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- 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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| 3. |
- Kristan, Matej, et al.
(author)
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The Ninth Visual Object Tracking VOT2021 Challenge Results
- 2021
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In: 2021 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2021). - : IEEE COMPUTER SOC. - 9781665401913 ; , s. 2711-2738
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2021 is the ninth annual tracker benchmarking activity organized by the VOT initiative. Results of 71 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in recent years. The VOT2021 challenge was composed of four sub-challenges focusing on different tracking domains: (i) VOT-ST2021 challenge focused on short-term tracking in RGB, (ii) VOT-RT2021 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2021 focused on long-term tracking, namely coping with target disappearance and reappearance and (iv) VOT-RGBD2021 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2021 dataset was refreshed, while VOT-RGBD2021 introduces a training dataset and sequestered dataset for winner identification. The source code for most of the trackers, the datasets, the evaluation kit and the results along with the source code for most trackers are publicly available at the challenge website(1).
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- Kanoni, Stavroula, et al.
(author)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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In: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Journal article (peer-reviewed)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 5. |
- Han, Meng, et al.
(author)
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Experimental study of the effect of air split ratio on thermoacoustic instability in a centrally-staged swirl burner
- 2022
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In: Physics of Fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 34:6
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Journal article (peer-reviewed)abstract
- This study focuses on one of the critical design parameters of lean premixed (LPM) combustors-the air split ratio (ASR) between the pilot and main stages. The effect of the air split ratio on thermoacoustic instability is experimentally studied based on a centrally staged model combustor. It is found that the thermoacoustic instability is suppressed with the ASR higher than 20%. The acoustic modes of ASR lower than 20% are dominated by the main stage mode, while the others are controlled by the pilot stage mode. The time-averaged flame shapes and the flame dynamics are processed and discussed. With the increase in ASR, the pilot flame becomes longer, whereas the main flame becomes shorter. Meanwhile, the pilot and main flames become less separated. Moreover, the flame in the outer shear layer (OSL) is extinguished, which is the key to suppressing the thermoacoustic instability. The flame with lower ASR exhibits large-scale periodic axial motion of flame dynamics. The flow fields of ASR = 15% (unstable) and ASR = 30% (stable) are analyzed and discussed to help reveal the differences in thermoacoustic instability between the two cases. It is found that the primary recirculation zone is smaller with ASR = 30%. Higher vorticity and strain rate distributions found in the OSL are believed to quench the flame there. The present study illustrates that a higher air split ratio improves the thermoacoustic stability, which is helpful in designing LPM combustors.
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| 8. |
- Han, Ziming, et al.
(author)
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Three-Year Consecutive Field Application of Erythromycin Fermentation Residue Following Hydrothermal Treatment: Cumulative Effect on Soil Antibiotic Resistance Genes
- 2022
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In: Engineering. - : Elsevier BV. - 2095-8099. ; 15, s. 78-88
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Journal article (peer-reviewed)abstract
- Fermentation-based antibiotic production results in abundant nutrient-rich fermentation residue with high potential for recycling, but the high antibiotic residual concentration restricts its usefulness (e.g., in land application as organic fertilizer). In this study, an industrial-scale hydrothermal facility for the treatment of erythromycin fermentation residue (EFR) was investigated, and the potential risk of the long-term soil application of treated EFR promoting environmental antibiotic resistance development was evaluated. The treatment effectively removed bacteria and their DNA, and an erythromycin removal ratio of up to approximately 98% was achieved. The treated EFR was utilized as organic fertilizer for consecutive field applications from 2018 to 2020, with dosages ranging from 3750 to 15 000 kg∙hm−2, resulting in sub-inhibitory levels of erythromycin (ranging from 0.83–76.00 μg∙kg−1) in soils. Metagenomic shotgun sequencing was then used to characterize the antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial community composition of the soils. The soil ARG abundance and diversity did not respond to the treated EFR application in the first year, but gradually changed in the second and third year of application. The highest fold change in relative abundance of macrolide–lincosamide–streptogramin (MLS) and total ARGs were 12.59 and 2.75 times, compared with the control (CK; without application), respectively. The soil MGEs and taxonomic composition showed similar temporal trends to those of the ARGs, and appeared to assist in driving increasing ARG proliferation, as revealed by correlation analysis and structural equation models (SEMs). The relative abundance of particular erm resistance genes (RNA methyltransferase genes) increased significantly in the third year of treated EFR application. The close association of erm with MGEs suggested that horizontal gene transfer played a critical role in the observed erm gene enrichment. Metagenomic binning results demonstrated that the proliferation of mac gene-carrying hosts was responsible for the increased abundance of mac genes (efflux pump genes). This study shows that sub-inhibitory levels of erythromycin in soils had a cumulative effect on soil ARGs over time and emphasizes the importance of long-term monitoring for assessing the risk of soil amendment with treated industrial waste.
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| 9. |
- Jiang, Xia, et al.
(author)
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ITGB4 as a novel serum diagnosis biomarker and potential therapeutic target for colorectal cancer
- 2021
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In: Cancer Medicine. - : Wiley. - 2045-7634. ; 10:19, s. 6823-6834
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Journal article (peer-reviewed)abstract
- Purpose To develop new and effective biomarkers for the diagnosis of colorectal cancer (CRC). Experimental design The serum expression of ITGB4 (49 CRC and 367 HC) was detected by enzyme-linked immunosorbent assay (ELISA), and its diagnostic value was analyzed using the receiver operating characteristic (ROC) curve. The sensitivity and specificity of ITGB4 in CRC diagnosis were calculated through statistical analysis. The optimal clinical cutoff value was calculated using the Youden index, and diagnostic efficacy was analyzed in a larger serum sample (98 CRC and 1631 non-CRC). The expression of ITGB4 was measured by CyTOF (cell experimental technology) at the single-cell level, and characteristics were analyzed using viSNE and SPADE TREE. Results Serum ITGB4 and CEA levels were significantly higher in CRC patients than in HC and non-CRC patients. The use of serum ITGB4 levels for the diagnosis of CRC has a high sensitivity (79%) but not high specificity when the clinical cutoff value was 0.70 ng/mL. However, the optimal cutoff value was 1.6 ng/mL with 86.2% specificity and 52.0% sensitivity, and the diagnostic efficacy was greatly improved with high specificity (82.0%) and sensitivity (71.4%) when combined with CEA. ITGB4 expression characteristics were measured and related to the expression of EpCAM, Ck8/18, and perforin at the single-cell level. Single-cell analysis showed that cell clusters with low expression of CK8/18 and ITGB4 were more sensitive to 5FU and radiotherapy (RT). Conclusions ITGB4 is an effective diagnostic serum biomarker and a potential therapeutic target for CRC.
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| 10. |
- Kristan, Matej, et al.
(author)
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The first visual object tracking segmentation VOTS2023 challenge results
- 2023
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In: 2023 IEEE/CVF International conference on computer vision workshops (ICCVW). - : Institute of Electrical and Electronics Engineers Inc.. - 9798350307443 - 9798350307450 ; , s. 1788-1810
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking Segmentation VOTS2023 challenge is the eleventh annual tracker benchmarking activity of the VOT initiative. This challenge is the first to merge short-term and long-term as well as single-target and multiple-target tracking with segmentation masks as the only target location specification. A new dataset was created; the ground truth has been withheld to prevent overfitting. New performance measures and evaluation protocols have been created along with a new toolkit and an evaluation server. Results of the presented 47 trackers indicate that modern tracking frameworks are well-suited to deal with convergence of short-term and long-term tracking and that multiple and single target tracking can be considered a single problem. A leaderboard, with participating trackers details, the source code, the datasets, and the evaluation kit are publicly available at the challenge website1
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