| 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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| 3. |
- Liang, Jiawei, et al.
(författare)
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Performance and microbial communities of a novel integrated industrial-scale pulp and paper wastewater treatment plant
- 2021
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Ingår i: Journal of Cleaner Production. - : Elsevier BV. - 0959-6526. ; 278
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Tidskriftsartikel (refereegranskat)abstract
- Ltd Paper production generates pulp and paper wastewater (PPW), and it is difficult to remove the high-level pollutants in PPW efficiently. Herein, an efficient industrial-scale pulp and paper wastewater treatment plant (PP-WWTP) that integrated physicochemical and biological processes is investigated and reported. This PP-WWTP treated 2.3 Mt of wastewater with 17,388 ± 1436 mg/L chemical oxygen demand (COD) annually. The PP-WWTP can effectively remove over 99.81% of the COD. In detail, the physical, anaerobic, aerobic and chemical steps accounted for 41.6%, 40.0%, 11.9%, and 6.5% of COD removal, respectively. The microbial communities of the bioreactors removed the pollutants efficiently and contained diverse microbes. Further metagenomic analyses of the bioreactors identified more than 90,000 genes/gene fragments encoding for carbohydrate-active enzymes (CAZys), demonstrating high lignocellulose degradation ability of the bioreactors at molecular level. The xylanase activity assay showed some lignocellulase in the bioreactors were functional. Recycling the residual heat from the PPW along with energy recovered from biological treatment of the PPW, in the form of biogas (20,000 m³/d), could generate more than 1.5 M USD benefits/y. The results of this study demonstrated that the integrated physicochemical and biological process for PPWW treatment could effectively remove pollutants while generating revenue.
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| 4. |
- Picklo, Matthew J., et al.
(författare)
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Denoising Particle-In-Cell data via Smoothness-Increasing Accuracy-Conserving filters with application to Bohm speed computation
- 2024
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Ingår i: Journal of Computational Physics. - : Elsevier BV. - 0021-9991 .- 1090-2716. ; 502
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Tidskriftsartikel (refereegranskat)abstract
- The simulation of plasma physics is computationally expensive because the underlying physical system is of high dimensions, requiring three spatial dimensions and three velocity dimensions. One popular numerical approach is Particle-In-Cell (PIC) methods owing to its ease of implementation and favorable scalability in high-dimensional problems. An unfortunate drawback of the method is the introduction of statistical noise resulting from the use of finitely many particles. In this paper we examine the application of the Smoothness-Increasing Accuracy-Conserving (SIAC) family of convolution kernel filters as denoisers for moment data arising from PIC simulations. We show that SIAC filtering is a promising tool to denoise PIC data in the physical space as well as capture the appropriate scales in the Fourier space. Furthermore, we demonstrate how the application of the SIAC technique reduces the amount of information necessary in the computation of quantities of interest in plasma physics such as the Bohm speed.
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| 5. |
- Bhat, Goutam, et al.
(författare)
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NTIRE 2022 Burst Super-Resolution Challenge
- 2022
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Ingår i: 2022 IEEE/CVF CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION WORKSHOPS (CVPRW 2022). - : IEEE. - 9781665487399 - 9781665487405 ; , s. 1040-1060
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Konferensbidrag (refereegranskat)abstract
- Burst super-resolution has received increased attention in recent years due to its applications in mobile photography. By merging information from multiple shifted images of a scene, burst super-resolution aims to recover details which otherwise cannot be obtained using a simple input image. This paper reviews the NTIRE 2022 challenge on burst super-resolution. In the challenge, the participants were tasked with generating a clean RGB image with 4x higher resolution, given a RAW noisy burst as input. That is, the methods need to perform joint denoising, demosaicking, and super-resolution. The challenge consisted of 2 tracks. Track 1 employed synthetic data, where pixel-accurate high-resolution ground truths are available. Track 2 on the other hand used real-world bursts captured from a handheld camera, along with approximately aligned reference images captured using a DSLR. 14 teams participated in the final testing phase. The top performing methods establish a new state-of-the-art on the burst super-resolution task.
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| 6. |
- Ding, Xue Bing, et al.
(författare)
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Impaired meningeal lymphatic drainage in patients with idiopathic Parkinson’s disease
- 2021
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:3, s. 411-418
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Tidskriftsartikel (refereegranskat)abstract
- Animal studies implicate meningeal lymphatic dysfunction in the pathogenesis of neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease (PD). However, there is no direct evidence in humans to support this role1–5. In this study, we used dynamic contrast-enhanced magnetic resonance imaging to assess meningeal lymphatic flow in cognitively normal controls and patients with idiopathic PD (iPD) or atypical Parkinsonian (AP) disorders. We found that patients with iPD exhibited significantly reduced flow through the meningeal lymphatic vessels (mLVs) along the superior sagittal sinus and sigmoid sinus, as well as a notable delay in deep cervical lymph node perfusion, compared to patients with AP. There was no significant difference in the size (cross-sectional area) of mLVs in patients with iPD or AP versus controls. In mice injected with α-synuclein (α-syn) preformed fibrils, we showed that the emergence of α-syn pathology was followed by delayed meningeal lymphatic drainage, loss of tight junctions among meningeal lymphatic endothelial cells and increased inflammation of the meninges. Finally, blocking flow through the mLVs in mice treated with α-syn preformed fibrils increased α-syn pathology and exacerbated motor and memory deficits. These results suggest that meningeal lymphatic drainage dysfunction aggravates α-syn pathology and contributes to the progression of PD.
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| 7. |
- Guan, Qi, et al.
(författare)
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Eutrophication changes in fifty large lakes on the Yangtze Plain of China derived from MERIS and OLCI observations
- 2020
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Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257. ; 246
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Tidskriftsartikel (refereegranskat)abstract
- The eutrophication problems in lakes on the Yangtze Plain of China have attracted global concern. However, a comprehensive assessment of the eutrophication status and its evolution is still lacking for these regional lakes, mostly because of technical difficulties and/or insufficient data to cover the large region. Our study attempts to fill this knowledge gap by using the entire archive of remote sensing images from two satellite ocean color missions (MEdium Resolution Imaging Spectrometer, or MERIS (2003−2011), and Ocean and Land Color Instrument, or OLCI (2017–2018)), together with in situ data on remote sensing reflectance and chlorophyll-a (Chla) concentrations across various lakes on the Yangtze Plain. A machine learning-based piecewise Chla algorithm was developed in this study, with special considerations to improve algorithm performance under lower Chla conditions. Remotely sensed Chla and algal bloom areas were then used to classify the eutrophication status of 50 large lakes on the Yangtze Plain, and the frequent satellite observations enabled us to estimate the probability of eutrophication occurrence (PEO) for each examined lake. The long-term mean Chla ranged from 17.58 mg m−3 to 43.86 mg m−3 on the Yangtze Plain, and severe floating algal blooms were found in 7 lakes. All 50 lakes had high climatological PEO values (50%) during the study period, indicating a generally high probability of eutrophication in lakes on the Yangtze Plain. However, 21 out of 51 lakes exhibited statistically significant (p < .05) decreasing trends in PEO during the observation period, suggesting an overall improvement in the water quality of lakes on the Yangtze Plain in recent years. The methods developed here are expected to contribute to real-time monitoring of drinking water safety for local regions, and the long-term results provide valuable baseline information for future lake conservation and restoration efforts.
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| 8. |
- Guan, Qi, et al.
(författare)
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Long-term changes of nitrogen leaching and the contributions of terrestrial nutrient sources to lake eutrophication dynamics on the Yangtze Plain of China
- 2023
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Ingår i: Biogeosciences. - 1726-4170. ; 20:8, s. 1635-1648
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Tidskriftsartikel (refereegranskat)abstract
- Over the past half-century, drastically increased chemical fertilizers have entered agricultural ecosystems to promote crop production on the Yangtze Plain, potentially enhancing agricultural nutrient sources for eutrophication in freshwater ecosystems. However, long-term trends of nitrogen dynamics in terrestrial ecosystems and their impacts on eutrophication changes in this region remain poorly studied. Using a process-based ecosystem model, we investigated the temporal and spatial patterns of nitrogen use efficiency (NUE) and nitrogen leaching on the Yangtze Plain from 1979-2018. The agricultural NUE for the Yangtze Plain significantly decreased from 50g€¯% in 1979 to 25g€¯% in 2018, with the largest decline of NUE in soybean, rice, and rapeseed. Simultaneously, the leached nitrogen from cropland and natural land increased, with annual rates of 4.5 and 0.22g€¯kgg€¯Ng€¯ha-1g€¯yr-2, respectively, leading to an overall increase of nitrogen inputs to the 50 large lakes. We further examined the correlations between terrestrial nutrient sources (i.e., the leached nitrogen, total phosphorus sources, and industrial wastewater discharge) and the satellite-observed probability of eutrophication occurrence (PEO) at an annual scale and showed that PEO was positively correlated with the changes in terrestrial nutrient sources for most lakes. Agricultural nitrogen and phosphorus sources were found to explain the PEO trends in lakes in the western and central part of the Yangtze Plain, and industrial wastewater discharge was associated with the PEO trends in eastern lakes. Our results revealed the importance of terrestrial nutrient sources for long-term changes in eutrophic status over the 50 lakes of the Yangtze Plain. This calls for region-specific sustainable nutrient management (i.e., nitrogen and phosphorus applications in agriculture and industry) to improve the water quality of lake ecosystems.
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| 9. |
- Guan, Qi, et al.
(författare)
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Trends in River Total Suspended Sediments Driven by Dams and Soil Erosion : A Comparison Between the Yangtze and Mekong Rivers
- 2022
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Ingår i: Water Resources Research. - 0043-1397. ; 58:10
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Tidskriftsartikel (refereegranskat)abstract
- Global river systems are experiencing rapid changes in sediment transport under growing anthropogenic and climatic stresses. However, the response of sediment discharge to the coupled influence of anthropogenic and natural factors and the associated impacts on the fluvial geomorphology in the Yangtze and Mekong rivers are not comprehensively assessed. Here, we recalibrated a seamless retrieval algorithm of the total suspended sediment (TSS) concentrations using in situ data and concurrent satellite data sets to analyze spatiotemporal patterns of the TSS concentrations in the lower Yangtze and Mekong rivers. Combined with soil erosion rates estimated by the Revised Universal Soil Loss Equation for the past 20 years, we examined the contributions of different factors to TSS trends. The results show that TSS concentrations in the Yangtze River decreased from 0.47 g L−1 in 2000 to 0.23 g L−1 in 2018 due to the construction of the Three Gorges Dam (TGD), especially in the Jingjiang reach, with a declining magnitude of 0.3 g L−1 (∼56%) since the TGD began operating. The Mekong River experienced increasing TSS concentration trends upstream and decreasing trends downstream from 2000 to 2018, possibly attributed to increased upstream soil erosion and decreased downstream water discharge. Declining TSS concentrations in both rivers have driven varying degrees of river channel erosion over the past two decades. This study investigated long-term changes in the TSS concentrations and soil erosion in the Yangtze and Mekong rivers, and the results provide baseline information for the sustainable development of river sediment delivery.
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| 10. |
- Han, Xiaolei, et al.
(författare)
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Accelerometer-measured sedentary behavior patterns, brain structure, and cognitive function in dementia-free older adults : a population-based study
- 2023
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Ingår i: Journal of Alzheimer's Disease. - : IOS Press. - 1387-2877 .- 1875-8908. ; 96:2, s. 657-668
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Tidskriftsartikel (refereegranskat)abstract
- Background: Sedentary behavior is associated with cognitive impairment, but the neuropathological mechanisms underlying their associations are poorly understood.Objective: To investigate the associations of accelerometer-measured sedentary behavior patterns with brain structure and cognition, and further to explore the potential mechanisms.Methods: This community-based study included 2,019 older adults (age≥60 years, 59% women) without dementia derived from participants in the baseline examination of MIND-China (2018-2020). We assessed sedentary parameters using an accelerometer and cognitive function using a neuropsychological test battery. Structural brain markers were assessed on the structural brain MRI scans in a subsample (n = 1,009). Data were analyzed using the general linear, isotemporal substitution, and mediation models.Results: In the total sample (n = 2,019), adjusting for multiple covariates and moderate-to-vigorous-intensity physical activity, longer mean sedentary bout duration was linearly related with lower z-scores of global cognition, verbal fluency, and memory (ptrend < 0.05), whereas greater total sedentary time was linearly associated with lower z-scores of global cognition, verbal fluency, and memory only among individuals with long sedentary time (>10 h/day) (ptrend < 0.05); Breaking up sedentary time with same amount of light-intensity physical activity was significantly associated with higher verbal fluency and memory z-scores (p < 0.05). In the MRI subsample (n = 1,009), separately entering structural brain MRI markers into the mediation models substantially attenuated the associations of mean sedentary bout duration with global cognition, verbal fluency, and memory z-scores.Conclusion: Prolonged uninterrupted sedentary time is associated with poor global cognition, memory, and verbal fluency among rural older adults, and structural brain markers could partially mediate the association.
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