| 1. |
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| 2. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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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| 3. |
- Kristan, Matej, et al.
(author)
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The Ninth Visual Object Tracking VOT2021 Challenge Results
- 2021
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In: 2021 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2021). - : IEEE COMPUTER SOC. - 9781665401913 ; , s. 2711-2738
-
Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2021 is the ninth annual tracker benchmarking activity organized by the VOT initiative. Results of 71 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in recent years. The VOT2021 challenge was composed of four sub-challenges focusing on different tracking domains: (i) VOT-ST2021 challenge focused on short-term tracking in RGB, (ii) VOT-RT2021 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2021 focused on long-term tracking, namely coping with target disappearance and reappearance and (iv) VOT-RGBD2021 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2021 dataset was refreshed, while VOT-RGBD2021 introduces a training dataset and sequestered dataset for winner identification. The source code for most of the trackers, the datasets, the evaluation kit and the results along with the source code for most trackers are publicly available at the challenge website(1).
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| 4. |
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| 5. |
- Kanoni, Stavroula, et al.
(author)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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In: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Journal article (peer-reviewed)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 6. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 7. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 8. |
- Luo, Yifei, et al.
(author)
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Technology Roadmap for Flexible Sensors
- 2023
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In: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
-
Research review (peer-reviewed)abstract
- Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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| 9. |
- Ding, Xue Bing, et al.
(author)
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Impaired meningeal lymphatic drainage in patients with idiopathic Parkinson’s disease
- 2021
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In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:3, s. 411-418
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Journal article (peer-reviewed)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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| 10. |
- Jin, Ying-Hui, et al.
(author)
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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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In: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
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Journal article (peer-reviewed)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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| 11. |
- Liu, Lihui, et al.
(author)
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Ablation of ERO1A induces lethal endoplasmic reticulum stress responses and immunogenic cell death to activate anti-tumor immunity
- 2023
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In: Cell Reports Medicine. - : Cell Press. - 2666-3791. ; 4:10
-
Journal article (peer-reviewed)abstract
- Immunophenotyping of the tumor microenvironment (TME) is essential for enhancing immunotherapy effi-cacy. However, strategies for characterizing the TME exhibit significant heterogeneity. Here, we show that endoplasmic reticular oxidoreductase-1a (ERO1A) mediates an immune-suppressive TME and attenuates the response to PD-1 blockade. Ablation of ERO1A in tumor cells substantially incites anti-tumor T cell im-munity and promotes the efficacy of aPD-1 in therapeutic models. Single-cell RNA-sequencing analyses confirm that ERO1A correlates with immunosuppression and dysfunction of CD8+ T cells along anti-PD-1 treatment. In human lung cancer, high ERO1A expression is associated with a higher risk of recurrence following neoadjuvant immunotherapy. Mechanistically, ERO1A ablation impairs the balance between IRE1a and PERK signaling activities and induces lethal unfolded protein responses in tumor cells undergoing endoplasmic reticulum stress, thereby enhancing anti-tumor immunity via immunogenic cell death. These findings reveal how tumor ERO1A induces immunosuppression, highlighting its potential as a therapeutic target for cancer immunotherapy.
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| 12. |
- Liu, Lihui, et al.
(author)
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Dynamic toxicity landscape of immunotherapy for solid tumors across treatment lines
- 2023
-
In: Journal of the National Cancer Center. - : Elsevier. - 2667-0054. ; 3:3, s. 186-196
-
Journal article (peer-reviewed)abstract
- Objective: Immune checkpoint inhibitors (ICIs) targeting programmed cell death-1/ligand-1 (PD-1/PD-L1), cytotoxic T lymphocyte antigen-4 (CTLA-4), and lymphocyte-activation gene-3 (LAG-3) have been widely studied and applied throughout the course of cancer treatment. This study aimed to provide a comprehensive profile of ICI-associated toxicity and elucidate the toxicity patterns of ICIs across different treatment lines. Methods: In total, 155 cohorts comprising 24 539 eligible patients were included in the safety analysis. Trial name, registration number, cancer type, trial phase, clinical setting, trial design, regimen, dosing schedule, age, sex and ethnicity distributions, number of patients, number of treatment-related adverse events (trAEs), and number of treatment-related death were extracted. We defined a timeline from the neoadjuvant setting to the third-line setting. We also introduced a synthesizing principle for adverse event rates (SPAER) of immunotherapy to ensure the comparability and reliability across different treatment lines. The study protocol was registered and approved by the PROSPERO protocol review committee (CRD42021242368). Results: After excluding the neoadjuvant setting group, we observed a distinct reduction in the incidence of treatment-related adverse events (trAEs) with an advancement of the line of ICI treatment. The incidence of trAEs was negatively correlated with the line of treatment, irrespective of whether monotherapy or dual-ICI combination therapy was administered. Sensitivity analyses also confirmed the coincident negative correlations. Conclusion: In summary, using a timeline-based concept centered around treatment lines, we revealed the dynamic landscape of ICI-associated toxicity and found that patients treated with ICIs during later lines of therapy may have a lower risk of trAEs.
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| 13. |
- Ramdas, S., et al.
(author)
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A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids
- 2022
-
In: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 109:8, s. 1366-1387
-
Journal article (peer-reviewed)abstract
- A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.
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| 14. |
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| 15. |
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| 16. |
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| 17. |
- Liu, Hui, et al.
(author)
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Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
-
In: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
-
Journal article (peer-reviewed)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
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| 18. |
- Sun, Q., et al.
(author)
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Prevalence and cardiovascular risk factors of asymptomatic intracranial arterial stenosis : the Kongcun Town Study in Shandong, China
- 2020
-
In: European Journal of Neurology. - : Wiley. - 1351-5101 .- 1468-1331. ; 27:4, s. 729-735
-
Journal article (peer-reviewed)abstract
- Background and purpose This study was to investigate the prevalence and cardiovascular risk factors (CRFs) of asymptomatic intracranial atherosclerotic stenosis (aICAS) amongst middle-aged and older adults living in rural communities in China. Methods This population-based study included 2019 subjects (aged >= 40 years, 52.3% women) who were free of stroke and living in rural communities in China. From October 2017 to May 2018, data on demographics, CRFs and health conditions were collected through face-to-face interviews, physical examination and laboratory tests. Asymptomatic ICAS was detected through a two-phase procedure: a screening phase with transcranial Doppler ultrasound, followed by a diagnostic phase with magnetic resonance angiography examination. Multivariable logistic regression models were used to analyse CRFs associated with aICAS. Results Of the 2019 participants, aICAS was detected in 153 persons. The overall prevalence of aICAS was 7.6%, and the prevalence of moderate-to-severe aICAS was 5.0%. The multi-adjusted odds ratio (95% confidence interval) of aICAS associated with CRFs was 2.40 (1.56-3.69) for hypertension, 1.91 (1.32-2.76) for high hypersensitive C-reactive protein, 1.68 (1.14-2.49) for diabetes and 1.61 (1.08-2.41) for overweight or obesity. When these four CRFs were aggregated, compared with participants without any of these factors, the multi-adjusted odds ratios (95% confidence interval) of aICAS for persons concurrently having one, two and three or more of these factors were 1.14 (0.52-2.48), 2.91 (1.42-5.99) and 5.51 (2.64-11.50), respectively (P for linear trend <0.001). Conclusions Asymptomatic ICAS is common amongst rural-dwelling middle-aged and older Chinese people. Hypertension, diabetes, overweight or obesity and high hypersensitive C-reactive protein, especially when coexisting, are strongly associated with aICAS.
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| 19. |
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| 20. |
- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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| 21. |
- Cheng, Shi-Ping, et al.
(author)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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In: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Journal article (peer-reviewed)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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| 22. |
- Morawska, Lidia, et al.
(author)
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The state of science on severe air pollution episodes : Quantitative and qualitative analysis
- 2021
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In: Environment International. - : Elsevier BV. - 1873-6750 .- 0160-4120. ; 156, s. 106732-106732
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Journal article (peer-reviewed)abstract
- Severe episodic air pollution blankets entire cities and regions and have a profound impact on humans and their activities. We compiled daily fine particle (PM2.5) data from 100 cities in five continents, investigated the trends of number, frequency, and duration of pollution episodes, and compared these with the baseline trend in air pollution. We showed that the factors contributing to these events are complex; however, long-term measures to abate emissions from all anthropogenic sources at all times is also the most efficient way to reduce the occurrence of severe air pollution events. In the short term, accurate forecasting systems of such events based on the meteorological conditions favouring their occurrence, together with effective emergency mitigation of anthropogenic sources, may lessen their magnitude and/or duration. However, there is no clear way of preventing events caused by natural sources affected by climate change, such as wildfires and desert dust outbreaks.
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| 23. |
- Wang, Hao-Tian, et al.
(author)
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Insights into the missing apiosylation step in flavonoid apiosides biosynthesis of Leguminosae plants
- 2023
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Journal article (peer-reviewed)abstract
- Apiose is a natural pentose containing an unusual branched-chain structure. Apiosides are bioactive natural products widely present in the plant kingdom. However, little is known on the key apiosylation reaction in the biosynthetic pathways of apiosides. In this work, we discover an apiosyltransferase GuApiGT from Glycyrrhiza uralensis. GuApiGT could efficiently catalyze 2″-O-apiosylation of flavonoid glycosides, and exhibits strict selectivity towards UDP-apiose. We further solve the crystal structure of GuApiGT, determine a key sugar-binding motif (RLGSDH) through structural analysis and theoretical calculations, and obtain mutants with altered sugar selectivity through protein engineering. Moreover, we discover 121 candidate apiosyltransferase genes from Leguminosae plants, and identify the functions of 4 enzymes. Finally, we introduce GuApiGT and its upstream genes into Nicotiana benthamiana, and complete de novo biosynthesis of a series of flavonoid apiosides. This work reports an efficient phenolic apiosyltransferase, and reveals mechanisms for its sugar donor selectivity.
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| 24. |
- Wang, Shaoying, et al.
(author)
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Characterizing lipid profiles associated with asymptomatic intracranial arterial stenosis in rural-dwelling adults : A population-based study
- 2020
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In: Journal of Clinical Lipidology. - : Elsevier BV. - 1933-2874 .- 1876-4789. ; 14:3, s. 371-380
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Journal article (peer-reviewed)abstract
- BACKGROUND: Although individual lipid parameters have been frequently examined in association with asymptomatic intracranial arterial stenosis (aICAS), few population-based studies have investigated the lipid profiles associated with aICAS among Chinese adults. OBJECTIVE: This study aims to characterize the lipid profiles associated with aICAS in rural-dwelling adults in China. METHODS: This population-based study included 2027 persons who were aged >= 40 years and free of stroke. Data were collected via interviews, clinical examinations, and laboratory testing. We diagnosed aICAS by integrating transcranial color Doppler with magnetic resonance angiography. Data were analyzed using binary and multinomial logistic regression models. RESULTS: Of the 2027 participants, 154 were detected with aICAS. The multiadjusted odds ratio (95% confidence interval) of aICAS was 1.41 (0.997-2.00) for high small dense low-density lipoprotein cholesterol, 1.44 (1.02-2.04) for high lipoprotein(a), 1.71 (1.21-2.44) for low apolipoprotein A-1, 1.43 (1.00-2.04) for low high-density lipoprotein cholesterol (HDL-C), 1.61 (1.14-2.27) for high apolipoprotein B/apolipoprotein A-1 ratio, 1.95 (1.38-2.76) for high low-density lipoprotein cholesterol/HDL-C ratio, and 1.51 (1.06-2.14) for high total cholesterol/HDL-C ratio. When severity of aICAS was analyzed, high levels of lipoprotein(a), small dense low-density lipoprotein cholesterol, and lipid ratios were significantly associated with an increased likelihood of moderate-to-severe aICAS (P < .05). An increasing number of abnormal lipid measurements was associated with an increased likelihood of aICAS (P for trend <.001). CONCLUSION: These findings suggest that lipid profiles for aICAS among rural residents in China are characterized by high atherogenic cholesterol, low antiatherogenic cholesterol, and high ratios of atherogenic-to-antiatherogenic cholesterol or lipoproteins.
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| 25. |
- Wang, Wen‐Bo, et al.
(author)
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Chromosome‐scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata
- 2023
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In: New Phytologist. - : John Wiley & Sons. - 0028-646X .- 1469-8137. ; 238:5, s. 2016-2032
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Journal article (peer-reviewed)abstract
- Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated.First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation.Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays.Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.
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| 26. |
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| 27. |
- Zhao, Xue-Ke, et al.
(author)
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Focal amplifications are associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma
- 2021
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 12
-
Journal article (peer-reviewed)abstract
- The role of focal amplifications and extrachromosomal DNA (ecDNA) is unknown in gastric cardia adenocarcinoma (GCA). Here, we identify frequent focal amplifications and ecDNAs in Chinese GCA patient samples, and find focal amplifications in the GCA cohort are associated with the chromothripsis process and may be induced by accumulated DNA damage due to local dietary habits. We observe diverse correlations between the presence of oncogene focal amplifications and prognosis, where ERBB2 focal amplifications positively correlate with prognosis and EGFR focal amplifications negatively correlate with prognosis. Large-scale ERBB2 immunohistochemistry results from 1668 GCA patients show survival probability of ERBB2 positive patients is lower than that of ERBB2 negative patients when their surviving time is under 2 years, however, the tendency is opposite when their surviving time is longer than 2 years. Our observations indicate that the ERBB2 focal amplifications may represent a good prognostic marker in GCA patients.
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| 28. |
- Bi, Zenghui, et al.
(author)
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Highly dispersed La−O/N−C sites anchored in hierarchically porous nitrogen-doped carbon as bifunctional catalysts for high-performance rechargeable Zn−air batteries
- 2023
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In: Energy Storage Materials. - : Elsevier. - 2405-8289 .- 2405-8297. ; 54, s. 313-322
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Journal article (peer-reviewed)abstract
- Inexpensive, high-activity bifunctional catalysts for the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) are imperative for the development of energy storage and conversion systems. A nitrogen-doped carbon material with a micro−meso−macroporous structure doped with La (LaPNC) containing La−O/N−C active sites is prepared using SiO2 particle templating of carbon and a metal node exchange strategy. The coordination environment of La sites stabilized by two oxygen and four nitrogen atoms (LaO2N4), is further verified by X-ray absorption spectroscopy. The ORR half-wave potential reaches 0.852 V, and the OER overpotential reaches 263 mV at 10 mA cm−2. The Zn−air battery, with LaPNC as the air cathode, has a maximum power density of 202 mW cm−2 and achieves stable charge−discharge for at least 100 h without a significant increase or decrease in the charge or discharge voltages, respectively. Density functional theory calculations suggest that LaO2N4 sites exhibit the lowest activation free energy and the most easily desorbed oxygen capacity. This study provides new insights into the design of efficient, durable bifunctional catalysts as alternatives to precious-metal-based catalysts.
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| 29. |
- Chen, Jie, et al.
(author)
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Bidirectional Mendelian Randomisation Analysis Provides Evidence for the Causal Involvement of Dysregulation of CXCL9, CCL11 and CASP8 in the Pathogenesis of Ulcerative Colitis
- 2023
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In: Journal of Crohn's & Colitis. - : Oxford University Press. - 1873-9946 .- 1876-4479. ; 17:5, s. 777-785
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Journal article (peer-reviewed)abstract
- Background and Aims Systemic inflammation is well recognised to be associated with ulcerative colitis [UC], but whether these effects are causal or consequential remains unclear. We aimed to define potential causal relationship of cytokine dysregulation with different tiers of evidence. Methods We first synthesised serum proteomic profiling data from two multicentred observational studies, in which a panel of systemic inflammatory proteins was analysed to examine their associations with UC risk. To further dissect observed associations, we then performed a bidirectional two-sample Mendelian randomisation [TSMR] analysis from both forward and reverse directions using five genome-wide association study [GWAS] summary level data for serum proteomic profiles and the largest GWAS of 28 738 European-ancestry individuals for UC risk. Results Pooled analysis of serum proteomic data identified 14 proteins to be associated with the risk of UC. Forward MR analysis using only cis-acting protein quantitative trait loci [cis-pQTLs] or trans-pQTLs further validated causal associations of two chemokines and the increased risk of UC: C-X-C motif chemokine ligand 9 [CXCL9] [OR 1.45, 95% CI 1.08, 1.95, p = 0.012] and C-C motif chemokine ligand 11 [CCL11] [OR 1.14, 95% CI 1.09, 1.18, p = 3.89 x 10(-10)]. Using both cis- and trans-acting pQTLs, an association of caspase-8 [CASP8] [OR 1.04, 95% CI 1.03, 1.05, p = 7.63 x 10(-19)] was additionally identified. Reverse MR did not find any influence of genetic predisposition to UC on any of these three inflammation proteins. Conclusion Pre-existing elevated levels of CXCL9, CCL11 and CASP8 may play a role in the pathogenesis of UC.
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| 30. |
- Du, Shixiong, et al.
(author)
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Evaluating the potential benefits of float solar photovoltaics through the water footprint recovery period
- 2024
-
In: Journal of Cleaner Production. - 0959-6526. ; 446
-
Journal article (peer-reviewed)abstract
- In the context of higher demands on the development of clean energy technologies due to the issue of water shortage in China and the implementation of the 2060 carbon-neutral objective, floating photovoltaic (FPV) systems present novel opportunities for transforming the energy structure through land conservation and enhancement of power generation efficiency compared to conventional solar systems. However, there is currently a lack of comprehensive analysis on the potential benefits of FPV. Utilizing reservoir databases and employing a professional FPV system design, a methodology for determining the water footprint recovery period was introduced, which enables the assessment of potential FPV benefits. The water footprint recovery period for constructing FPV on 909 reservoirs in China was found that ranges from 1.86 yr to 10.48 yr. It is found that reservoir evaporation, latitude, and climate are closely related to the water footprint recovery period of FPV. Furthermore, by implementing FPV panels with an optimal tilt angle, covering 30% of the area in each reservoir, the annual electricity generation can amount to 1429.19 TWh, leading to savings of 5.76 billion m3 of water. This achievement corresponds to 19.41% of the national electricity consumption and a 6.86% reduction in the national residential water consumption in 2020. The overall economic benefit is 5.61 myriads RMB, equivalent to 5.76% of the national GDP. These benefits are unevenly distributed and mainly concentrated in areas with more reservoirs. The anticipated enhancement of FPV system benefits is foreseen with the ongoing development and implementation of future reservoir power infrastructure and energy storage technology. These results demonstrate the significant potential of installing FPV systems on the reservoirs in China. This study proposes a method to comprehensively evaluate the comprehensive benefits of constructing FPV in China and conduct a thorough analysis of the feasibility of FPV, which could provide reference for the development of regional industries and the achievement of sustainable development goals (SDGs).
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| 31. |
- Gong, Zheng, et al.
(author)
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A targetable fluorescent probe for detecting mitochondrial viscosity in live cells by using fluorescence lifetime imaging
- 2024
-
In: New Journal of Chemistry. - : ROYAL SOC CHEMISTRY. - 1144-0546 .- 1369-9261.
-
Journal article (peer-reviewed)abstract
- Intracellular viscosity plays an important role in regulating cellular morphology and physiology and is closely related to a host of diseases. Especially, the changes in mitochondrial viscosity will cause some common diseases such as hyperlipidemia, Alzheimer's disease and cancer. In this work, we report the design of a red-emissive molecular rotor for the detection of mitochondrial viscosity in live cells. The probe showed fascinating performance, such as specific targeting to mitochondria, high sensitivity to viscosity, and rapid fluorescence response, especially the dual response mode of fluorescence intensity and fluorescence lifetime. By using this probe, we realized monitoring of the mitochondrial viscosity variations in live cells under different physiological processes. Our study offers an opportunity to discover potential tools for mitochondria-related physiology and pathology investigation. A D-pi-A typed fluorescence lifetime probe for sensitively detecting viscosity has been designed and synthesized. BSOH has been successfully applied to real-time monitoring mitochondrial viscosity in live cells by fluorescence lifetime imaging.
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| 32. |
- Han, Bo-Yun, et al.
(author)
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A highly selective C-rhamnosyltransferase from Viola tricolor and insights into its mechanisms
- 2023
-
In: Acta Pharmaceutica Sinica B. - : Elsevier. - 2211-3835 .- 2211-3843. ; 13:8, s. 3535-3544
-
Journal article (peer-reviewed)abstract
- C-Glycosides are important natural products with various bioactivities. In plant biosynthetic pathways, the C-glycosylation step is usually catalyzed by C-glycosyltransferases (CGTs), and most of them prefer to accept uridine 5′-diphosphate glucose (UDP-Glc) as sugar donor. No CGTs favoring UDP-rhamnose (UDP-Rha) as sugar donor has been reported, thus far. Herein, we report the first selective C-rhamnosyltransferase VtCGTc from the medicinal plant Viola tricolor. VtCGTc could efficiently catalyze C-rhamnosylation of 2-hydroxynaringenin 3-C-glucoside, and exhibited high selectivity towards UDP-Rha. Mechanisms for the sugar donor selectivity of VtCGTc were investigated by molecular dynamics (MD) simulations and molecular mechanics with generalized Born and surface area solvation (MM/GBSA) binding free energy calculations. Val144 played a vital role in recognizing UDP-Rha, and the V144T mutant could efficiently utilize UDP-Glc. This work provides a new and efficient approach to prepare flavonoid C-rhamnosides such as violanthin and iso-violanthin.
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| 33. |
- Han, Xin-Bao, et al.
(author)
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Fe-substituted cobalt-phosphate polyoxometalates as enhanced oxygen evolution catalysts in acidic media
- 2020
-
In: Cuihuà xuébào. - : Science Press. - 0253-9837 .- 1872-2067. ; 41:5, s. 853-857
-
Journal article (peer-reviewed)abstract
- All-inorganic and earth-abundant bi-/trimetallic hydr(oxy)oxides are widely used as oxygen evolution electrocatalysts owing to their remarkable performance. However, their atomically precise structures remain undefined, complicating their optimization and limiting the understanding of their enhanced performance. Here, the underlying structure-property correlation is explored by using a well-defined cobalt-phosphate polyoxometalate cluster [{Co-4(OH)(3)(PO4)}(4)(SiW9O34)(4)](32-) (1), which may serve as a molecular model of multimetal hydr(oxy)oxides. The catalytic activity is enhanced upon replacing Co by Fe in 1, resulting in a reduced overpotential (385 mV) for oxygen evolution (by 66 mV) compared to that of the parent 1 at 10 mA cm(-2) in an acidic medium; this overpotential is comparable to that for the IrO2 catalyst. These abundant-metal-based polyoxometalates exhibit high stability, with no evidence of degradation even after 24 h of operation.
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| 34. |
- He, YQ, et al.
(author)
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A polygenic risk score for nasopharyngeal carcinoma shows potential for risk stratification and personalized screening
- 2022
-
In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 1966-
-
Journal article (peer-reviewed)abstract
- Polygenic risk scores (PRS) have the potential to identify individuals at risk of diseases, optimizing treatment, and predicting survival outcomes. Here, we construct and validate a genome-wide association study (GWAS) derived PRS for nasopharyngeal carcinoma (NPC), using a multi-center study of six populations (6 059 NPC cases and 7 582 controls), and evaluate its utility in a nested case-control study. We show that the PRS enables effective identification of NPC high-risk individuals (AUC = 0.65) and improves the risk prediction with the PRS incremental deciles in each population (Ptrend ranging from 2.79 × 10−7 to 4.79 × 10−44). By incorporating the PRS into EBV-serology-based NPC screening, the test’s positive predictive value (PPV) is increased from an average of 4.84% to 8.38% and 11.91% in the top 10% and 5% PRS, respectively. In summary, the GWAS-derived PRS, together with the EBV test, significantly improves NPC risk stratification and informs personalized screening.
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| 35. |
- Ji, Longjuan, et al.
(author)
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Structure and thermoacoustic instability of turbulent swirling lean premixed methane/hydrogen/air flames in a model combustor
- 2024
-
In: International Journal of Hydrogen Energy. - 0360-3199. ; 60, s. 890-901
-
Journal article (peer-reviewed)abstract
- The structure and thermoacoustic instability (TI) of premixed CH4/H2/air swirling flames were experimentally investigated for a range of hydrogen fraction (ηH2) up to 80% under different equivalence ratio (Φ) and swirl number (S) conditions. It is shown that the onset of TI is enhanced when increasing either ηH2, S, or Φ. The dominant frequency of TI increases dramatically with ηH2. The higher dominant frequency in the hydrogen-enriched flames can be attributed to a shorter flame length which results in a reduced flame convection time. It is observed that the unstable flames are always accompanied by the appearance of outer recirculation zone (ORZ) flame. Therefore, the flame kernel residing in the ORZ can be an indicator of the occurrence of TI. The flame front of thermoacoustic unstable flames was observed to be more wrinkled, e.g., with larger mean absolute curvature (κ abs) and local flame surface area ratio (δΣmax). Importantly, the phase-locked analysis shows that κ abs and δΣmax can be modified at different oscillation phases, and their maximum and minimum values are simultaneously achieved at phase angles θ of about 0° and 180°, respectively. Variations of κ abs and δΣmax are in phase with the heat release rate, indicating a strong correlation between the TI and flame structure modification; however, they show a phase lag of about 72° behind the pressure in this work. These results are vital when understanding and predicting the TI based on the flame structure, especially when adopting a visual detection method of the instability.
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| 36. |
- Jia, Kai-Hua, et al.
(author)
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Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
- 2021
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In: Horticulture Research. - : Oxford University Press (OUP). - 2052-7276 .- 2662-6810. ; 8:1
-
Journal article (peer-reviewed)abstract
- Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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| 37. |
- Jin, Feng, et al.
(author)
-
Enhanced rate capability and high-voltage cycling stability of single-crystal nickel-rich cathode by surface anchoring dielectric BaTiO3
- 2022
-
In: Journal of Colloid and Interface Science. - : Elsevier. - 0021-9797 .- 1095-7103. ; 619, s. 65-74
-
Journal article (peer-reviewed)abstract
- The single-crystal Ni-rich Li(NixCoyMn1_x_y)O-2 cathode (NCM) demonstrates better cycle performance, enhanced tap density and improved mechanical structure stability, compared with polycrystalline NCM. However, limited Li+ transports, (003) plane slips and microcracks in large single particles hinder rate capability and cycle performance. To overcome these shortcomings, single-crystal NCM cathodes have been modified by nanosized tetragonal BaTiO3. Due to the dielectric properties, BaTiO(3 )particles induce electric field concentration at the BaTiO3-NCM-electrolyte interface. Thus, a large amount of lithium vacancies can be formed, providing sufficient sites for the hopping diffusion of lithium ions, thereby significantly enhancing the diffusion coefficient of Li+. Moreover, the redistribution of charges can inhibit the formation and accumulation of cathode-electrolyte-interface. Owing to the synergetic effect of BaTiO3, the BT-modified single-crystal NCM with the optimized loading shows a remarkable initial discharge capacity of 138.5 mAh g(_1) and maintains 53.8% of its initial discharge capacity after 100 cycles under 5C at 4.5 V cut-off voltage. Overall, the proposed dielectric cathode-electrolyte-interface strategy can enhance Li+ ion transport and stabilize the interface structure, leading to improved rate performance. Meanwhile, the diffusion-induced state of charge gradient can also be inhibited, resulting in high structure stability of single-crystal NCMs under high rate and cut-off voltage cycling. (C) 2022 Elsevier Inc. All rights reserved.
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| 38. |
- Li, Xuechao, et al.
(author)
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Direct transformation of n-alkane into all-trans conjugated polyene via cascade dehydrogenation
- 2021
-
In: National Science Review. - : Oxford University Press. - 2095-5138 .- 2053-714X. ; 8:10
-
Journal article (peer-reviewed)abstract
- Selective C(sp(3))-H activation is of fundamental importance in processing alkane feedstocks to produce high-value-added chemical products. By virtue of an on-surface synthesis strategy, we report selective cascade dehydrogenation of n-alkane molecules under surface constraints, which yields monodispersed all-trans conjugated polyenes with unprecedented length controllability. We are also able to demonstrate the generality of this concept for alkyl-substituted molecules with programmable lengths and diverse functionalities, and more importantly its promising potential in molecular wiring.
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| 39. |
- Li, Xin, et al.
(author)
-
Halide Double Perovskite Nanocrystals Doped with Rare-Earth Ions for Multifunctional Applications
- 2023
-
In: Advanced Science. - 2198-3844. ; 10:20
-
Journal article (peer-reviewed)abstract
- Most lead-free halide double perovskite materials display low photoluminescence quantum yield (PLQY) due to the indirect bandgap or forbidden transition. Doping is an effective strategy to tailor the optical properties of materials. Herein, efficient blue-emitting Sb3+-doped Cs2NaInCl6 nanocrystals (NCs) are selected as host, rare-earth (RE) ions (Sm3+, Eu3+, Tb3+, and Dy3+) are incorporated into the host, and excellent PLQY of 80.1% is obtained. Femtosecond transient absorption measurement found that RE ions not only served as the activator ions but also filled the deep vacancy defects. Anti-counterfeiting, optical thermometry, and white-light-emitting diodes (WLEDs) are exhibited using these RE ions-doped halide double perovskite NCs. For the optical thermometry based on Sm3+-doped Cs2NaInCl6:Sb3+ NCs, the maximum relative sensitivity is 0.753% K−1, which is higher than those of most temperature-sensing materials. Moreover, the WLED fabricated by Sm3+-doped Cs2NaInCl6:Sb3+ NCs@PMMA displays CIE color coordinates of (0.30, 0.28), a luminous efficiency of 37.5 lm W−1, a CCT of 8035 K, and a CRI over 80, which indicate that Sm3+-doped Cs2NaInCl6:Sb3+ NCs are promising single-component white-light-emitting phosphors for next-generation lighting and display technologies.
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| 40. |
- Li, Youbing, et al.
(author)
-
A-site alloying-guided universal design of noble metal-based MAX phases
- 2024
-
In: Matter. - : Cell Press. - 2590-2393 .- 2590-2385. ; 7:2, s. 523-538
-
Journal article (peer-reviewed)abstract
- Mn+1AXn (MAX) phases have attracted significant attention due to their structural diversity and potential applications. Designing MAX phases with single-atom-thick A layers featuring 4d/5d-orbital electronic elements is interesting work. Here, we present a comprehensive report on noble metal-based M2(A1-xA′x)C (M = V, Ti, Nb; A = Al, Sn, In, Ga, Ge; A′ = Ru, Rh, Pd, Ir, Pt, Au and combinations thereof; 0 < x ≤ 0.4) phases featuring A sublayers of 4d/5d-orbital electronic elements through an A-site alloying strategy. The chemical composition of MAX phases can be adjusted by selecting different M- and A-site elements, with morphology tailored by distinct C sources. Furthermore, the V2(Sn0.8Pt0.2)C (15.7 wt % Pt) catalyst showed better performance for hydrogen evolution reaction compared to the commercial Pt/C (20 wt % Pt) electrode. This study highlights the prospects of A-site alloying for the design of novel MAX phases with unique properties and promising applications in electrocatalysis and beyond.
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| 41. |
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| 42. |
- Liu, Shaohui, et al.
(author)
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Data-Driven Controlled Synthesis of Oriented Quasi-Spherical CsPbBr3 Perovskite Materials
- 2024
-
In: Angewandte Chemie International Edition. - : WILEY-V C H VERLAG GMBH. - 1433-7851 .- 1521-3773. ; 63:14
-
Journal article (peer-reviewed)abstract
- Controlled synthesis of lead-halide perovskite crystals is challenging yet attractive because of the pivotal role played by the crystal structure and growth conditions in regulating their properties. This study introduces data-driven strategies for the controlled synthesis of oriented quasi-spherical CsPbBr3, alongside an investigation into the synthesis mechanism. High-throughput rapid characterization of absorption spectra and color under ultraviolet illumination was conducted using 23 possible ligands for the synthesis of CsPbBr3 crystals. The links between the absorption spectra slope (difference in the absorbance at 400 nm and 450 nm divided by a wavelength interval of 50 nm) and crystal size were determined through statistical analysis of more than 100 related publications. Big data analysis and machine learning were employed to investigate a total of 688 absorption spectra and 652 color values, revealing correlations between synthesis parameters and properties. Ex situ characterization confirmed successful synthesis of oriented quasi-spherical CsPbBr3 perovskites using polyvinylpyrrolidone and Acacia. Density functional theory calculations highlighted strong adsorption of Acacia on the (110) facet of CsPbBr3. Optical properties of the oriented quasi-spherical perovskites prepared with these data-driven strategies were significantly improved. This study demonstrates that data-driven controlled synthesis facilitates morphology-controlled perovskites with excellent optical properties.
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| 43. |
- Liu, Shentan, et al.
(author)
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Effects of bioelectricity generation processes on methane emission and bacterial community in wetland and carbon fate analysis
- 2022
-
In: Bioresources and Bioprocessing. - : Springer Science and Business Media LLC. - 2197-4365. ; 9:1
-
Journal article (peer-reviewed)abstract
- Wetlands are an important carbon sink for greenhouse gases (GHGs), and embedding microbial fuel cell (MFC) into constructed wetland (CW) has become a new technology to control methane (CH4) emission. Rhizosphere anode CW–MFC was constructed by selecting rhizome-type wetland plants with strong hypoxia tolerance, which could provide photosynthetic organics as alternative fuel. Compared with non-planted system, CH4 emission flux and power output from the planted CW–MFC increased by approximately 0.48 ± 0.02 mg/(m2·h) and 1.07 W/m3, respectively. The CH4 emission flux of the CW–MFC operated under open-circuit condition was approximately 0.46 ± 0.02 mg/(m2·h) higher than that under closed-circuit condition. The results indicated that plants contributed to the CH4 emission from the CW–MFC, especially under open-circuit mode conditions. The CH4 emission from the CW–MFC was proportional to external resistance, and it increased by 0.67 ± 0.01 mg/(m2·h) when the external resistance was adjusted from 100 to 1000 Ω. High throughput sequencing further showed that there was a competitive relationship between electrogenic bacteria and methanogens. The flora abundance of electrogenic bacteria was high, while methanogens mainly consisted of Methanothrix, Methanobacterium and Methanolinea. The form and content of element C were analysed from solid phase, liquid phase and gas phase. It was found that a large amount of carbon source (TC = 254.70 mg/L) was consumed mostly through microbial migration and conversion, and carbon storage and GHGs emission accounted for 60.38% and 35.80%, respectively. In conclusion, carbon transformation in the CW–MFC can be properly regulated via competition of microorganisms driven by environmental factors, which provides a new direction and idea for the control of CH4 emission from wetlands. Graphical Abstract: [Figure not available: see fulltext.].
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| 44. |
- Liu, Yanrong, et al.
(author)
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Ionic liquids as a new cornerstone to support hydrogen energy
- 2023
-
In: Green Chemistry. - : Royal Society of Chemistry. - 1463-9262 .- 1463-9270. ; 25:13, s. 4981-4994
-
Research review (peer-reviewed)abstract
- As a fuel or energy carrier, hydrogen has been identified as a key way to decarbonize electricity, industry, transportation, and heating sectors. Hydrogen can be produced by a variety of methods, among which water electrolysis driven by renewable energy is sustainable and nearly carbon-free. To use hydrogen widely, storage and transportation over long distances are another key issue. Apart from storage at high pressure and low temperature, hydrogen can be stored in organic compounds via chemical bonding under relatively mild conditions. Efficient utilization of hydrogen includes hydrogen fuel cells as an alternative to internal combustion engines. From the above scenarios, catalysis and reaction media are the key factors for realizing hydrogen energy implementation. Ionic liquids (ILs) offer new opportunities due to their tunable functional groups, low vapor pressure, and stable structures as additives, solvents, and charge transfer materials. ILs are known to produce solid catalysts with controllable properties, decorate solid catalysts with modified electrons and geometric structures, and serve as electrolytes and hydrogen storage media. This review summarizes and recaps the recent progress in how ILs act as a cornerstone to support the production, storage, and utilization of hydrogen. Furthermore, critical challenges and future research directions of ILs in hydrogen energy applications are also outlined.
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| 45. |
- Mehta, Raghav, et al.
(author)
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QU-BraTS : MICCAI BraTS 2020 Challenge on QuantifyingUncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results
- 2022
-
In: Journal of Machine Learning for Biomedical Imaging. - 2766-905X. ; , s. 1-54
-
Journal article (peer-reviewed)abstract
- Deep learning (DL) models have provided the state-of-the-art performance in a wide variety of medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder the translation of DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties, could enable clinical review of the most uncertain regions, thereby building trust and paving the way towards clinical translation. Recently, a number of uncertainty estimation methods have been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019-2020 task on uncertainty quantification (QU-BraTS), and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions, and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentages of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, and hence highlight the need for uncertainty quantification in medical image analyses. Our evaluation code is made publicly available at https://github.com/RagMeh11/QU-BraTS
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| 46. |
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| 47. |
- Peng, Ningxin, et al.
(author)
-
Platelet mitochondrial DNA methylation : A novel biomarker for myocardial infarction – A preliminary study
- 2023
-
In: International Journal of Cardiology. - 0167-5273.
-
Journal article (peer-reviewed)abstract
- Background: Platelet activation and thrombus formation play critical roles in the pathogenesis of myocardial infarction (MI). In addition to their role in energy production, platelet mitochondria also regulate cellular functions related to apoptosis, oxidative stress, and inflammation. Epigenetic modifications of platelet mitochondrial DNA (mtDNA) may influence platelet function and are believed to be an important factor in MI. Therefore, the aim of this study was to investigate the differences in platelet mtDNA methylation levels between MI patients and controls. Methods: The present study utilized propensity score matching to generate 45 multivariate matched apparently healthy controls for 45 patients with newly-onset acute MI. Platelet mtDNA methylation levels were assessed through bisulfite-PCR pyrosequencing and compared between the two groups, with further adjustments made in the sensitivity analysis. Results: Among the measured mitochondrial genes (MT-COX1, MT-COX2, MT-COX3, MT-ND5, MT-ATP6 and tRNA_Leu), patients with MI exhibited statistically significant differences in mtDNA methylation levels as compared to matched controls. Specifically, higher levels of mtDNA methylation were observed in MT-COX1, MT-COX3, and tRNA_Leu, while a lower level was observed in MT-ATP6 (all p < 0.0001). These results remained robust in the sensitivity analysis. Conclusion: Our study demonstrated significant variations in platelet mtDNA methylation levels between patients with MI and controls. Platelet mtDNA methylation may serve as a novel biomarker for MI. This observation also provided some insights into the etiology of MI.
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| 48. |
- Shao, Xue-Feng, et al.
(author)
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Screening of sugar alcohols and their binary eutectic mixtures as phase change materials for low-to-medium temperature thermal energy storage. (III) : Thermal endurance
- 2020
-
In: Energy. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0360-5442 .- 1873-6785. ; 209
-
Journal article (peer-reviewed)abstract
- The thermal endurance of four pure and three binary eutectic mixture sugar alcohols were examined as a complementary work to the previous screening efforts based on the phase change behaviors towards latent heat storage. It was shown that both the melting point and latent heat of fusion of these sugar alcohols degrade with increasing the heating duration, and that a higher degree of superheat leads to faster degradation. The melting point drift mainly attributes to the shrinking range of hydrogen bonding, whereas the decay of latent heat is likely resulted from the disruption of hydrogen bond networks and incomplete crystallization. Among the various candidates, erythritol exhibits the best thermal endurance. The infrared spectra demonstrated that sugar alcohols can be oxidized to generate aldehydes upon heating when exposed to air. It was also found that the duration for 10% degradation of the latent heat of fusion of inositol can be extended by similar to 9 times when being protected by nitrogen gas. However, although the introduction of nitrogen gas could efficiently improve the thermal endurance, other complex reactions can still occur in inert gas atmosphere at high temperatures, leaving the room for further improving the thermal endurance of sugar alcohols toward real-world applications.
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| 49. |
- Shi, Tian-Le, et al.
(author)
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Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values
- 2023
-
In: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
-
Journal article (peer-reviewed)abstract
- Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.
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| 50. |
- Shi, Tian-Le, et al.
(author)
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High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar
- 2024
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In: Plant Physiology. - : Oxford University Press. - 0032-0889 .- 1532-2548. ; 195:1, s. 652-670
-
Journal article (peer-reviewed)abstract
- Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
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