taiwan. This study investigated associations between meteorological factors (temperature, precipitation) and burden of age-cause-specific diarrheal diseases in six regions of Taiwan using 13 years of (2004-2016) population-based data.METHODS: Weekly cause-specific diarrheal and meteorological data were obtained from 2004 to 2016. We used distributed lag non-linear model to assess age (under five, all age) and cause-specific (viral, bacterial) diarrheal disease burden associated with extreme high (99th percentile) and low (5th percentile) of climate variables up to lag 8 weeks in six regions of Taiwan. Random-effects meta-analysis was used to pool these region-specific estimates.RESULTS: Extreme low temperature (15.30 °C) was associated with risks of all-infectious and viral diarrhea, with the highest risk for all-infectious diarrheal found at lag 8 weeks among all age [Relative Risk (RR): 1.44; 95 % Confidence Interval (95 % CI): 1.24-1.67]. The highest risk of viral diarrheal infection was observed at lag 2 weeks regardless the age. Extreme high temperature (30.18 °C) was associated with risk of bacterial diarrheal among all age (RR: 1.07; 95 % CI: 1.02-1.13) at lag 8 weeks. Likewise, extreme high precipitation (290 mm) was associated with all infectious diarrheal, with the highest risk observed for bacterial diarrheal among population under five years (RR: 2.77; 95 % CI: 1.60-4.79) at lag 8 weeks. Extreme low precipitation (0 mm) was associated with viral diarrheal in all age at lag 1 week (RR: 1.08; 95 % CI: 1.01-1.15)].CONCLUSION: In Taiwan, extreme low temperature is associated with an increased burden of viral diarrheal, while extreme high temperature and precipitation elevated burden of bacterial diarrheal. This distinction in cause-specific and climate-hazard specific diarrheal disease burden underscore the importance of incorporating differences in public health preparedness measures designed to enhance community resilience against climate change.
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| 9. |
- Hsu, Yu-Kai, et al.
(author)
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Highly hydrophilic electrodeposited NiS/Ni3S2 interlaced nanosheets with surface-enriched Ni3+ sites as binder-free flexible cathodes for high-rate hybrid supercapacitors
- 2022
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In: Applied Surface Science. - : Elsevier. - 0169-4332 .- 1873-5584. ; 579
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Journal article (peer-reviewed)abstract
- In this study, nanostructured nickel sulfides (NiS, Ni3S2 and NiS/Ni3S2) were fabricated directly on the surface of flexible carbon fiber cloths by simply modifying the deposition parameters of pulse-reversal (PR) electrodeposition method and utilized as binder-free flexible electrodes for aqueous hybrid supercapacitors (SCs). X-ray photoelectron spectroscopy and contact angle measurement studies verifies that the surface of heterostructure NiS/Ni3S2 electrode has enriched Ni3+ sites and highly hydrophilic nature. Consequently, the heterostructure NiS/Ni3S2 electrode demonstrated superior rate capability than that of both single phase NiS and Ni3S2 electrodes. Additionally, the hybrid SC device based on the flexible NiS/Ni3S2 electrode delivered a capacity of 40.4 mAh g−1 at a current density of 2 A g−1 and representing a maximum energy density of 32.3 Wh kg−1 at an impressive power density of 1.6 kW kg−1. Furthermore, the device provided excellent electrochemical stability with a capacity retention of 86.2%, even after a 120-h floating test. Hence, the heterostructure NiS/Ni3S2 with interlaced nanosheets morphology should be considered as promising binder-free flexible electrode materials for next-generation energy storage applications.
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| 10. |
- King, Sontoria D., et al.
(author)
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Genetic Susceptibility to Nonalcoholic Fatty Liver Disease and Risk for Pancreatic Cancer: Mendelian Randomization
- 2023
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In: Cancer Epidemiology, Biomarkers and Prevention. - : American Association For Cancer Research (AACR). - 1055-9965 .- 1538-7755. ; 32:9, s. 1265-1269
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Journal article (peer-reviewed)abstract
- BACKGROUND: There are conflicting data on whether nonalcoholic fatty liver disease (NAFLD) is associated with susceptibility to pancreatic cancer. Using Mendelian randomization (MR), we investigated the relationship between genetic predisposition to NAFLD and risk for pancreatic cancer.METHODS: Data from genome-wide association studies (GWAS) within the Pancreatic Cancer Cohort Consortium (PanScan; cases n = 5,090, controls n = 8,733) and the Pancreatic Cancer Case Control Consortium (PanC4; cases n = 4,163, controls n = 3,792) were analyzed. We used data on 68 genetic variants with four different MR methods [inverse variance weighting (IVW), MR-Egger, simple median, and penalized weighted median] separately to predict genetic heritability of NAFLD. We then assessed the relationship between each of the four MR methods and pancreatic cancer risk, using logistic regression to calculate ORs and 95% confidence intervals (CI), adjusting for PC risk factors, including obesity and diabetes.RESULTS: No association was found between genetically predicted NAFLD and pancreatic cancer risk in the PanScan or PanC4 samples [e.g., PanScan, IVW OR, 1.04; 95% confidence interval (CI), 0.88-1.22; MR-Egger OR, 0.89; 95% CI, 0.65-1.21; PanC4, IVW OR, 1.07; 95% CI, 0.90-1.27; MR-Egger OR, 0.93; 95% CI, 0.67-1.28]. None of the four MR methods indicated an association between genetically predicted NAFLD and pancreatic cancer risk in either sample.CONCLUSIONS: Genetic predisposition to NAFLD is not associated with pancreatic cancer risk.IMPACT: Given the close relationship between NAFLD and metabolic conditions, it is plausible that any association between NAFLD and pancreatic cancer might reflect host metabolic perturbations (e.g., obesity, diabetes, or metabolic syndrome) and does not necessarily reflect a causal relationship between NAFLD and pancreatic cancer.
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