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152. Protein Biomarkers Predict Risk of Gastrointestinal Bleeding in Left Ventricular Assist Device Patients

Author

Cavallo, K., primary, Kanwar, M., additional, Diao, G., additional, Sinha, S.S., additional, Singh, R., additional, Tang, D., additional, Isseh, I., additional, Brocious, J., additional, Bagchi, P., additional, Crandall, D., additional, Farrar, D.J., additional, Murali, S., additional, Walenga, J., additional, Lindenfeld, J., additional, deFilippi, C., additional, and Shah, P., additional

Published
2022
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155. Post-peak dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022

Author

Elliott, P, Eales, O, Bodinier, B, Tang, D, Wang, H, Jonnerby, J, Haw, D, Elliott, J, Whitaker, M, Walters, C, Atchison, C, Diggle, P, Page, A, Trotter, A, Ashby, D, Barclay, W, Taylor, G, Ward, H, Darzi, A, Cooke, G, Chadeau-Hyam, M, and Donnelly, C

Subjects
SARS-CoV-2 coronavirus research
Abstract

Background: Rapid transmission of the SARS-CoV-2 Omicron variant has led to the highest ever recorded case incidence levels in many countries around the world. Methods: The REal-time Assessment of Community Transmission-1 (REACT-1) study has been characterising the transmission of the SARS-CoV-2 virus using RT-PCR test results from self-administered throat and nose swabs from randomly-selected participants in England at ages 5 years and over, approximately monthly since May 2020. Round 17 data were collected between 5 and 20 January 2022 and provide data on the temporal, socio-demographic and geographical spread of the virus, viral loads and viral genome sequence data for positive swabs. Results: From 102,174 valid tests in round 17, weighted prevalence of swab positivity was 4.41% (95% credible interval [CrI], 4.25% to 4.56%), which is over three-fold higher than in December 2021 in England. Of 3,028 sequenced positive swabs, 2,393 lineages were determined and 2,374 (99.2%) were Omicron including 19 (0.80% of all Omicron lineages) cases of BA.2 sub-lineage and one BA.3 (0.04% of all Omicron) detected on 17 January 2022, and only 19 (0.79%) were Delta. The growth of the BA.2 Omicron sub-lineage against BA.1 and its sub-lineage BA.1.1 indicated a daily growth rate advantage of 0.14 (95% CrI, 0.03, 0.28) for BA.2, which corresponds to an additive R advantage of 0.46 (95% CrI, 0.10, 0.92). Within round 17, prevalence was decreasing overall (R=0.95, 95% CrI, 0.93, 0.97) but increasing in children aged 5 to 17 years (R=1.13, 95% CrI, 1.09, 1.18). Those 75 years and older had a swab-positivity prevalence of 2.46% (95% CI, 2.16%, 2.80%) reflecting a high level of infection among a highly vulnerable group. Among the 3,613 swab-positive individuals reporting whether or not they had had previous infection, 2,334 (64.6%) reported previous confirmed COVID-19. Of these, 64.4% reported a positive test from 1 to 30 days before their swab date. Risks of infection were increased among essential/key workers (other than healthcare or care home workers) with mutually adjusted Odds Ratio (OR) of 1.15 (95% CI, 1.05, 1.26), people living in large compared to single-person households (6+ household size OR 1.73; 95% CI, 1.44, 2.08), those living in urban vs rural areas (OR 1.24, 95% CI, 1.13, 1.35) and those living in the most vs least deprived areas (OR 1.34, 95% CI, 1.20, 1.49). Conclusions: We observed unprecedented levels of infection with SARS-CoV-2 in England in January 2022, an almost complete replacement of Delta by Omicron, and evidence for a growth advantage for BA.2 compared to BA.1. The increase in the prevalence of infection with Omicron among children (aged 5 to 17 years) during January 2022 could pose a risk to adults, despite the current trend for prevalence in adults to decline. (Funded by the Department of Health and Social Care in England.)

Published
2022

161. Rapid increase in Omicron infections in England during December 2021: REACT-1 study

Author

Elliott, P, Bodinier, B, Eales, O, Wang, H, Haw, D, Elliott, J, Whitaker, M, Jonnerby, J, Tang, D, Walters, C, Atchison, C, Diggle, P, Page, A, Trotter, A, Ashby, D, Barclay, W, Taylor, G, Ward, H, Darzi, A, Cooke, G, Chadeau-Hyam, M, and Donnelly, C

Subjects
COVID-19, SARS-CoV-2 coronavirus research
Abstract

Background: The highest-ever recorded numbers of daily severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in England has been observed during December 2021 and have coincided with a rapid rise in the highly transmissible Omicron variant despite high levels of vaccination in the population. Although additional COVID-19 measures have been introduced in England and internationally to contain the epidemic, there remains uncertainty about the spread and severity of Omicron infections among the general population. Methods: The REal-time Assessment of Community Transmission–1 (REACT-1) study has been monitoring the prevalence of SARS-CoV-2 infection in England since May 2020. REACT-1 obtains self-administered throat and nose swabs from a random sample of the population of England at ages 5 years and over. Swabs are tested for SARS-CoV-2 infection by reverse transcription polymerase chain reaction (RT-PCR) and samples testing positive are sent for viral genome sequencing. To date 16 rounds have been completed, each including ~100,000 or more participants with data collected over a period of 2 to 3 weeks per month. Socio-demographic, lifestyle and clinical information (including previous history of COVID-19 and symptoms prior to swabbing) is collected by online or telephone questionnaire. Here we report results from round 14 (9-27 September 2021), round 15 (19 October - 05 November 2021) and round 16 (23 November - 14 December 2021) for a total of 297,728 participants with a valid RT-PCR test result, of whom 259,225 (87.1%) consented for linkage to their NHS records including detailed information on vaccination (vaccination status, date). We used these data to estimate community prevalence and trends by age and region, to evaluate vaccine effectiveness against infection in children ages 12 to 17 years, and effect of a third (booster) dose in adults, and to monitor the emergence of the Omicron variant in England. Results: We observed a high overall prevalence of 1.41% (1.33%, 1.51%) in the community during round 16. We found strong evidence of an increase in prevalence during round 16 with an estimated reproduction number R of 1.13 (1.06, 1.09) for the whole of round 16 and 1.27 (1.14, 1.40) when restricting to observations from 1 December onwards. The reproduction number in those aged 18-54 years was estimated at 1.23 (1.14, 1.33) for the whole of round 16 and 1.41 (1.23, 1.61) from 1 December. Our data also provide strong evidence of a steep increase in prevalence in London with an estimated R of 1.62 (1.34, 1.93) from 1 December onwards and a daily prevalence reaching 6.07% (4.06%, 9.00%) on 14 December 2021. As of 1 to 11 December 2021, of the 275 lineages determined, 11 (4.0%) corresponded to the Omicron variant. The first Omicron infection was detected in London on 3 December, and subsequent infections mostly appeared in the South of England. The 11 Omicron cases were all aged 18 to 54 years, double-vaccinated (reflecting the large numbers of people who have received two doses of vaccine in this age group) but not boosted, 9 were men, 5 lived in London and 7 were symptomatic (5 with classic COVID-19 symptoms: loss or change of sense of smell or taste, fever, persistent cough), 2 were asymptomatic, and symptoms were unknown for 2 cases. The proportion of Omicron (vs Delta or Delta sub-lineages) was found to increase rapidly with a daily increase of 66.0% (32.7%, 127.3%) in the odds of Omicron (vs. Delta) infection, conditional on swab positivity. Highest prevalence of swab positivity by age was observed in (unvaccinated) children aged 5 to 11 years (4.74% [4.15%, 5.40%]) similar to the prevalence observed at these ages in round 15. In contrast, prevalence in children aged 12 to 17 years more than halved from 5.35% (4.78%, 5.99%) in round 15 to 2.31% (1.91%, 2.80%) in round 16. As of 14 December 2021, 76.6% children at ages 12 to 17 years had received at least one vaccine dose; we estimated that vaccine effectiveness against infection was 57.9% (44.1%, 68.3%) in this age group. In addition, the prevalence of swab positivity in adults aged 65 years and over fell by over 40% from 0.84% (0.72%, 0.99%) in round 15 to 0.48% (0.39%,0.59%) in round 16 and for those aged 75 years and over it fell by two-thirds from 0.63% (0.48%,0.82%) to 0.21% (0.13%,0.32%). At these ages a high proportion of participants (>90%) had received a third vaccine dose; we estimated that adults having received a third vaccine dose had a three- to four-fold lower risk of testing positive compared to those who had received two doses. Conclusion: A large fall in swab positivity from round 15 to round 16 among 12 to 17 year olds, most of whom have been vaccinated, contrasts with the continuing high prevalence among 5 to 11 year olds who have largely not been vaccinated. Likewise there were large falls in swab positivity among people aged 65 years and over, the vast majority of whom have had a third (booster) vaccine dose; these results reinforce the importance of the vaccine and booster campaign. However, the rapidly increasing prevalence of SARS-CoV-2 infections in England during December 2021, coincident with the rapid rise of Omicron infections, may lead to renewed pressure on health services. Additional measures beyond vaccination may be needed to control the current wave of infections and prevent health services (in England and other countries) from being overwhelmed.

Published
2021

170. Melanoma secretion of transforming growth factor‐β2 leads to loss of epidermal AMBRA1 threatening epidermal integrity and facilitating tumour ulceration*

Author

Cosgarea, I., primary, McConnell, A.T., additional, Ewen, T., additional, Tang, D., additional, Hill, D.S., additional, Anagnostou, M., additional, Elias, M., additional, Ellis, R.A., additional, Murray, A., additional, Spender, L.C., additional, Giglio, P., additional, Gagliardi, M., additional, Greenwood, A., additional, Piacentini, M., additional, Inman, G.J., additional, Fimia, G.M., additional, Corazzari, M., additional, Armstrong, J.L., additional, and Lovat, P.E., additional

Published
2021
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171. Prenatal findings of 2q13 Duplication and Deletion: Further Evidence for Lack of Phenotypic-Genotype Correlation

Author

Chen J, Li L, Dai Y, Tang D, Liao Q, Guo H, Ye M, Zeng Z, Hu W, and Huang X

Subjects
Correlation, Genetics, Text mining, business.industry, Genotype, Gene duplication, Biology, business, Phenotype, humanities
Abstract

2q13 CNV was associated with various diseases, with a lack of consensus. By CMA analysis, we found that four fetuses had deletion in the proximal region of 2q13, one had duplication, and one had duplication in the distal region of 2q13; however, they had variable outcomes.

Published
2021

177. Physiological responses and drought resistance evaluation of 12 plants to drought stress and rehydration in the northern piedmont of Tianshan Mountains in Xinjiang

Author

CHENG Ping, TANG Dong, WANG Kai, YANG Lu, ZHANG Zhigang, and LI Hong

Subjects
northern piedmont of tianshan mountains in xinjiang, drought stress, vegetation restoration, drought resistance evaluation, Biology (General), QH301-705.5, Botany, QK1-989
Abstract

[ Objective ] The front piedmont belt of the northern slope of the Tianshan Mountains in Xinjiang is a crucial component of the mountain-oasis-desert ecosystem of the Tianshan northern slope. Investiga- ting the dynamic physiological adaptations of plants to drought stress and assessing methods for drought resistance , as well as selecting suitable tree species for vegetation restoration holds significant importance for the ecological restoration in this region. [ Methods ] 12 plant species planted in the piedmont belt of the northern slope of the Tianshan Mountains in Xinjiang were selected as the subjects. The study observed the spatiotemporal distribution of soil moisture following irrigation and analyzed the impact of drought stress and rewatering treatment on plant photosynthetic and physiological indicators. The drought resist- ance of these 12 species was evaluated using principal component analysis. [ Results ] ( 1 ) Following drought stress , soil moisture depletion occurred most rapidly in the 0-20 cm layer , followed by the 20- 40 cm layer , and was slowest in the 40-60 cm layer. Different plants employed different strategies to adapt their growth to drought stress. ( 2 ) Following drought stress , net photosynthetic rate ( P n ), stoma- tal conductance ( G s ), transpiration rate ( T r ), intercellular CO 2 concentration ( C i ), potential activity of PSⅡ ( F v / F o ), maximum photochemical efficiency of PSⅡ ( F v / F m ), electron transport rate ( ETR ), and chlorophyll content were decreased , while the activity of superoxide dismutase ( SOD ), proline content , malondialdehyde ( MDA ) content , and non-photochemical quenching coefficient ( q N ) were increased. Af- ter rehydration , there was a certain degree of recovery in each parameter , but none of them reached the in- itial levels. ( 3 ) The results of principal component analysis highlighted that factors like P n , chlorophyll content , ETR , and MDA content were major contributors. Species such as Haloxylon ammodendron , Tamarix chinensis , Rosa acicularis , and Caragana korshinskii demonstrated significant drought resili- ence. Hippophae rhamnoides , H . rhamnoides ‘ Xinji 5 ’, H . rhamnoides ‘ Xinji 1 ’, and Prunus sibirica showed moderate levels of drought resistance , while H . rhamnoides ‘ Xinji 4 ’, H . rhamnoides ‘ Xinji 3 ’, Xanthoceras sorbifolium , and H . rhamnoides ‘ Xinji 2 ’ exhibited relatively lower drought tolerance. [ Conclusion ] P n , chlorophyll content , ETR , and MDA content were crucial indicators for evaluating the adaptability of various plant species to drought stress. In the context of ecological restoration efforts in the piedmont belt of the Tianshan Mountains􀆴 northern slope in Xinjiang , prioritizing the cultivation of H . ammodendron , T . chinensis , R . acicularis , and C . korshinskii were recommended.

Published
2024
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178. Deciphering smooth muscle cell heterogeneity in atherosclerotic plaques and constructing model: a multi-omics approach with focus on KLF15/IGFBP4 axis

Author

Zhanli Peng, Qinghui Kan, Kangjie Wang, Tang Deng, Shenming Wang, Ridong Wu, and Chen Yao

Subjects
Atherosclerosis, Smooth muscle cell, Single-cell, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Ruptured atherosclerotic plaques often precipitate severe ischemic events, such as stroke and myocardial infarction. Unraveling the intricate molecular mechanisms governing vascular smooth muscle cell (VSMC) behavior in plaque stabilization remains a formidable challenge. Methods In this study, we leveraged single-cell and transcriptomic datasets from atherosclerotic plaques retrieved from the gene expression omnibus (GEO) database. Employing a combination of single-cell population differential analysis, weighted gene co-expression network analysis (WGCNA), and transcriptome differential analysis techniques, we identified specific genes steering the transformation of VSMCs in atherosclerotic plaques. Diagnostic models were developed and validated through gene intersection, utilizing the least absolute shrinkage and selection operator (LASSO) and random forest (RF) methods. Nomograms for plaque assessment were constructed. Tissue localization and expression validation were performed on specimens from animal models, utilizing immunofluorescence co-localization, western blot, and reverse-transcription quantitative-polymerase chain reaction (RT-qPCR). Various online databases were harnessed to predict transcription factors (TFs) and their interacting compounds, with determination of the cell-specific localization of TF expression using single-cell data. Results Following rigorous quality control procedures, we obtained a total of 40,953 cells, with 6,261 representing VSMCs. The VSMC population was subsequently clustered into 5 distinct subpopulations. Analyzing inter-subpopulation cellular communication, we focused on the SMC2 and SMC5 subpopulations. Single-cell subpopulation and WGCNA analyses revealed significant module enrichments, notably in collagen-containing extracellular matrix and cell-substrate junctions. Insulin-like growth factor binding protein 4 (IGFBP4), apolipoprotein E (APOE), and cathepsin C (CTSC) were identified as potential diagnostic markers for early and advanced plaques. Notably, gene expression pattern analysis suggested that IGFBP4 might serve as a protective gene, a hypothesis validated through tissue localization and expression analysis. Finally, we predicted TFs capable of binding to IGFBP4, with Krüppel-like family 15 (KLF15) emerging as a prominent candidate showing relative specificity within smooth muscle cells. Predictions about compounds associated with affecting KLF15 expression were also made. Conclusion Our study established a plaque diagnostic and assessment model and analyzed the molecular interaction mechanisms of smooth muscle cells within plaques. Further analysis revealed that the transcription factor KLF15 may regulate the biological behaviors of smooth muscle cells through the KLF15/IGFBP4 axis, thereby influencing the stability of advanced plaques via modulation of the PI3K-AKT signaling pathway. This could potentially serve as a target for plaque stability assessment and therapy, thus driving advancements in the management and treatment of atherosclerotic plaques.

Published
2024
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179. FANCA facilitates G1/S cell cycle advancement, proliferation, migration and invasion in gastric cancer

Author

Wang Wei, Baral Shantanu, Liu Bin, Sun Qiannan, Wang Liuhua, Ren Jun, Tang Dong, and Wang Daorong

Subjects
gastric cancer, FANCA, proliferation, migration, invasion, cell cycle, Biochemistry, QD415-436, Genetics, QH426-470
Abstract

The present study explores the function of FANCA gene, a pivotal member of the Fanconi anaemia (FA) pathway crucial for preserving genomic stability and preventing cancer, particularly in the context of gastric cancer (GC). Using immunohistochemistry, quantitative real-time PCR, and western blot analysis, we evaluate FANCA mRNA and protein expressions in GC cell lines. The relationship between FANCA expression and clinicopathological characteristics is also explored. Various assays, including CCK8, colony formation, wound healing, and Transwell assays, are used to assess functional changes in cells associated with FANCA. Flow cytometry is utilized to evaluate alterations in the cell cycle resulted from FANCA knockdown and overexpression. Our findings show elevated FANCA expression in GC cell lines, with levels correlated with pathologic stage and lymphatic metastasis. FANCA knockdown impedes cell proliferation, migration, and invasion and induces G1/S phase cell cycle arrest. Conversely, FANCA overexpression stimulates cell proliferation, migration, and invasion. In vivo xenograft experiments confirm the promotional role of FANCA in GC tumor progression. Moreover, FANCA overexpression is associated with the activation of cell cycle. Collectively, our results suggest that FANCA drives malignant cell behaviors in GC through the cell cycle pathway, highlighting its potential as a therapeutic target for the treatment of GC.

Published
2024
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180. Correlation analysis of serum miR-499 and severity of coronary lesions in patients with acute coronary syndrome

Author

TANG Dongjuan, JIANG Lai, and JIANG Ye

Subjects
mir-499, acute coronary syndrome, biomarker, coronary artery stenosis, Medicine
Abstract

Objective·To explore the value of miR-499 expression levels in the serum of patients with acute coronary syndrome (ACS) in predicting the severity of coronary artery disease.Methods·Seventy-four patients with ACS admitted to Xinhua Hospital, Shanghai Jiao Tong University School of Medicine were included and divided into a mild group of 30 cases, a moderate group of 21 cases, and a severe group of 23 cases according to the Gensini score. Real-time quantitative polymerase chain reaction (qPCR) technology was used to detect the expression level of serum miR-499, while troponin (cTnI), creatine kinase isoenzyme (CK-MB), myoglobin (Mb), brain natriuretic peptide (BNP), left ventricular ejection fraction (LVEF), and other laboratory indicators were measured. Spearman correlation analysis was used to analyze the correlation between the expression level of miR-499 and Gensini score, as well as the number of vessel branches in coronary artery disease. The evaluation value of miR-499 in assessing the severity of coronary artery disease was analyzed by using receiver operating characteristic (ROC) curve.Results·The expression level of miR-499 increased with the severity of coronary artery disease (P=0.000). The expression level of miR-499 was positively correlated with Gensini score and cTnI (r=0.331, r=0.143, P0.05), while Gensini score was not correlated with cTnI and LVEF (P>0.05). ROC analysis showed that the AUC of miR-499 for assessing the severity of coronary artery disease was 0.802 (95% CI 0.698‒0.906), with sensitivity of 65.2% and specificity of 80.4%. The expression level of miR-499 increased with the increase of the number of coronary artery lesions, and was positively correlated with the number of coronary artery lesions (r=0.368, P

Published
2024
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181. Emerging role and function of SPDL1 in human health and diseases

Author

Feng Yuejiao, Tang Donghao, and Wang Jie

Subjects
cancer, ccdc99, cell cycle, hspindly, spdl1, Medicine
Abstract

SPDL1 (spindle apparatus coiled-coil protein 1), also referred to as CCDC99, is a recently identified gene involved in cell cycle regulation. SPDL1 encodes a protein, hSpindly, which plays a critical role in the maintenance of spindle checkpoint silencing during mitosis. hSpindly coordinates microtubule attachment by promoting kinesin recruitment and mitotic checkpoint signaling. Moreover, the protein performs numerous biological functions in vivo and its aberrant expression is closely associated with abnormal neuronal development, pulmonary interstitial fibrosis, and malignant tumor development. In this review, we provide an overview of studies that reveal the characteristics of SPDL1 and of the protein encoded by it, as well as its biological and tumor-promoting functions.

Published
2024
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182. Embodied intelligent driving: concept, methods, the state of the art and beyond

Author

SHEN Tianyu, LI Zhiwei, FAN Lili, ZHANG Tingzhen, TANG Dandan, ZHOU Meihua, LIU Huaping, and WANG Kunfeng

Subjects
embodied intelligence, autonomous driving, embodied perception, embodied execution, embodied evolution, Electronic computers. Computer science, QA75.5-76.95
Abstract

Embodied intelligence transcends the boundaries of traditional artificial intelligence by emphasizing the importance of interaction between machines and the physical world, facilitating the development of intelligent entities that combine hardware and software to learn from and adapt to their environments, thereby solving real-world problems. Inspired by this philosophy, the concept and framework of embodied intelligent driving are introduced, aiming at integrating the idea of embodied intelligence into the development and application of autonomous vehicles. Through the continuous interaction between physical agents, virtual agents, and real traffic scenes, intelligent driving systems can achieve precise perception, efficient execution, and autonomous evolution in complex scenes, enhancing the long-term adaptability of autonomous vehicles in open traffic environments. Based on the embodied intelligent driving framework, the relevant technologies are summarize and the development status and existing problems of such technologies are analyzed. Furthermore, thoughts and prospects in this field are demonstrated by exploring the important roles and application potential of virtual-real interactive data intelligence, foundation models and foundation intelligence, continuous learning and parallel intelligence. This paper is expected to promote innovative research and the application on embodied intelligent driving in a wider range of scenarios, and provide new ideas and solutions for the development of mobile robot systems such as intelligent vehicles.

Published
2024
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188. Transparent Ceramics

Author

Kong, Ling Bing, primary, Huang, Y. Z., additional, Que, W. X., additional, Zhang, T. S., additional, Li, S., additional, Zhang, J., additional, Dong, Z. L., additional, and Tang, D. Y., additional

Published
2015
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190. OPTIMAL LIGHT INTENSITY AND PHOTOPERIOD FOR THE GROWTH AND QUALITY OF PLATOSTOMA PALUSTRE IN A PLANT FACTORY.

Author

Huang, Y. F., Quan, C. Q., Wei, F., and Tang, D. F.

Subjects
LIGHT intensity, LABOR costs, ROOT growth, COST control, LEAF area
Abstract

Platostoma palustre (Blume) A. J. Paton is an important medicinal and edible plant in China and Southeast Asian countries with great market and economic value. In recent years, due to the high labor cost of cultivation and management of P. palustre and limited economic benefits, domestic farmers have been hesitant to plant it. This has led to an inadequate supply of raw materials for P. palustre in China, necessitating the import of large quantities from Southeast Asian countries. Consequently, alternative methods for planting and cultivating P. palustre beyond traditional field practices are needed. In this study, a hydroponic experiment was conducted to investigate suitable lighting conditions for P. palustre growth in a plant factory. The experiment involved a two-factor, four-level design incorporating red light intensities of 50, 100, 150, 200 µmol/(m2•s) and photoperiods of 8h/16h, 12h/12h, 16h/8h, 20h/4h Light/Darkness (L/D). The results showed that increasing red light intensity and duration promoted the whole plant weight and stem diameter of P. palustre to some extent, while extending light duration was beneficial for the leaf area. Light intensities ranging from 50 to 150 µmol/(m2•s) combined with a 20h/4h L/D photoperiod favored the accumulation of total chlorophyll, chlorophyll a, chlorophyll b, and carotenoid. Prolonged photoperiods and higher light intensities facilitated the root growth of P. palustre. Light intensitiesbetween 100 and 200 µmol/(m2•s) with an 8h/16h L/D photoperiod were helpful for the accumulation of total pectin and soluble sugar content. Membership function analysis indicated that the T12 treatment (150 µmol/(m2•s) light intensity and 20h/4h L/D photoperiod) was more suitable for the cultivation and quality production of P. palustre in the plant factory. The current study provided scientific data for plant factory or indoor large-scale cultivation and planting of P. palustre. [ABSTRACT FROM AUTHOR]

Published
2024
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191. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Author

Grapotte M., Saraswat M., Bessiere C., Menichelli C., Ramilowski J. A., Severin J., Hayashizaki Y., Itoh M., Tagami M., Murata M., Kojima-Ishiyama M., Noma S., Noguchi S., Kasukawa T., Hasegawa A., Suzuki H., Nishiyori-Sueki H., Frith M. C., Abugessaisa I., Aitken S., Aken B. L., Alam I., Alam T., Alasiri R., Alhendi A. M. N., Alinejad-Rokny H., Alvarez M. J., Andersson R., Arakawa T., Araki M., Arbel T., Archer J., Archibald A. L., Arner E., Arner P., Asai K., Ashoor H., Astrom G., Babina M., Baillie J. K., Bajic V. B., Bajpai A., Baker S., Baldarelli R. M., Balic A., Bansal M., Batagov A. O., Batzoglou S., Beckhouse A. G., Beltrami A. P., Beltrami C. A., Bertin N., Bhattacharya S., Bickel P. J., Blake J. A., Blanchette M., Bodega B., Bonetti A., Bono H., Bornholdt J., Bttcher M., Bougouffa S., Boyd M., Breda J., Brombacher F., Brown J. B., Bult C. J., Burroughs A. M., Burt D. W., Busch A., Caglio G., Califano A., Cameron C. J., Cannistraci C. V., Carbone A., Carlisle A. J., Carninci P., Carter K. W., Cesselli D., Chang J. -C., Chen J. C., Chen Y., Chierici M., Christodoulou J., Ciani Y., Clark E. L., Coskun M., Dalby M., Dalla E., Daub C. O., Davis C. A., de Hoon M. J. L., de Rie D., Denisenko E., Deplancke B., Detmar M., Deviatiiarov R., Di Bernardo D., Diehl A. D., Dieterich L. C., Dimont E., Djebali S., Dohi T., Dostie J., Drablos F., Edge A. S. B., Edinger M., Ehrlund A., Ekwall K., Elofsson A., Endoh M., Enomoto H., Enomoto S., Faghihi M., Fagiolini M., Farach-Carson M. C., Faulkner G. J., Favorov A., Fernandes A. M., Ferrai C., Forrest A. R. R., Forrester L. M., Forsberg M., Fort A., Francescatto M., Freeman T. C., Frith M., Fukuda S., Funayama M., Furlanello C., Furuno M., Furusawa C., Gao H., Gazova I., Gebhard C., Geier F., Geijtenbeek T. B. H., Ghosh S., Ghosheh Y., Gingeras T. R., Gojobori T., Goldberg T., Goldowitz D., Gough J., Greco D., Gruber A. J., Guhl S., Guigo R., Guler R., Gusev O., Gustincich S., Ha T. J., Haberle V., Hale P., Hallstrom B. M., Hamada M., Handoko L., Hara M., Harbers M., Harrow J., Harshbarger J., Hase T., Hashimoto K., Hatano T., Hattori N., Hayashi R., Herlyn M., Hettne K., Heutink P., Hide W., Hitchens K. J., Sui S. H., 't Hoen P. A. C., Hon C. C., Hori F., Horie M., Horimoto K., Horton P., Hou R., Huang E., Huang Y., Hugues R., Hume D., Ienasescu H., Iida K., Ikawa T., Ikemura T., Ikeo K., Inoue N., Ishizu Y., Ito Y., Ivshina A. V., Jankovic B. R., Jenjaroenpun P., Johnson R., Jorgensen M., Jorjani H., Joshi A., Jurman G., Kaczkowski B., Kai C., Kaida K., Kajiyama K., Kaliyaperumal R., Kaminuma E., Kanaya T., Kaneda H., Kapranov P., Kasianov A. S., Katayama T., Kato S., Kawaguchi S., Kawai J., Kawaji H., Kawamoto H., Kawamura Y. I., Kawasaki S., Kawashima T., Kempfle J. S., Kenna T. J., Kere J., Khachigian L., Kiryu H., Kishima M., Kitajima H., Kitamura T., Kitano H., Klaric E., Klepper K., Klinken S. P., Kloppmann E., Knox A. J., Kodama Y., Kogo Y., Kojima M., Kojima S., Komatsu N., Komiyama H., Kono T., Koseki H., Koyasu S., Kratz A., Kukalev A., Kulakovskiy I., Kundaje A., Kunikata H., Kuo R., Kuo T., Kuraku S., Kuznetsov V. A., Kwon T. J., Larouche M., Lassmann T., Law A., Le-Cao K. -A., Lecellier C. -H., Lee W., Lenhard B., Lennartsson A., Li K., Li R., Lilje B., Lipovich L., Lizio M., Lopez G., Magi S., Mak G. K., Makeev V., Manabe R., Mandai M., Mar J., Maruyama K., Maruyama T., Mason E., Mathelier A., Matsuda H., Medvedeva Y. A., Meehan T. F., Mejhert N., Meynert A., Mikami N., Minoda A., Miura H., Miyagi Y., Miyawaki A., Mizuno Y., Morikawa H., Morimoto M., Morioka M., Morishita S., Moro K., Motakis E., Motohashi H., Mukarram A. K., Mummery C. L., Mungall C. J., Murakawa Y., Muramatsu M., Nagasaka K., Nagase T., Nakachi Y., Nakahara F., Nakai K., Nakamura K., Nakamura Y., Nakazawa T., Nason G. P., Nepal C., Nguyen Q. H., Nielsen L. K., Nishida K., Nishiguchi K. M., Nishiyori H., Nitta K., Notredame C., Ogishima S., Ohkura N., Ohno H., Ohshima M., Ohtsu T., Okada Y., Okada-Hatakeyama M., Okazaki Y., Oksvold P., Orlando V., Ow G. S., Ozturk M., Pachkov M., Paparountas T., Parihar S. P., Park S. -J., Pascarella G., Passier R., Persson H., Philippens I. H., Piazza S., Plessy C., Pombo A., Ponten F., Poulain S., Poulsen T. M., Pradhan S., Prezioso C., Pridans C., Qin X. -Y., Quackenbush J., Rackham O., Ramilowski J., Ravasi T., Rehli M., Rennie S., Rito T., Rizzu P., Robert C., Roos M., Rost B., Roudnicky F., Roy R., Rye M. B., Sachenkova O., Saetrom P., Sai H., Saiki S., Saito M., Saito A., Sakaguchi S., Sakai M., Sakaue S., Sakaue-Sawano A., Sandelin A., Sano H., Sasamoto Y., Sato H., Saxena A., Saya H., Schafferhans A., Schmeier S., Schmidl C., Schmocker D., Schneider C., Schueler M., Schultes E. A., Schulze-Tanzil G., Semple C. A., Seno S., Seo W., Sese J., Sheng G., Shi J., Shimoni Y., Shin J. W., SimonSanchez J., Sivertsson A., Sjostedt E., Soderhall C., Laurent G. S., Stoiber M. H., Sugiyama D., Summers K. M., Suzuki A. M., Suzuki K., Suzuki M., Suzuki N., Suzuki T., Swanson D. J., Swoboda R. K., Taguchi A., Takahashi H., Takahashi M., Takamochi K., Takeda S., Takenaka Y., Tam K. T., Tanaka H., Tanaka R., Tanaka Y., Tang D., Taniuchi I., Tanzer A., Tarui H., Taylor M. S., Terada A., Terao Y., Testa A. C., Thomas M., Thongjuea S., Tomii K., Triglia E. T., Toyoda H., Tsang H. G., Tsujikawa M., Uhlen M., Valen E., van de Wetering M., van Nimwegen E., Velmeshev D., Verardo R., Vitezic M., Vitting-Seerup K., von Feilitzen K., Voolstra C. R., Vorontsov I. E., Wahlestedt C., Wasserman W. W., Watanabe K., Watanabe S., Wells C. A., Winteringham L. N., Wolvetang E., Yabukami H., Yagi K., Yamada T., Yamaguchi Y., Yamamoto M., Yamamoto Y., Yamanaka Y., Yano K., Yasuzawa K., Yatsuka Y., Yo M., Yokokura S., Yoneda M., Yoshida E., Yoshida Y., Yoshihara M., Young R., Young R. S., Yu N. Y., Yumoto N., Zabierowski S. E., Zhang P. G., Zucchelli S., Zwahlen M., Chatelain C., Brehelin L., Grapotte, M., Saraswat, M., Bessiere, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., Abugessaisa, I., Aitken, S., Aken, B. L., Alam, I., Alam, T., Alasiri, R., Alhendi, A. M. N., Alinejad-Rokny, H., Alvarez, M. J., Andersson, R., Arakawa, T., Araki, M., Arbel, T., Archer, J., Archibald, A. L., Arner, E., Arner, P., Asai, K., Ashoor, H., Astrom, G., Babina, M., Baillie, J. K., Bajic, V. B., Bajpai, A., Baker, S., Baldarelli, R. M., Balic, A., Bansal, M., Batagov, A. O., Batzoglou, S., Beckhouse, A. G., Beltrami, A. P., Beltrami, C. A., Bertin, N., Bhattacharya, S., Bickel, P. J., Blake, J. A., Blanchette, M., Bodega, B., Bonetti, A., Bono, H., Bornholdt, J., Bttcher, M., Bougouffa, S., Boyd, M., Breda, J., Brombacher, F., Brown, J. B., Bult, C. J., Burroughs, A. M., Burt, D. W., Busch, A., Caglio, G., Califano, A., Cameron, C. J., Cannistraci, C. V., Carbone, A., Carlisle, A. J., Carninci, P., Carter, K. W., Cesselli, D., Chang, J. -C., Chen, J. C., Chen, Y., Chierici, M., Christodoulou, J., Ciani, Y., Clark, E. L., Coskun, M., Dalby, M., Dalla, E., Daub, C. O., Davis, C. A., de Hoon, M. J. L., de Rie, D., Denisenko, E., Deplancke, B., Detmar, M., Deviatiiarov, R., Di Bernardo, D., Diehl, A. D., Dieterich, L. C., Dimont, E., Djebali, S., Dohi, T., Dostie, J., Drablos, F., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Elofsson, A., Endoh, M., Enomoto, H., Enomoto, S., Faghihi, M., Fagiolini, M., Farach-Carson, M. C., Faulkner, G. J., Favorov, A., Fernandes, A. M., Ferrai, C., Forrest, A. R. R., Forrester, L. M., Forsberg, M., Fort, A., Francescatto, M., Freeman, T. C., Frith, M., Fukuda, S., Funayama, M., Furlanello, C., Furuno, M., Furusawa, C., Gao, H., Gazova, I., Gebhard, C., Geier, F., Geijtenbeek, T. B. H., Ghosh, S., Ghosheh, Y., Gingeras, T. R., Gojobori, T., Goldberg, T., Goldowitz, D., Gough, J., Greco, D., Gruber, A. J., Guhl, S., Guigo, R., Guler, R., Gusev, O., Gustincich, S., Ha, T. J., Haberle, V., Hale, P., Hallstrom, B. M., Hamada, M., Handoko, L., Hara, M., Harbers, M., Harrow, J., Harshbarger, J., Hase, T., Hashimoto, K., Hatano, T., Hattori, N., Hayashi, R., Herlyn, M., Hettne, K., Heutink, P., Hide, W., Hitchens, K. J., Sui, S. H., 't Hoen, P. A. C., Hon, C. C., Hori, F., Horie, M., Horimoto, K., Horton, P., Hou, R., Huang, E., Huang, Y., Hugues, R., Hume, D., Ienasescu, H., Iida, K., Ikawa, T., Ikemura, T., Ikeo, K., Inoue, N., Ishizu, Y., Ito, Y., Ivshina, A. V., Jankovic, B. R., Jenjaroenpun, P., Johnson, R., Jorgensen, M., Jorjani, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kajiyama, K., Kaliyaperumal, R., Kaminuma, E., Kanaya, T., Kaneda, H., Kapranov, P., Kasianov, A. S., Katayama, T., Kato, S., Kawaguchi, S., Kawai, J., Kawaji, H., Kawamoto, H., Kawamura, Y. I., Kawasaki, S., Kawashima, T., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L., Kiryu, H., Kishima, M., Kitajima, H., Kitamura, T., Kitano, H., Klaric, E., Klepper, K., Klinken, S. P., Kloppmann, E., Knox, A. J., Kodama, Y., Kogo, Y., Kojima, M., Kojima, S., Komatsu, N., Komiyama, H., Kono, T., Koseki, H., Koyasu, S., Kratz, A., Kukalev, A., Kulakovskiy, I., Kundaje, A., Kunikata, H., Kuo, R., Kuo, T., Kuraku, S., Kuznetsov, V. A., Kwon, T. J., Larouche, M., Lassmann, T., Law, A., Le-Cao, K. -A., Lecellier, C. -H., Lee, W., Lenhard, B., Lennartsson, A., Li, K., Li, R., Lilje, B., Lipovich, L., Lizio, M., Lopez, G., Magi, S., Mak, G. K., Makeev, V., Manabe, R., Mandai, M., Mar, J., Maruyama, K., Maruyama, T., Mason, E., Mathelier, A., Matsuda, H., Medvedeva, Y. A., Meehan, T. F., Mejhert, N., Meynert, A., Mikami, N., Minoda, A., Miura, H., Miyagi, Y., Miyawaki, A., Mizuno, Y., Morikawa, H., Morimoto, M., Morioka, M., Morishita, S., Moro, K., Motakis, E., Motohashi, H., Mukarram, A. K., Mummery, C. L., Mungall, C. J., Murakawa, Y., Muramatsu, M., Nagasaka, K., Nagase, T., Nakachi, Y., Nakahara, F., Nakai, K., Nakamura, K., Nakamura, Y., Nakazawa, T., Nason, G. P., Nepal, C., Nguyen, Q. H., Nielsen, L. K., Nishida, K., Nishiguchi, K. M., Nishiyori, H., Nitta, K., Notredame, C., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Ohtsu, T., Okada, Y., Okada-Hatakeyama, M., Okazaki, Y., Oksvold, P., Orlando, V., Ow, G. S., Ozturk, M., Pachkov, M., Paparountas, T., Parihar, S. P., Park, S. -J., Pascarella, G., Passier, R., Persson, H., Philippens, I. H., Piazza, S., Plessy, C., Pombo, A., Ponten, F., Poulain, S., Poulsen, T. M., Pradhan, S., Prezioso, C., Pridans, C., Qin, X. -Y., Quackenbush, J., Rackham, O., Ramilowski, J., Ravasi, T., Rehli, M., Rennie, S., Rito, T., Rizzu, P., Robert, C., Roos, M., Rost, B., Roudnicky, F., Roy, R., Rye, M. B., Sachenkova, O., Saetrom, P., Sai, H., Saiki, S., Saito, M., Saito, A., Sakaguchi, S., Sakai, M., Sakaue, S., Sakaue-Sawano, A., Sandelin, A., Sano, H., Sasamoto, Y., Sato, H., Saxena, A., Saya, H., Schafferhans, A., Schmeier, S., Schmidl, C., Schmocker, D., Schneider, C., Schueler, M., Schultes, E. A., Schulze-Tanzil, G., Semple, C. A., Seno, S., Seo, W., Sese, J., Sheng, G., Shi, J., Shimoni, Y., Shin, J. W., Simonsanchez, J., Sivertsson, A., Sjostedt, E., Soderhall, C., Laurent, G. S., Stoiber, M. H., Sugiyama, D., Summers, K. M., Suzuki, A. M., Suzuki, K., Suzuki, M., Suzuki, N., Suzuki, T., Swanson, D. J., Swoboda, R. K., Taguchi, A., Takahashi, H., Takahashi, M., Takamochi, K., Takeda, S., Takenaka, Y., Tam, K. T., Tanaka, H., Tanaka, R., Tanaka, Y., Tang, D., Taniuchi, I., Tanzer, A., Tarui, H., Taylor, M. S., Terada, A., Terao, Y., Testa, A. C., Thomas, M., Thongjuea, S., Tomii, K., Triglia, E. T., Toyoda, H., Tsang, H. G., Tsujikawa, M., Uhlen, M., Valen, E., van de Wetering, M., van Nimwegen, E., Velmeshev, D., Verardo, R., Vitezic, M., Vitting-Seerup, K., von Feilitzen, K., Voolstra, C. R., Vorontsov, I. E., Wahlestedt, C., Wasserman, W. W., Watanabe, K., Watanabe, S., Wells, C. A., Winteringham, L. N., Wolvetang, E., Yabukami, H., Yagi, K., Yamada, T., Yamaguchi, Y., Yamamoto, M., Yamamoto, Y., Yamanaka, Y., Yano, K., Yasuzawa, K., Yatsuka, Y., Yo, M., Yokokura, S., Yoneda, M., Yoshida, E., Yoshida, Y., Yoshihara, M., Young, R., Young, R. S., Yu, N. Y., Yumoto, N., Zabierowski, S. E., Zhang, P. G., Zucchelli, S., Zwahlen, M., Chatelain, C., Brehelin, L., Institute of Biotechnology, Biosciences, Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), National Institute of Advanced Industrial Science and Technology (AIST), SANOFI Recherche, University of British Columbia (UBC), Experimental Immunology, Infectious diseases, AII - Infectious diseases, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)

Subjects
0301 basic medicine, General Physics and Astronomy, Genome, Mice, 0302 clinical medicine, Transcription (biology), Promoter Regions, Genetic, Transcription Initiation, Genetic, 0303 health sciences, Multidisciplinary, 1184 Genetics, developmental biology, physiology, High-Throughput Nucleotide Sequencing, Neurodegenerative Diseases, 222 Other engineering and technologies, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], humanities, Enhancer Elements, Genetic, Microsatellite Repeat, Transcription Initiation Site, Sequence motif, Transcription Initiation, Human, Enhancer Elements, Neural Networks, Science, 610 Medicine & health, Computational biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, Promoter Regions, 03 medical and health sciences, Computer, Deep Learning, Tandem repeat, Genetic, Clinical Research, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Machine learning, Genetics, Animals, Humans, Polymorphism, Enhancer, Transcriptomics, Gene, A549 Cell, 030304 developmental biology, Polymorphism, Genetic, Neurodegenerative Disease, Base Sequence, Animal, Genome, Human, Human Genome, Computational Biology, Promoter, General Chemistry, 113 Computer and information sciences, Cap analysis gene expression, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Cardiovascular and Metabolic Diseases, A549 Cells, Minion, Generic health relevance, 3111 Biomedicine, Neural Networks, Computer, 610 Medizin und Gesundheit, 030217 neurology & neurosurgery, FANTOM consortium, Microsatellite Repeats
Abstract

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism., Nature Communications, 12 (1), ISSN:2041-1723

Published
2020

195. Artifact Peaks Due to Minor Decomposition of Sample Diluent DMSO in Head Space-GC Analysis: Mass Spectrometric Investigation Using Deuterated DMSO and Quadrupole Time-of-Flight Mass Detection

Author

Tang D, Weiliang Zhu, Li Q, Junling Wang, Chen W, Lin J, Zhu Y, Meng Li, and Zhou Q

Subjects
chemistry.chemical_compound, Deuterated DMSO, Chromatography, Chemistry, Dimethyl sulfoxide, Formic acid, Methanethiol, Gas chromatography, Gas chromatography–mass spectrometry, Decomposition, Diluent
Abstract

Rationale: Head space gas chromatography (HS-GC) has become a widely used analytical technique for residual solvents determination in drug substances and drug products. During our method development of residual solvents by HS-GC for certain drug substances, four unknown peaks were observed when dimethyl sulfoxide (DMSO) was employed as sample diluent.Methods: Use of other sample diluents replacing DMSO did not show these unknown peaks in the HS-GC analysis. HS-GC-MS was then utilized to investigate these peaks. As part of the investigation, DMSO-d6 was used to trace the origins of these unknown peaks to DMSO. A stress study of methanethiol and formic acid was carried out to provide further evidence that S-methyl methanethioate was one of the unknown peaks observed during the original HS-GC analysis.Results: The four unknown peaks have been identified as methanethiol, dimethylsulfide, S-methyl methanethioate, and dimethyldisulfide, respectively, and it has been demonstrated that the four peaks are clearly related to DMSO through the use of its deuterated counterpart. Plausible formation mechanisms of these species are proposed.Conclusions: The occurrence of the peaks is due to minor degradation of DMSO, facilitated by certain drug substances as analytes of the analysis. These peaks are artifacts, rather than genuine impurities of the drug substances. These artifact peaks could widely occur in HS-GC analysis, when DMSO is used as sample diluent.

Published
2021

200. High quantum efficiency of 1.8 μm luminescence in Tm3+ fluoride tellurite glass

Author

Tang, D, Liu, Qingsong, Liu, X, Wang, Xu, Yang, X, Liu, Yongyan, Ying, Tian, Renguang, Ye, Zhang, Xianghua, Xu, Shiqing, China Jiliang University (CJLU), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), National Key Research and Development Project of China [2018YFE0207700], Zhejiang Provincial Natur- al Science Foundation of China [LZ21F050002], and National Natur- al Science Foundation of China [61775205]

Subjects
Maximum half height width, Fluorotellurite glass, [CHIM]Chemical Sciences, Mid infrared luminescence, Condensed Matter Physics, Atomic and Molecular Physics, and Optics, Quantum efficiency, Electronic, Optical and Magnetic Materials
Abstract

International audience; In this paper, Tm3+ doped fluorotellurite glasses are synthesized by melt-quenching technique. The thermal and spectral properties of the glasses are characterized. The effect of the 1.8 mu m emission properties for different Tm3+ concentrations are investigated. Delta T (153 celcius) of the glass indicates it has good thermal stability. Spectroscopic parameters of Tm3+ such as radiative transition probability, branching ratio, spectroscopic quality factor, integrated emission cross section and radiative lifetime are calculated on the basis of Judd-Ofelt analysis. The maximum half-height width corresponding to 1.8 mu m broadens as Tm3+ increases and reaches a maximum of 216 nm, as well as the longer lifetime (5.68 ms). For 1.8 mu m (3F4 -> 3H6) emission band, the calculated Tm3+ doped fluorotellurite glass has a high quantum efficiency of 75.93%. Furthermore, the theoretical analysis of the energy transfer mechanism between Tm3+ ions were represented. Therefore, these results demonstrate that prepared Tm3+ doped fluorotellurite glass is an ideal laser material for 1.8 mu m band solid-state laser applications.

Published
2022

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