| 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. |
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| 3. |
- Kristanl, Matej, et al.
(author)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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In: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 4. |
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| 5. |
- Kristan, Matej, et al.
(author)
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The Visual Object Tracking VOT2016 Challenge Results
- 2016
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In: COMPUTER VISION - ECCV 2016 WORKSHOPS, PT II. - Cham : SPRINGER INT PUBLISHING AG. - 9783319488813 - 9783319488806 ; , s. 777-823
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2016 aims at comparing short-term single-object visual trackers that do not apply pre-learned models of object appearance. Results of 70 trackers are presented, with a large number of trackers being published at major computer vision conferences and journals in the recent years. The number of tested state-of-the-art trackers makes the VOT 2016 the largest and most challenging benchmark on short-term tracking to date. For each participating tracker, a short description is provided in the Appendix. The VOT2016 goes beyond its predecessors by (i) introducing a new semi-automatic ground truth bounding box annotation methodology and (ii) extending the evaluation system with the no-reset experiment.
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| 6. |
- Zhang, Guojie, et al.
(author)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Journal article (peer-reviewed)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 7. |
- de las Fuentes, Lisa, et al.
(author)
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Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci
- 2021
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In: Molecular Psychiatry. - : Springer Nature. - 1359-4184 .- 1476-5578. ; 26:6, s. 2111-2125
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Journal article (peer-reviewed)abstract
- Educational attainment is widely used as a surrogate for socioeconomic status (SES). Low SES is a risk factor for hypertension and high blood pressure (BP). To identify novel BP loci, we performed multi-ancestry meta-analyses accounting for gene-educational attainment interactions using two variables, “Some College” (yes/no) and “Graduated College” (yes/no). Interactions were evaluated using both a 1 degree of freedom (DF) interaction term and a 2DF joint test of genetic and interaction effects. Analyses were performed for systolic BP, diastolic BP, mean arterial pressure, and pulse pressure. We pursued genome-wide interrogation in Stage 1 studies (N = 117 438) and follow-up on promising variants in Stage 2 studies (N = 293 787) in five ancestry groups. Through combined meta-analyses of Stages 1 and 2, we identified 84 known and 18 novel BP loci at genome-wide significance level (P < 5 × 10-8). Two novel loci were identified based on the 1DF test of interaction with educational attainment, while the remaining 16 loci were identified through the 2DF joint test of genetic and interaction effects. Ten novel loci were identified in individuals of African ancestry. Several novel loci show strong biological plausibility since they involve physiologic systems implicated in BP regulation. They include genes involved in the central nervous system-adrenal signaling axis (ZDHHC17, CADPS, PIK3C2G), vascular structure and function (GNB3, CDON), and renal function (HAS2 and HAS2-AS1, SLIT3). Collectively, these findings suggest a role of educational attainment or SES in further dissection of the genetic architecture of BP.
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| 8. |
- 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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| 9. |
- Cheng, Li, et al.
(author)
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Safety and Protection Measures of Underground Non-Coal Mines with Mining Depth over 800 m: A Case Study in Shandong, China
- 2022
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In: Sustainability. - : MDPI. - 2071-1050. ; 14:20
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Journal article (peer-reviewed)abstract
- With the increase in mining depth, the risk of ground pressure disasters in yellow gold mines is becoming more and more serious. This paper carries out a borehole test for the pressure behavior in a non-coal mining area with a mining depth of more than 800 m in the Jiaodong area. The test results show that under a depth of 1050 m, the increase in the vertical principal stress is the same as the increase in the minimum horizontal principal stress, which is about 3 MPa per 100 m. When the depth increases to 1350 m, the vertical principal stress increases by about 3% per 100 m, and the self-weight stress and the maximum horizontal principal stress maintain a steady growth rate of about 3 MPa per 100 m. In addition, based on the test results, the operation of the ground pressure monitoring system in each mine is investigated. The investigation results show that in some of the roadway and stope mines with depths of more than 800 m, varying degrees of rock mass instability have occurred, and a few mines have had sporadic slight rockbursts, accounting for about 5%. There was a stress concentration area in the lower part of the goaf formed in the early stage of mining, and slight rockburst phenomena such as rock mass ejection have occurred; meanwhile, the area stability for normal production and construction was good, and there was no obvious ground pressure. This paper compares the researched mines horizontally as well as to international high-level mines and puts forward some suggestions, including: carrying out ground pressure investigations and improving the level of intelligence, which would provide countermeasures to balance the safety risks of deep mining, reducing all kinds of safety production accidents and providing a solid basis for risk prevention and supervision.
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| 10. |
- Li, Jingjing, et al.
(author)
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Photothermal Aerogel Beads Based on Polysaccharides: Controlled Fabrication and Hybrid Applications in Solar-Powered Interfacial Evaporation, Water Remediation, and Soil Enrichment
- 2022
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In: ACS Applied Materials & Interfaces. - : American Chemical Society (ACS). - 1944-8252 .- 1944-8244. ; 14:44, s. 50266-50279
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Journal article (peer-reviewed)abstract
- Solar-powered interfacial evaporation has emerged as an innovative and sustainable technology for clean water production. However, the rapid, mass and shape-controlled fabrication of three-dimensional (3D) steam generators (SGs) for versatile hybrid applications remains challenging. Herein, composite aerogel beads with self-contained properties (i.e., hydrophilic, porous, photothermal, and durable) are developed and demonstrated for threefold hybrid applications including efficient solar-powered interfacial evaporation, water remediation, and controlled soil enrichment. The rational incorporation of selected polysaccharides enables us to fabricate bead-like aerogels with rapid gelation, continuous processing, and enhanced ion adsorption. The composite beads can attain a high water evaporation rate of 1.62 kg m-2 h-1 under 1 sun. Meanwhile, high phosphate adsorption capacity of over 120 mg g-1 is achieved in broad pH (2.5-12.4) and concentration (200-1000 mg L-1) ranges of phosphate solutions. Gratifyingly, we demonstrate the first example of recycling biomaterials from interfacial SGs for controlled nutrient release, soil enrichment, and sustainable agriculture. The phosphate-saturated beads can be gradually broken down in the soil. Macronutrients (N, P, and K) can be slowly released in 50 days, sustaining the plant germination and growth in a whole growth stage. This work shines light on the mass and controlled fabrication of aerogel beads based on double-network biopolymers, not merely scaling up solar-powered interfacial evaporation but also considering water remediation, waste material disposal, and value-added conversion.
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