| 1. |
- Jin, Ying-Hui, et al.
(författare)
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Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
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Ingår i: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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| 2. |
- Li, Feiran, 1993, et al.
(författare)
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Deep learning-based k(cat) prediction enables improved enzyme-constrained model reconstruction
- 2022
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Ingår i: Nature Catalysis. - : Springer Science and Business Media LLC. - 2520-1158. ; 5:8, s. 662-672
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Tidskriftsartikel (refereegranskat)abstract
- Enzyme turnover numbers (k(cat)) are key to understanding cellular metabolism, proteome allocation and physiological diversity, but experimentally measured k(cat) data are sparse and noisy. Here we provide a deep learning approach (DLKcat) for high-throughput k(cat) prediction for metabolic enzymes from any organism merely from substrate structures and protein sequences. DLKcat can capture k(cat) changes for mutated enzymes and identify amino acid residues with a strong impact on k(cat) values. We applied this approach to predict genome-scale k(cat) values for more than 300 yeast species. Additionally, we designed a Bayesian pipeline to parameterize enzyme-constrained genome-scale metabolic models from predicted k(cat) values. The resulting models outperformed the corresponding original enzyme-constrained genome-scale metabolic models from previous pipelines in predicting phenotypes and proteomes, and enabled us to explain phenotypic differences. DLKcat and the enzyme-constrained genome-scale metabolic model construction pipeline are valuable tools to uncover global trends of enzyme kinetics and physiological diversity, and to further elucidate cellular metabolism on a large scale.
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| 3. |
- Li, Qian, et al.
(författare)
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Genome-wide identification of resistance genes and cellular analysis of key gene knockout strain under 5-hydroxymethylfurfural stress in Saccharomyces cerevisiae
- 2023
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Ingår i: BMC Microbiology. - 1471-2180. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- In bioethanol production, the main by-product, 5-hydroxymethylfurfural (HMF), significantly hinders microbial fermentation. Therefore, it is crucial to explore genes related to HMF tolerance in Saccharomyces cerevisiae for enhancing the tolerance of ethanol fermentation strains. A comprehensive analysis was conducted using genome-wide deletion library scanning and SGAtools, resulting in the identification of 294 genes associated with HMF tolerance in S. cerevisiae. Further KEGG and GO enrichment analysis revealed the involvement of genes OCA1 and SIW14 in the protein phosphorylation pathway, underscoring their role in HMF tolerance. Spot test validation and subcellular structure observation demonstrated that, following a 3-h treatment with 60mM HMF, the SIW14 gene knockout strain exhibited a 12.68% increase in cells with abnormal endoplasmic reticulum (ER) and a 22.41% increase in the accumulation of reactive oxygen species compared to the BY4741 strain. These findings indicate that the SIW14 gene contributes to the protection of the ER structure within the cell and facilitates the clearance of reactive oxygen species, thereby confirming its significance as a key gene for HMF tolerance in S. cerevisiae.
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| 4. |
- Liu, Tao, et al.
(författare)
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16% efficiency all-polymer organic solar cells enabled by a finely tuned morphology via the design of ternary blend
- 2021
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Ingår i: Joule. - : CELL PRESS. - 2542-4351. ; 5:4, s. 914-930
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Tidskriftsartikel (refereegranskat)abstract
- A SUMMARY There is an urgent demand for all-polymer organic solar cells (AP-OSCs) to gain higher efficiency. Here, we successfully improve the performance to 16.09% by introducing a small amount of BN-T, a B <- N-type polymer acceptor, into the PM6:PY-IT blend. It has been found that BN-T makes the active layer, based on the PM6:PY-IT:BN-T ternary blend, more crystalline but meanwhile slightly reduces the phase separation, leading to enhancement of both exciton harvesting and charge transport. From a thermodynamic viewpoint, BN-T prefers to reside between PM6 and PY-IT, and the fraction of this fine-tunes the morphology. Besides, a significantly reduced nonradiative energy loss occurs in the ternary blend, along with the coexistence of energy and charge transfer between the two acceptors. The progressive performance facilitated by these improved properties demonstrates that AP-OSCs can possibly comparably efficient with those based on small molecule acceptors, further enhancing the competitiveness of this device type.
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| 5. |
- Lu, Hongzhong, 1987, et al.
(författare)
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Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection
- 2021
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Ingår i: Molecular Systems Biology. - : EMBO. - 1744-4292. ; 17:10
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Tidskriftsartikel (refereegranskat)abstract
- Yeasts are known to have versatile metabolic traits, while how these metabolic traits have evolved has not been elucidated systematically. We performed integrative evolution analysis to investigate how genomic evolution determines trait generation by reconstructing genome-scale metabolic models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize trait diversity and predict enzyme functionality, thereby signifying that sequence-level evolution has shaped reaction networks towards new metabolic functions. Strikingly, using GEMs, we can mechanistically map different evolutionary events, e.g. horizontal gene transfer and gene duplication, onto relevant subpathways to explain metabolic plasticity. This demonstrates that gene family expansion and enzyme promiscuity are prominent mechanisms for metabolic trait gains, while GEM simulations reveal that additional factors, such as gene loss from distant pathways, contribute to trait losses. Furthermore, our analysis could pinpoint to specific genes and pathways that have been under positive selection and relevant for the formulation of complex metabolic traits, i.e. thermotolerance and the Crabtree effect. Our findings illustrate how multidimensional evolution in both metabolic network structure and individual enzymes drives phenotypic variations.
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| 6. |
- Lu, Jing, et al.
(författare)
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Ameliorated Snake Optimizer-Based Approximate Merging of Disk Wang-Ball Curves
- 2024
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Ingår i: BIOMIMETICS. - : MDPI. - 2313-7673. ; 9:3
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Tidskriftsartikel (refereegranskat)abstract
- A method for the approximate merging of disk Wang-Ball (DWB) curves based on the modified snake optimizer (BEESO) is proposed in this paper to address the problem of difficulties in the merging of DWB curves. By extending the approximate merging problem for traditional curves to disk curves and viewing it as an optimization problem, an approximate merging model is established to minimize the merging error through an error formulation. Considering the complexity of the model built, a BEESO with better convergence accuracy and convergence speed is introduced, which combines the snake optimizer (SO) and three strategies including bi-directional search, evolutionary population dynamics, and elite opposition-based learning. The merging results and merging errors of numerical examples demonstrate that BEESO is effective in solving approximate merging models, and it provides a new method for the compression and transfer of product shape data in Computer-Aided Geometric Design.
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| 7. |
- Ma, Ruijie, et al.
(författare)
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All-polymer solar cells with over 16% efficiency and enhanced stability enabled by compatible solvent and polymer additives
- 2022
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Ingår i: Aggregate. - : Wiley. - 2692-4560 .- 2766-8541. ; 3:3
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Tidskriftsartikel (refereegranskat)abstract
- Considering the robust and stable nature of the active layers, advancing the power conversion efficiency (PCE) has long been the priority for all-polymer solar cells (all-PSCs). Despite the recent surge of PCE, the photovoltaic parameters of the state-of-the-art all-PSC still lag those of the polymer:small molecule-based devices. To compete with the counterparts, judicious modulation of the morphology and thus the device electrical properties are needed. It is difficult to improve all the parameters concurrently for the all-PSCs with advanced efficiency, and one increase is typically accompanied by the drop of the other(s). In this work, with the aids of the solvent additive (1-chloronaphthalene) and the n-type polymer additive (N2200), we can fine-tune the morphology of the active layer and demonstrate a 16.04% efficient all-PSC based on the PM6:PY-IT active layer. The grazing incidence wide-angle X-ray scattering measurements show that the shape of the crystallites can be altered, and the reshaped crystallites lead to enhanced and more balanced charge transport, reduced recombination, and suppressed energy loss, which lead to concurrently improved and device efficiency and stability.
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| 8. |
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| 9. |
- Sarris, Theodore E., et al.
(författare)
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Daedalus MASE (mission assessment through simulation exercise): A toolset for analysis of in situ missions and for processing global circulation model outputs in the lower thermosphere-ionosphere
- 2023
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Ingår i: Frontiers in Astronomy and Space Sciences. - : Frontiers Media SA. - 2296-987X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Daedalus MASE (Mission Assessment through Simulation Exercise) is an open-source package of scientific analysis tools aimed at research in the Lower Thermosphere-Ionosphere (LTI). It was created with the purpose to assess the performance and demonstrate closure of the mission objectives of Daedalus, a mission concept targeting to perform in-situ measurements in the LTI. However, through its successful usage as a mission-simulator toolset, Daedalus MASE has evolved to encompass numerous capabilities related to LTI science and modeling. Inputs are geophysical observables in the LTI, which can be obtained either through in-situ measurements from spacecraft and rockets, or through Global Circulation Models (GCM). These include ion, neutral and electron densities, ion and neutral composition, ion, electron and neutral temperatures, ion drifts, neutral winds, electric field, and magnetic field. In the examples presented, these geophysical observables are obtained through NCAR’s Thermosphere-Ionosphere-Electrodynamics General Circulation Model. Capabilities of Daedalus MASE include: 1) Calculations of products that are derived from the above geophysical observables, such as Joule heating, energy transfer rates between species, electrical currents, electrical conductivity, ion-neutral collision frequencies between all combinations of species, as well as height-integrations of derived products. 2) Calculation and cross-comparison of collision frequencies and estimates of the effect of using different models of collision frequencies into derived products. 3) Calculation of the uncertainties of derived products based on the uncertainties of the geophysical observables, due to instrument errors or to uncertainties in measurement techniques. 4) Routines for the along-orbit interpolation within gridded datasets of GCMs. 5) Routines for the calculation of the global coverage of an in situ mission in regions of interest and for various conditions of solar and geomagnetic activity. 6) Calculations of the statistical significance of obtaining the primary and derived products throughout an in situ mission’s lifetime. 7) Routines for the visualization of 3D datasets of GCMs and of measurements along orbit. Daedalus MASE code is accompanied by a set of Jupyter Notebooks, incorporating all required theory, references, codes and plotting in a user-friendly environment. Daedalus MASE is developed and maintained at the Department for Electrical and Computer Engineering of the Democritus University of Thrace, with key contributions from several partner institutions.
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| 10. |
- Sarris, Theodoros, et al.
(författare)
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Plasma-neutral interactions in the lower thermosphere-ionosphere : The need for in situ measurements to address focused questions
- 2023
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Ingår i: Frontiers in Astronomy and Space Sciences. - : Frontiers Media SA. - 2296-987X. ; 9
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Forskningsöversikt (refereegranskat)abstract
- The lower thermosphere-ionosphere (LTI) is a key transition region between Earth's atmosphere and space. Interactions between ions and neutrals maximize within the LTI and in particular at altitudes from 100 to 200 km, which is the least visited region of the near-Earth environment. The lack of in situ co-temporal and co-spatial measurements of all relevant parameters and their elusiveness to most remote-sensing methods means that the complex interactions between its neutral and charged constituents remain poorly characterized to this date. This lack of measurements, together with the ambiguity in the quantification of key processes in the 100-200 km altitude range affect current modeling efforts to expand atmospheric models upward to include the LTI and limit current space weather prediction capabilities. We present focused questions in the LTI that are related to the complex interactions between its neutral and charged constituents. These questions concern core physical processes that govern the energetics, dynamics, and chemistry of the LTI and need to be addressed as fundamental and long-standing questions in this critically unexplored boundary region. We also outline the range of in situ measurements that are needed to unambiguously quantify key LTI processes within this region, and present elements of an in situ concept based on past proposed mission concepts.
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