| 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. |
- Kristan, Matej, et al.
(author)
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The Sixth Visual Object Tracking VOT2018 Challenge Results
- 2019
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In: Computer Vision – ECCV 2018 Workshops. - Cham : Springer Publishing Company. - 9783030110086 - 9783030110093 ; , s. 3-53
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative. Results of over eighty 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 and a “real-time” experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. A long-term tracking subchallenge has been introduced to the set of standard VOT sub-challenges. The new subchallenge focuses on long-term tracking properties, namely coping with target disappearance and reappearance. A new dataset has been compiled and a performance evaluation methodology that focuses on long-term tracking capabilities has been adopted. The VOT toolkit has been updated to support both standard short-term and the new long-term tracking subchallenges. 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 (http://votchallenge.net).
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| 3. |
- 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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| 4. |
- Bettegowda, Chetan, et al.
(author)
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Detection of circulating tumor DNA in early- and late-stage human malignancies
- 2014
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In: Science Translational Medicine. - : American Association for the Advancement of Science (AAAS). - 1946-6234 .- 1946-6242. ; 6:224, s. 224ra24-
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Journal article (peer-reviewed)abstract
- The development of noninvasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital polymerase chain reaction-based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. We found that ctDNA was detectable in >75% of patients with advanced pancreatic, ovarian, colorectal, bladder, gastroesophageal, breast, melanoma, hepatocellular, and head and neck cancers, but in less than 50% of primary brain, renal, prostate, or thyroid cancers. In patients with localized tumors, ctDNA was detected in 73, 57, 48, and 50% of patients with colorectal cancer, gastroesophageal cancer, pancreatic cancer, and breast adenocarcinoma, respectively. ctDNA was often present in patients without detectable circulating tumor cells, suggesting that these two biomarkers are distinct entities. In a separate panel of 206 patients with metastatic colorectal cancers, we showed that the sensitivity of ctDNA for detection of clinically relevant KRAS gene mutations was 87.2% and its specificity was 99.2%. Finally, we assessed whether ctDNA could provide clues into the mechanisms underlying resistance to epidermal growth factor receptor blockade in 24 patients who objectively responded to therapy but subsequently relapsed. Twenty-three (96%) of these patients developed one or more mutations in genes involved in the mitogen-activated protein kinase pathway. Together, these data suggest that ctDNA is a broadly applicable, sensitive, and specific biomarker that can be used for a variety of clinical and research purposes in patients with multiple different types of cancer.
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| 5. |
- Liu, Tiefeng, et al.
(author)
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Ground-state electron transfer in all-polymer donor:acceptor blends enables aqueous processing of water-insoluble conjugated polymers
- 2023
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In: Nature Communications. - : NATURE PORTFOLIO. - 2041-1723. ; 14:1
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Journal article (peer-reviewed)abstract
- Water-based conductive inks are vital for the sustainable manufacturing and widespread adoption of organic electronic devices. Traditional methods to produce waterborne conductive polymers involve modifying their backbone with hydrophilic side chains or using surfactants to form and stabilize aqueous nanoparticle dispersions. However, these chemical approaches are not always feasible and can lead to poor material/device performance. Here, we demonstrate that ground-state electron transfer (GSET) between donor and acceptor polymers allows the processing of water-insoluble polymers from water. This approach enables macromolecular charge-transfer salts with 10,000x higher electrical conductivities than pristine polymers, low work function, and excellent thermal/solvent stability. These waterborne conductive films have technological implications for realizing high-performance organic solar cells, with efficiency and stability superior to conventional metal oxide electron transport layers, and organic electrochemical neurons with biorealistic firing frequency. Our findings demonstrate that GSET offers a promising avenue to develop water-based conductive inks for various applications in organic electronics. Chemical approaches to improve aqueous dispersions of conjugated polymers are limited by the feasibility of modifying the backbone or lead to poor performance. Here, Liu et al. show that ground-state electron transfer in donor:acceptor blends aids aqueous dispersion, for high conductivity and solubility.
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| 6. |
- Wang, Kang, et al.
(author)
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Luminescent metal-halide perovskites: fundamentals, synthesis, and light-emitting devices
- 2024
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In: Science in China Series B. - : SCIENCE PRESS. - 1674-7291 .- 1869-1870. ; 67:6, s. 1776-1838
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Research review (peer-reviewed)abstract
- Metal-halide perovskites have garnered considerable research attention as highly efficient light emitters in recent years due to their outstanding optoelectronic properties with remarkable tunability and excellent solution processabilities. Substantial advancements have been achieved in the development of novel halide perovskites, and the exploitations of these materials in light-emitting devices. This review comprehensively outlines recent breakthroughs in metal-halide perovskites, encompassing the rational design of perovskite materials with tunable light emission properties, the controllable growth of single crystal for a deeper understanding of their structure-property relationships, as well as the fundamental insights into the photophysics and carrier dynamics in perovskite systems. Additionally, it provides an overview of recent applications of perovskite materials in high-performance light-emitting diodes (LEDs) and lasers.
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| 7. |
- Wang, Yuxuan, et al.
(author)
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A deep learning approach to real-time CO concentration prediction at signalized intersection
- 2020
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In: Atmospheric Pollution Research. - : Elsevier BV. - 1309-1042. ; 11:8, s. 1370-1378
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Journal article (peer-reviewed)abstract
- Vehicle exhaust emissions at signalized intersections are the essential source of traffic-related pollution to pedestrians. Therefore, it is critical to predicting traffic emissions, especially the hazardous CO gas, with practical and accurate methods. However, the CO emission and concentration at crosswalks can be influenced by the complex traffic conditions in a complicated way, making the prediction of CO concentration a challenging task for traditional statistical models. To this end, a hybrid machine learning framework is proposed in this study to investigate the concentration of CO emissions at pedestrian crosswalks. The proposed method firstly ranks key influencing factors with a random forest approach. Then a prediction model with Multi-Variate Long Short-Term Memory (LSTM) neural networks based on the selected factors is developed. Data is collected at the field intersection for model training and validation. The autoregressive integrated moving average (ARIMA), support vector machines (SVM), radial basis functions network (RBFN), nonlinear vector autoregressive (VAR) and gated recurrent unit ( GRU) neural network are selected as the benchmark models to verify the performance of the proposed model. The Root Mean Square Errors (RMSE), Mean Absolute Error (MAE) and R square are calculated to evaluate the performance of models comprehensively. The results indicated that the proposed model overwhelms the benchmark models in terms of prediction accuracy.
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| 8. |
- Wang, Yuxuan, et al.
(author)
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Are shared electric scooters energy efficient?
- 2021
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In: Communications in Transportation Research. - : Elsevier BV. - 2772-4247. ; 1
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Journal article (peer-reviewed)abstract
- Shared electric scooters (e-scooter) are booming across the world and widely regarded as a sustainable mobility service. An increasing number of studies have investigated the e-scooter trip patterns, safety risks, and environmental impacts, but few considered the energy efficiency of e-scooters. In this research, we collected the operational data of e-scooters from a major provider in Gothenburg to shed light on the energy efficiency performance of e-scooters in real cases. We first develop a multiple logarithmic regression model to examine the energy consumption of single trips and influencing factors. With the regression model, a Monte Carlo simulation framework is proposed to estimate the fleet energy consumption in various scenarios, taking into account both trip-related energy usage and energy loss in idle status. The results indicate that 40% of e-scooter battery energy was wasted in idle status in the current practice, mainly due to the relatively low usage rate (0.83) of e-scooters. If the average usage rate drops below 0.5, the wasted energy could reach up to 53%. In the end, we present a field example to showcase how to optimally integrate public transport with e-scooters from the perspective of energy efficiency. We hope the findings of this study could help understand and resolve the current and future challenges regarding the ever-growing e-scooter services.
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