| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Hering, Alessa, et al.
(författare)
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Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning
- 2023
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Ingår i: IEEE Transactions on Medical Imaging. - : Institute of Electrical and Electronics Engineers (IEEE). - 0278-0062 .- 1558-254X. ; 42:3, s. 697-712
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Tidskriftsartikel (refereegranskat)abstract
- Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration data set for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https:// learn2reg.grand-challenge.org. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, as well as results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias. While no single approach worked best across all tasks, many methodological aspects could be identified that push the performance of medical image registration to new state-of-the-art performance. Furthermore, we demystified the common belief that conventional registration methods have to be much slower than deep-learning-based methods.
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| 3. |
- Chirico, Nicola, et al.
(författare)
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In silico approaches for the prediction of the breakthrough of organic contaminants in wastewater treatment plants
- 2024
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Ingår i: Environmental Science. - 2050-7887 .- 2050-7895. ; 26:2, s. 400-410
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Tidskriftsartikel (refereegranskat)abstract
- The removal efficiency (RE) of organic contaminants in wastewater treatment plants (WWTPs) is a major determinant of the environmental impact of chemicals which are discharged to wastewater. In a recent study, non-target screening analysis was applied to quantify the percentage removal efficiency (RE%) of more than 300 polar contaminants, by analyzing influent and effluent samples from a Swedish WWTP with direct injection UHPLC-Orbitrap-MS/MS. Based on subsets extracted from these data, we developed quantitative structure–property relationships (QSPRs) for the prediction of WWTP breakthrough (BT) to the effluent water. QSPRs were developed by means of multiple linear regression (MLR) and were selected after checking for overfitting and chance relationships by means of bootstrap and randomization procedures. A first model provided good fitting performance, showing that the proposed approach for the development of QSPRs for the prediction of BT is reasonable. By further populating the dataset with similar chemicals using a Tanimoto index approach based on substructure count fingerprints, a second QSPR indicated that the prediction of BT is also applicable to new chemicals sufficiently similar to the training set. Finally, a class-specific QSPR for PEGs and PPGs showed BT prediction trends consistent with known degradation pathways.
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| 4. |
- Hu, Xiaosong, et al.
(författare)
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Co-estimation of state of charge and state of health for lithium-ion batteries based on fractional-order calculus
- 2018
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Ingår i: IEEE Transactions on Vehicular Technology. - 0018-9545 .- 1939-9359. ; 67:11, s. 10319-10329
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Tidskriftsartikel (refereegranskat)abstract
- Lithium-ion batteries have emerged as the state-of-The-Art energy storage for portable electronics, electrified vehicles, and smart grids. An enabling Battery Management System holds the key for efficient and reliable system operation, in which State-of-Charge (SOC) estimation and State-of-Health (SOH) monitoring are of particular importance. In this paper, an SOC and SOH co-estimation scheme is proposed based on the fractional-order calculus. First, a fractional-order equivalent circuit model is established and parameterized using a Hybrid Genetic Algorithm/Particle Swarm Optimization method. This model is capable of predicting the voltage response with a root-mean-squared error less than 10 mV under various driving-cycle-based tests. Comparative studies show that it improves the modeling accuracy appreciably from its second-and third-order counterparts. Then, a dual fractional-order extended Kalman filter is put forward to realize simultaneous SOC and SOH estimation. Extensive experimental results show that the maximum steady-state errors of SOC and SOH estimation can be achieved within 1%, in the presence of initial deviation, noise, and disturbance. The resilience of the co-estimation scheme against battery aging is also verified through experimentation.
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| 5. |
- Li, Zhe, 1987-, et al.
(författare)
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A strategic screening approach to identify transformation products of organic micropollutants along rivers
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Many transformation products (TPs) from organic micropollutants are not included in routine monitoring programs due to limited knowledge of their occurrence and fate. An efficient method to identify and prioritize critical compounds in terms of environmental relevance is needed. In this study we applied a strategic screening approach based on a case-control concept to identify TPs with an increasing trend along a stretch in four wastewater-impacted rivers. Time-integrated samples were taken over one week at both ends of a river stretch downstream of a wastewater treatment plant (WWTP) outfall. The screening procedure consisted of three major steps: i) screening for parent compounds (PCs) attenuating along the stretch; ii) prediction of TPs for these PCs; and iii) screening for TPs with an increasing trend along the stretch. In total, 48 organic micropollutants were tentatively identified, of which 32 were decreasing along the stretches. From these PCs, 1315 TPs were predicted and eight out of which were tentatively identified with increasing concentrations along the stretches. Generally, good correlations were observed between the suspect screening results from this study and previous target analysis results on the same samples, suggesting high confidence of our screening approach. The case-control concept was proven efficient and reliable for identifying environmental relevant TPs formed along rivers.
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| 6. |
- Li, Zhe, 1987-
(författare)
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An integrated approach to study pharmaceuticals and their microbial transformation products: formation and environmental behavior in water/sediment systems
- 2014
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Pharmaceuticals are emerging organic micropollutants that are frequently detected in the aquatic environment. While information on their environmental occurrence is substantial, knowledge gaps exist with respect to their environmental transformation. This licentiate thesis focuses on this research deficit by (1) providing and applying tools for identifying biotransformation products, and (2) investigating the behavior of pharmaceuticals and their transformation products (TPs) in two different experimental systems.Study I established a data-processing method based on peak detection, time-trend filtration and structure assignment, and provides an efficient and reliable way for TP identification. Water/sediment tests were carried out with 9 pharmaceuticals. The method for identifying TPs is based on accurate mass data obtained from high resolution mass spectrometry and a comprehensive data-processing workflow. In total, 16 TPs were identified, 11 of which were confirmed by reference standards. Five of the TPs showed a continuous accumulation over the entire incubation period of 35 days.Study II aimed at studying the influence of water/sediment interactions on the environmental behavior of pharmaceuticals and their TPs. An artificial streaming channel was applied to simultaneously determine the concentrations of parent pharmaceuticals and key TPs in both surface water and sediment pore water under defined hydraulic conditions. All pharmaceuticals dissipated from the test system. The benefit from simultaneously analyzing parent compounds and TPs can be illustrated with carbamazepine, which is generally reported to be persistent. In study II, carbamazepine dissipated continuously from the test system, and the formation of a TP shows that this dissipation can be attributed to microbial biotransformation. The results also indicate that transformation predominantly occurs in the hyporheic zone, but also that TPs can be transported back into the streaming channel.This thesis confirms the crucial role of the hyporheic zone for the elimination of organic micropollutants from rivers and streams. Moreover, the developed workflow for TP identification provides opportunities to efficiently identify TPs for additional micropollutants in laboratory and field studies. In future work, we will study the influence of hydraulic conditions on transformation kinetics and formation of characteristic TPs, and we will extend the work to additional pharmaceuticals. Moreover, we will test the applicability of using TPs as indicators for characterizing ongoing biotransformation in field settings, thereby providing a more efficient way of characterizing the environmental fate of pharmaceuticals.
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| 7. |
- Li, Zhe, 1987-, et al.
(författare)
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Fate of Pharmaceuticals and Their Transformation Products in Four Small European Rivers Receiving Treated Wastewater
- 2016
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 50:11, s. 5614-5621
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Tidskriftsartikel (refereegranskat)abstract
- A considerable knowledge gap exists with respect to the fate and environmental relevance of transformation products (TPs) of polar organic micropollutants in surface water. To narrow this gap we investigated the fate of 20 parent compounds (PCs) and 11 characteristic TPs in four wastewater-impacted rivers. Samples were obtained from time-integrated active sampling as well as passive sampling using polar organic chemical integrative samplers (POCIS). Seventeen out of the 20 PCs were detected in at least one of the rivers. All the PCs except acesulfame, carbamazepine, and fluconazole were attenuated along the studied river stretches, with the largest decrease found in the smallest river which had an intense surface water-pore water exchange. Seven TPs were detected, all of which were already present directly downstream of the WWTP outfall, suggesting that the WWTPs were a major source of TPs to the recipients. For anionic compounds, attenuation was the highest in the two rivers with the lowest discharge, while the pattern was not as clear for neutral or cationic compounds. For most compounds the results obtained from active sampling were not significantly different from those using POCIS, demonstrating that the cost and labor efficient POCIS is suitable to determine the attenuation of organic micropollutants in rivers.
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| 8. |
- Li, Zhe, 1987-
(författare)
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Fate of Pharmaceuticals and Their Transformation Products in Rivers : An integration of target analysis and screening methods to study attenuation processes
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Pharmaceuticals are environmental contaminants causing steadily increasing concern due to their high usage, ubiquitous distribution in the aquatic environment, and potential to exert adverse effects on the ecosystems. After being discharged from wastewater treatment plants (WWTPs), pharmaceuticals can undergo transformation processes in surface waters, of which microbial degradation in river sediments is considered highly significant. In spite of a substantial number of studies on the occurrence of pharmaceuticals in aquatic systems, a comprehensive understanding of their environmental fate is still limited. First of all, very few consistent datasets from lab-based experiments to field studies exist to allow for a straightforward comparison of observations. Secondly, data on the identity and occurrence of transformation products (TPs) is insufficient and the relation of the behavior of TPs to that of their parent compounds (PCs) is poorly understood. In this thesis, these knowledge gaps were addressed by integrating the TP identification using suspect/non-target screening approaches and PC/TP fate determination. The overarching objective was to improve the understanding of the fate of pharmaceuticals in rivers, with a specific focus on water-sediment interactions, and formation and behavior of TPs. In paper I, 11 pharmaceutical TPs were identified in water-sediment incubation experiments using non-target screening. Bench-scale flume experiments were conducted in paper II to simultaneously investigate the behavior of PCs and TPs in both water and sediment compartments under more complex and realistic hydraulic conditions. The results illustrate that water-sediment interactions play a significant role for efficient attenuation of PCs, and demonstrate that TPs are formed in sediment and released back to surface water. In paper III the environmental behavior of PCs along stretches of four wastewater-impacted rivers was related to that of their TPs. The attenuation of PCs is highly compound and site specific. The highest attenuation rates of the PCs were observed in the river with the most efficient river water-pore water exchange. This research also indicates that WWTPs can be a major source of TPs to the receiving waters. In paper IV, suspect screening with a case-control concept was applied on water samples collected at both ends of the river stretches, which led to the identification of several key TPs formed along the stretches. The process-oriented strategies applied in this thesis provide a basis for prioritizing and identifying the critical PCs and TPs with respect to environmental relevance in future fate studies.
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| 9. |
- Li, Zhe, 1987-, et al.
(författare)
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Flume experiments to investigate the environmental fate of pharmaceuticals and their transformation products in streams
- 2015
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 49:10, s. 6009-6017
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Tidskriftsartikel (refereegranskat)abstract
- The hyporheic zone—the transition region beneath and alongside the stream bed—is a central compartment for attenuation of organic micropollutants in rivers. It provides abundant sorption sites and excellent conditions for biotransformation. We used a bench-scale flume to study the fate of 19 parent pharmaceuticals (PPs) and the formation of 11 characteristic transformation products (TPs) under boundary conditions similar to those in hyporheic zones. The persistence of PPs ranged from readily degradable with a dissipation half-life (DT50) as short as 1.8 days (acetaminophen, ibuprofen) to not degradable (chlorthalidone, fluconazole). The temporal and spatial patterns of PP and TP concentrations in pore water were heterogeneous, reflecting the complex hydraulic and biogeochemical conditions in hyporheic zones. Four TPs (carbamazepine-10,11-epoxide, metoprolol acid, 1-naphthol, and saluamine) were exclusively formed in the sediment compartment and released to surface water, highlighting their potential to be used as indicators for characterizing hyporheic transformation of micropollutants in streams. The accumulation of certain TPs over the experimental period illustrates that we might face a peak of secondary contamination by TPs far from the point of release of the original contaminants into a stream. Such TPs should be considered as priority candidates for a higher-tier environmental risk assessment.
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| 10. |
- Li, Zhe, 1987-, et al.
(författare)
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Screening for pharmaceutical transformation products formed in river sediment by combining ultrahigh performance liquid chromatography/high resolution mass spectrometry with a rapid data-processing method
- 2014
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Ingår i: Analytica Chimica Acta. - : Elsevier BV. - 0003-2670 .- 1873-4324. ; 810, s. 61-70
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Tidskriftsartikel (refereegranskat)abstract
- While the occurrence of pharmaceuticals in the aquatic environment has been extensively investigated, their environmental fate is less thoroughly explored. Scarce information on their transformation pathways and transformation products (TPs) limits conventional target analytical approaches. In this study, samples from water/sediment tests were analyzed by ultrahigh performance liquid chromatography interfaced with quadrupole time-of-flight mass spectrometry (UHPLC/QToF-MS). A data processing method based on peak detection, time-trend filtration and structure assignment was established to provide an efficient way for identifying the key TPs in terms of persistence; all software used for the individual steps of this method is freely available. The accurate mass and meaningful time-trends were major contributors in facilitating the isolation of plausible TP peaks. In total, 16 TPs from 9 parent pharmaceuticals were identified. Eleven out of the 16 TPs were confirmed by corresponding reference standards; no standards were available for the remaining TPs. For additional 6 potential TPs, a molecular formula was suggested but no additional structural information could be generated. Among the TPs identified in the water/sediment tests, carbamazepine-10,11-epoxide (parent: carbamazepine), saluamine (parent: furosemide), chlorothiazide and 4-amino-6-chloro-1,3-benzenedisulfonamide (parent of both: hydrochlorothiazide), and 1-naphthol (parent: propranolol) accumulated over the entire incubation period of 35 days.
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