| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- 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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| 4. |
- Chen, Fei'er, et al.
(författare)
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The effects of PM2.5 on asthmatic and allergic diseases or symptoms in preschool children of six Chinese cities, based on China, Children, Homes and Health (CCHH) project
- 2018
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Ingår i: Environmental Pollution. - : Elsevier BV. - 0269-7491 .- 1873-6424. ; 232, s. 329-337
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Tidskriftsartikel (refereegranskat)abstract
- The urbanization and industrialization in China is accompanied by bad air quality, and the prevalence of asthma in Chinese children has been increasing in recent years. To investigate the associations between ambient PM2.5 levels and asthmatic and allergic diseases or symptoms in preschool children in China, we assigned PM2.5 exposure data from the Global Burden of Disease (GBD) project to 205 kindergartens at a spatial resolution of 0.1° × 0.1° in six cities in China (Shanghai, Nanjing, Chongqing, Changsha, Urumqi, and Taiyuan). A hierarchical multiple logistical regression model was applied to analyze the associations between kindergarten-level PM2.5 exposure and individual-level outcomes of asthmatic and allergic symptoms. The individual-level variables, including gender, age, family history of asthma and allergic diseases, breastfeeding, parental smoking, indoor dampness, interior decoration pollution, household annual income, and city-level variable-annual temperature were adjusted. A total of 30,759 children (average age 4.6 years, 51.7% boys) were enrolled in this study. Apart from family history, indoor dampness, and decoration as predominant risk factors, we found that an increase of 10 μg/m3 of the annual PM2.5 was positively associated with the prevalence of allergic rhinitis by an odds ratio (OR) of 1.20 (95% confidence interval [CI] 1.11, 1.29) and diagnosed asthma by OR of 1.10 (95% CI 1.03, 1.18). Those who lived in non-urban (vs. urban) areas were exposed to more severe indoor air pollution arising from biomass combustion and had significantly higher ORs between PM2.5 and allergic rhinitis and current rhinitis. Our study suggested that long-term exposure to PM2.5 might increase the risks of asthmatic and allergic diseases or symptoms in preschool children in China. Compared to those living in urban areas, children living in suburban or rural areas had a higher risk of PM2.5 exposure.
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| 5. |
- Chen, Tianyi, et al.
(författare)
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Maternal exposure to PM2.5/BC during pregnancy predisposes children to allergic rhinitis which varies by regions and exclusive breastfeeding
- 2022
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Ingår i: Environment International. - : Elsevier. - 0160-4120 .- 1873-6750. ; 165
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundIncreasing prevalence of childhood allergic rhinitis(AR) needs a deeper understanding on the potential adverse effects of early life exposure to air pollution.ObjectivesThe main aim was to evaluate the effects of maternal exposure to PM2.5 and chemical constituents during pregnancy on preschool children’s AR, and further to explore the modification effects of regions and exclusive breastfeeding.MethodsA multi-center population-based study was performed in 6 cities from 3 regions of China in 2011–2012. Maternal exposure to ambient PM2.5 and main chemical constituents(BC, OM, SO42−, NO3−, NH4+) during pregnancy was assessed and a longitudinal prospective analysis was applied on preschool children’s AR. The modification effects of regions and exclusive breastfeeding were investigated.ResultsA total of 8.8% and 9.8% of children reported doctor-diagnosed allergic rhinitis(DDAR) and current hay fever, respectively, and 48.6% had less than 6 months of exclusive breastfeeding. The means of PM2.5 during pregnancy were 52.7 μg/m3, 70.3 μg/m3 and 76.4 μg/m3 in the east, north and central south of China, respectively. Multilevel log-binomial model regression showed that each interquartile range(IQR) increase of PM2.5 during pregnancy was associated with an average increase in prevalence ratio (PR) of DDAR by 1.43(95% confidence interval(CI): 1.11, 1.84) and current hay fever by 1.79(95% CI: 1.26, 2.55), respectively. Among chemical constituents, black carbon (BC) had the strongest associations. Across 3 regions, the eastern cities had the highest associations, followed by those in the central south and the north. For those equal to or longer than 6 months of exclusive breastfeeding, the associations were significantly reduced.ConclusionsChildren in east of China had the highest risks of developing AR per unit increase of maternal exposure to PM2.5 during pregnancy, especially BC constituent. Remarkable decline was found in association with an increase in breastfeeding for ≥6 months, in particular in east of China.
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| 6. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 7. |
- Du, Qian, et al.
(författare)
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Porcine circovirus type 2 infection promotes the SUMOylation of nucleophosmin-1 to facilitate the viral circular single-stranded DNA replication
- 2024
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Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 20:2
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Tidskriftsartikel (refereegranskat)abstract
- The mechanism of genome DNA replication in circular single-stranded DNA viruses is currently a mystery, except for the fact that it undergoes rolling-circle replication. Herein, we identified SUMOylated porcine nucleophosmin-1 (pNPM1), which is previously reported to be an interacting protein of the viral capsid protein, as a key regulator that promotes the genome DNA replication of porcine single-stranded DNA circovirus. Upon porcine circovirus type 2 (PCV2) infection, SUMO2/3 were recruited and conjugated with the K263 site of pNPM1's C-terminal domain to SUMOylate pNPM1, subsequently, the SUMOylated pNPM1 were translocated in nucleoli to promote the replication of PCV2 genome DNA. The mutation of the K263 site reduced the SUMOylation levels of pNPM1 and the nucleolar localization of pNPM1, resulting in a decrease in the level of PCV2 DNA replication. Meanwhile, the mutation of the K263 site prevented the interaction of pNPM1 with PCV2 DNA, but not the interaction of pNPM1 with PCV2 Cap. Mechanistically, PCV2 infection increased the expression levels of Ubc9, the only E2 enzyme involved in SUMOylation, through the Cap-mediated activation of ERK signaling. The upregulation of Ubc9 promoted the interaction between pNPM1 and TRIM24, a potential E3 ligase for SUMOylation, thereby facilitating the SUMOylation of pNPM1. The inhibition of ERK activation could significantly reduce the SUMOylation levels and the nucleolar localization of pNPM1, as well as the PCV2 DNA replication levels. These results provide new insights into the mechanism of circular single-stranded DNA virus replication and highlight NPM1 as a potential target for inhibiting PCV2 replication. Different types of DNA viruses employ different mechanisms to replicate their genome DNA. Porcine circovirus type 2 (PCV2) is the most representative circular single-stranded DNA virus that harms the pig industry all over the world. In this study, we found that the PCV2 Cap interacting protein pNPM1 also interacts with PCV2 DNA in a SUMOylated form to promote PCV2 DNA replication. The SUMOylation of pNPM1 at the conserved K263 site is critical for the interaction of pNPM1 with PCV2 DNA and the replication of PCV2 DNA. Furthermore, we found that PCV2 infection promotes the SUMO2/3 mediated SUMOylation of pNPM1, while does not significantly alter the expression level of pNPM1. PCV2 Cap is the major component that promotes pNPM1 SUMOylation by activating ERK/Ubc9/TRIM24 signalings. These results contribute to a better understanding of the replication mechanism of circular single-stranded DNA viruses, particularly PCV2.
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| 8. |
- Hao, Qian, et al.
(författare)
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Organic blue carbon sequestration in vegetated coastal wetlands: Processes and influencing factors
- 2024
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Ingår i: Earth-Science Reviews. - 0012-8252 .- 1872-6828. ; 255, s. 104853-104853
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Tidskriftsartikel (refereegranskat)abstract
- Coastal wetlands play a vital role in carbon (C) sequestration, named ‘blue carbon’. The review aims to disentangle the processes and influencing factors, including elevated atmospheric CO2, global climate warming, sea level rise and anthropogenic activities. Firstly, we provided an overview of C processes, including input, output, and deposition, in coastal wetlands. We then summarized the impacts of different factors on C processes by modifying soil physicochemical properties, plant growth, vegetation type, and microbial community composition. Vegetation composition was a major contributor to C inputs, and C outputs was mainly controlled by microbial decomposition. Increased atmospheric CO2 concentration and associated climate warming often enhanced vegetation growth, while climate warming also promoted soil C decomposition. As a result, C storage could increase under mild warming conditions in the short-term, but decrease in the long-term as the severity of warming intensifies. Elevated salinity, caused by sea level rise, can be harmful to plant growth and inhibit organic C decomposition because of the reduced biomass and the weakened metabolic capacity of microorganisms. Most of human activities, such as reclamation, can lead to less C input and more C output, resulting in decreased C storage in coastal wetlands. Additionally, we also illustrate various coastal wetland restoration methods aimed at enhancing C sequestration, including legal frameworks, scientific theories, vegetation management, hydrological restoration, and other relevant constructions. Vegetation management could benefit plant growth and enhance C input effectively, and hydrological restoration can maintain the harmonious development of coastal wetland ecosystems. Other constructions, including breakwater, spillway, and dredged material, could protect coastal wetlands, especially facing sea level rise. This review offers valuable theoretical support and scientific references for the sustainable development and management of coastal wetlands in a changing climate.
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| 9. |
- Hou, Cong wei, et al.
(författare)
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Parametric analysis on throttling components of multi-stage high pressure reducing valve
- 2018
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Ingår i: Applied Thermal Engineering. - : Elsevier BV. - 1359-4311. ; 128, s. 1238-1248
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Tidskriftsartikel (refereegranskat)abstract
- High pressure reducing valve (HPRV) is widely used for pressure and temperature control of heated steams in power plant and other related process engineering. The structures of throttling components inside HPRVs have important effects on the control performances. In this paper, a parametric study of throttling components in a multi-stage high pressure reducing valve (MSHPRV) is carried out, including the relative angle of inner and outer porous shrouded holes, the orifice plate thickness, the number of orifice plates and the diameter of plate holes. A numerical model is established to investigate internal flow and throttling characteristics with RNG k-ε model, and it is validated by the theoretical flux calculation. The results show that, the relative angle set as 180° can obtain the largest decompression pressure when steam flows through porous shrouded valve core, while the turbulence degree is the lowest. Setting one orifice plate can decrease the turbulent dissipation rate. The plate thickness has less influence on throttling effects. For ensuring the outlet flux, plate holes with smaller diameters should be chosen with a better flowing property on thermodynamic parameters. The work can be referred by the design work of throttling components in MSHPRV and it can also benefit the further research on similar HPRVs.
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| 10. |
- Kang, Shichang, et al.
(författare)
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Linking atmospheric pollution to cryospheric change in the Third Pole region : current progress and future prospects
- 2019
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Ingår i: National Science Review. - : Oxford University Press (OUP). - 2095-5138 .- 2053-714X. ; 6:4, s. 796-809
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Forskningsöversikt (refereegranskat)abstract
- The Tibetan Plateau and its surroundings are known as the Third Pole (TP). This region is noted for its high rates of glacier melt and the associated hydrological shifts that affect water supplies in Asia. Atmospheric pollutants contribute to climatic and cryospheric changes through their effects on solar radiation and the albedos of snow and ice surfaces; moreover, the behavior and fates within the cryosphere and environmental impacts of environmental pollutants are topics of increasing concern. In this review, we introduce a coordinated monitoring and research framework and network to link atmospheric pollution and cryospheric changes (APCC) within the TP region. We then provide an up-to-date summary of progress and achievements related to the APCC research framework, including aspects of atmospheric pollution's composition and concentration, spatial and temporal variations, trans-boundary transport pathways and mechanisms, and effects on the warming of atmosphere and changing in Indian monsoon, as well as melting of glacier and snow cover. We highlight that exogenous air pollutants can enter into the TP's environments and cause great impacts on regional climatic and environmental changes. At last, we propose future research priorities and map out an extended program at the global scale. The ongoing monitoring activities and research facilitate comprehensive studies of atmosphere-cryosphere interactions, represent one of China's key research expeditions to the TP and the polar regions and contribute to the global perspective of earth system science.
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