| 1. |
- 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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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Kamnitsas, Konstantinos, et al.
(författare)
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Transductive Image Segmentation : Self-training and Effect of Uncertainty Estimation
- 2021
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Ingår i: Domain Adaptation and Representation Transfer, and Affordable Healthcare and AI for Resource Diverse Global Health - 3rd MICCAI Workshop, DART 2021, and 1st MICCAI Workshop, FAIR 2021, Held in Conjunction with MICCAI 2021, Proceedings. - Cham : Springer International Publishing. - 1611-3349 .- 0302-9743. - 9783030877217 ; 12968 LNCS, s. 79-89
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Konferensbidrag (refereegranskat)abstract
- Semi-supervised learning (SSL) uses unlabeled data during training to learn better models. Previous studies on SSL for medical image segmentation focused mostly on improving model generalization to unseen data. In some applications, however, our primary interest is not generalization but to obtain optimal predictions on a specific unlabeled database that is fully available during model development. Examples include population studies for extracting imaging phenotypes. This work investigates an often overlooked aspect of SSL, transduction. It focuses on the quality of predictions made on the unlabeled data of interest when they are included for optimization during training, rather than improving generalization. We focus on the self-training framework and explore its potential for transduction. We analyze it through the lens of Information Gain and reveal that learning benefits from the use of calibrated or under-confident models. Our extensive experiments on a large MRI database for multi-class segmentation of traumatic brain lesions shows promising results when comparing transductive with inductive predictions. We believe this study will inspire further research on transductive learning, a well-suited paradigm for medical image analysis.
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| 4. |
- Karlsson, Max, et al.
(författare)
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Mixed halide perovskites for spectrally stable and high-efficiency blue light-emitting diodes
- 2021
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Bright and efficient blue emission is key to further development of metal halide perovskite light-emitting diodes. Although modifying bromide/chloride composition is straightforward to achieve blue emission, practical implementation of this strategy has been challenging due to poor colour stability and severe photoluminescence quenching. Both detrimental effects become increasingly prominent in perovskites with the high chloride content needed to produce blue emission. Here, we solve these critical challenges in mixed halide perovskites and demonstrate spectrally stable blue perovskite light-emitting diodes over a wide range of emission wavelengths from 490 to 451 nanometres. The emission colour is directly tuned by modifying the halide composition. Particularly, our blue and deep-blue light-emitting diodes based on three-dimensional perovskites show high EQE values of 11.0% and 5.5% with emission peaks at 477 and 467 nm, respectively. These achievements are enabled by a vapour-assisted crystallization technique, which largely mitigates local compositional heterogeneity and ion migration.
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| 5. |
- Kübler, André, et al.
(författare)
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Mycobacterium tuberculosis dysregulates MMP/TIMP balance to drive rapid cavitation and unrestrained bacterial proliferation.
- 2015
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Ingår i: Journal of Pathology. - : Wiley. - 0022-3417 .- 1096-9896. ; 235:3, s. 431-444
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Tidskriftsartikel (refereegranskat)abstract
- Active tuberculosis (TB) often presents with advanced pulmonary disease, including irreversible lung damage and cavities. Cavitary pathology contributes to antibiotic failure, transmission, morbidity and mortality. Matrix metalloproteinases (MMPs), in particular MMP-1 are implicated in TB pathogenesis. We explored the mechanisms relating MMP/TIMP imbalance to cavity formation in a modified rabbit model of cavitary TB. Our model results in consistent progression of consolidation to human-like cavities (100% by day 28) with resultant bacillary burdens (>10(7) CFU/g) far greater than those found in matched granulomatous tissue (10(5) CFU/g). Using a novel, breath-hold computerized tomography scanning and image analysis protocol. We show that cavities develop rapidly from areas of densely consolidated tissue. Radiological change correlated with a decrease in functional lung tissue as estimated by changes in lung density during controlled pulmonary expansion (R(2) =0.6356, p < 0.0001). We demonstrated that the expression of interstitial collagenase (MMP-1) is specifically greater in cavitary compared to granulomatous lesions (p < 0.01), and that TIMP-3 significantly decreases at the cavity surface. Our findings demonstrate that an MMP-1/TIMP imbalance, is associated with the progression of consolidated regions to cavities containing very high bacterial burdens. Our model provided mechanistic insight, correlating with human disease at the pathological, microbiological and molecular levels,. It also provides a strategy to investigate therapeutics in the context of complex TB pathology. We used these findings to predict a MMP/TIMP balance in active TB; and confirmed this in human plasma, revealing the potential of MMP/TIMP levels as key components of a diagnostic matrix aimed at distinguishing active from latent TB (PPV=92.9%; 95%CI 66.1-99.8%, NPV=85.6%; 95%CI 77.0-91.9%).
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| 6. |
- Li, Ziyue, et al.
(författare)
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Integrating life cycle assessment and a farmer survey of management practices to study environmental impacts of peach production in Beijing, China
- 2022
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Ingår i: Environmental Science and Pollution Research. - : Springer Nature. - 0944-1344 .- 1614-7499.
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Tidskriftsartikel (refereegranskat)abstract
- While intensive peach production has expanded rapidly in recent years, few studies have explored the environmental impacts associated with specific regional systems or the optimal management strategies to minimize associated environmental risks. Here, data from a survey of 290 native farmers were used to conduct a life cycle assessment to quantify the acidification potential (AP), global warming potential (GWP), eutrophication potential (EP), and reactive nitrogen (Nr) losses in peach production in Pinggu District, Beijing. Total annual Nr losses, and GWP, AP, and EP values for peach production in Pinggu District were respectively 10.7 kg N t−1, 857 kg CO2-eq t−1, 12.9 kg SO2-eq t−1, and 4.1 kg PO4-eq t−1. The principal driving factors were fertilizer production, transportation, and application, which together accounted for 94%, 67%, 75%, and 94% of Nr losses, GWP, AP, and EP, respectively. In the high yield, high nitrogen-use efficiency (HH) group, relative values of Nr losses, GWP, AP, and EP were respectively 33%, 25%, 39%, and 32% lower than the overall averages for 290 orchards. Further analyses indicate that improved farming practices such as decreasing application rates of fertilizers, increasing proportion of base fertilization rate, and proper fertilization frequency in the HH group were the main reasons for these orchards’ better performance in peach yields and partial factor productivity of nitrogen fertilizer, and their reduced environmental impacts. These results highlight the need to optimize nutrient management in peach production in order simultaneously to realize both environmental sustainability and high productivity in the peach production system.
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