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Li E, Zou XL, Xu LQ, Chu YQ, Feng X, Lian H, Liu HQ, Liu AD, Han MK, Dong JQ, Wang HH, Liu JW, Zang Q, Wang SX, Zhou TF, Huang YH, Hu LQ, Zhou C, Qu HX, Chen Y, Lin SY, Zhang B, Qian JP, Hu JS, Xu GS, Chen JL, Lu K, Liu FK, Song YT, Li JG, Gong XZ. Experimental Evidence of Intrinsic Current Generation by Turbulence in Stationary Tokamak Plasmas. PHYSICAL REVIEW LETTERS 2022; 128:085003. [PMID: 35275672 DOI: 10.1103/physrevlett.128.085003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 09/16/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
High-β_{θe} (a ratio of the electron thermal pressure to the poloidal magnetic pressure) steady-state long-pulse plasmas with steep central electron temperature gradient are achieved in the Experimental Advanced Superconducting Tokamak. An intrinsic current is observed to be modulated by turbulence driven by the electron temperature gradient. This turbulent current is generated in the countercurrent direction and can reach a maximum ratio of 25% of the bootstrap current. Gyrokinetic simulations and experimental observations indicate that the turbulence is the electron temperature gradient mode (ETG). The dominant mechanism for the turbulent current generation is due to the divergence of ETG-driven residual flux of current. Good agreement has been found between experiments and theory for the critical value of the electron temperature gradient triggering ETG and for the level of the turbulent current. The maximum values of turbulent current and electron temperature gradient lead to the destabilization of an m/n=1/1 kink mode, which by counteraction reduces the turbulence level (m and n are the poloidal and toroidal mode number, respectively). These observations suggest that the self-regulation system including turbulence, turbulent current, and kink mode is a contributing mechanism for sustaining the steady-state long-pulse high-β_{θe} regime.
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Chen JL, Yang SW, Qin YM, Cheng XY. [Thrombocytopenia after interventional closure of congenital heart disease]. ZHONGHUA XIN XUE GUAN BING ZA ZHI 2022; 50:191-194. [PMID: 35172468 DOI: 10.3760/cma.j.cn112148-20220104-00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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Chen JL, Zhang JY, Chen MM, Wang XZ. [Conservative management of Oehlers type Ⅲ dens invaginatus in maxillary lateral incisors with periapical periodontitis: a report of three cases]. ZHONGHUA KOU QIANG YI XUE ZA ZHI = ZHONGHUA KOUQIANG YIXUE ZAZHI = CHINESE JOURNAL OF STOMATOLOGY 2022; 57:182-185. [PMID: 35152655 DOI: 10.3760/cma.j.cn112144-20210823-00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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Bush JA, Aikawa H, Fuerst R, Li Y, Ursu A, Meyer SM, Benhamou RI, Chen JL, Khan T, Wagner-Griffin S, Van Meter MJ, Tong Y, Olafson H, McKee KK, Childs-Disney JL, Gendron TF, Zhang Y, Coyne AN, Wang ET, Yildirim I, Wang KW, Petrucelli L, Rothstein JD, Disney MD. Ribonuclease recruitment using a small molecule reduced c9ALS/FTD r(G 4C 2) repeat expansion in vitro and in vivo ALS models. Sci Transl Med 2021; 13:eabd5991. [PMID: 34705518 DOI: 10.1126/scitranslmed.abd5991] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Chen JL, Jin ML, Wang X, Yang XJ, Zhang N, Liu FN, Liu R, Guo JP, Chen Y, Wang CJ. [Fitting and predicting trend of COVID-19 by SVEPIUHDR dynamic model]. ZHONGHUA LIU XING BING XUE ZA ZHI = ZHONGHUA LIUXINGBINGXUE ZAZHI 2021; 42:1341-1346. [PMID: 34814551 DOI: 10.3760/cma.j.cn112338-20210225-00147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Objective: To fit and predict the trend of COVID-19 epidemics in the United States (USA) and the United Kingdom (UK), and analyze the effect of vaccination. Methods: Based on the SEIR dynamic model, considering the presymptomatic infections, isolation measures, vaccine vaccination coverage, etc., we developed a SEIR with vaccine inoculation, Presymptomatic infectious, unconfirmed infectious, hospital isolation and domiciliary isolation dynamics model. The publicly released incidence data of COVID-19 from November 6, 2020 to January 31, 2021 in USA and from November 23, 2020 to January 31, 2021 in UK were used to fit the model and the publicly released incidence data of COVID-19 from February 1, 2021 to April 1 were used to evaluate the predicting power of the model by software R 4.0.3 and predict changes in the daily new cases in the context of different vaccination coverage. Results: According to the cumulative confirmed cases, the fitting bias and the predicting bias of the SVEPIUHDR model for USA and UK were less than 5%, respectively. From the model prediction results, the cumulative cases after COVID-19 vaccination in USA in early April reached 31 864 970. If there had not had such vaccination, the cumulative cases of COVID-19 would have reached to 35 317 082, with a gap of more than 3.4 million cases. In UK, the cumulative cases of COVID-19 after the vaccination was estimated to be 4 195 538 in early April, compared with 4 268 786 cases if no COVID-19 vaccination had been provided, there would have heen a gap of more than 70 000 cases. Conclusion: SVEPIUHDR model shows a good prediction effect on the epidemic of COVID-19 in both USA and UK.
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Wagner-Griffin S, Abe M, Benhamou RI, Angelbello AJ, Vishnu K, Chen JL, Childs-Disney JL, Disney MD. A Druglike Small Molecule that Targets r(CCUG) Repeats in Myotonic Dystrophy Type 2 Facilitates Degradation by RNA Quality Control Pathways. J Med Chem 2021; 64:8474-8485. [PMID: 34101465 DOI: 10.1021/acs.jmedchem.1c00414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myotonic dystrophy type 2 (DM2) is one of >40 microsatellite disorders caused by RNA repeat expansions. The DM2 repeat expansion, r(CCUG)exp (where "exp" denotes expanded repeating nucleotides), is harbored in intron 1 of the CCHC-type zinc finger nucleic acid binding protein (CNBP). The expanded RNA repeat causes disease by a gain-of-function mechanism, sequestering various RNA-binding proteins including the pre-mRNA splicing regulator MBNL1. Sequestration of MBNL1 results in its loss-of-function and concomitant deregulation of the alternative splicing of its native substrates. Notably, this r(CCUG)exp causes retention of intron 1 in the mature CNBP mRNA. Herein, we report druglike small molecules that bind the structure adopted by r(CCUG)exp and improve DM2-associated defects. These small molecules were optimized from screening hits from an RNA-focused small-molecule library to afford a compound that binds r(CCUG)exp specifically and with nanomolar affinity, facilitates endogenous degradation of the aberrantly retained intron in which it is harbored, and rescues alternative splicing defects.
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Liu NX, Mu L, Ding R, Zhu YB, Li S, Xie H, Yan R, Peng J, Chen JL. Measurements of neutral particle energy spectrum on EAST using a time-of-flight low-energy neutral particle analyzer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:063507. [PMID: 34243563 DOI: 10.1063/5.0043769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/15/2021] [Indexed: 06/13/2023]
Abstract
The neutral particles generated by charge exchange reactions can play an important role in erosion of first wall materials in fusion devices. In order to measure the flux and energy of neutral particles to the first wall, a low-energy neutral particle analyzer (LENPA) based on the time-of-flight method has been developed and successfully applied on the Experimental Advanced Superconducting Tokamak (EAST)' to measure the neutrals with an energy of 20-3000 eV. The LENPA works in the counting mode, and the signal of photons is used as the reference for the flight time of neutrals. The energy spectrum of low-energy neutral particles on EAST has been obtained for the first time. The new diagnostics can help in understanding the neutral particle generation and deposition on the first wall materials in tokamaks under different plasma conditions.
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Alemanno F, An Q, Azzarello P, Barbato FCT, Bernardini P, Bi XJ, Cai MS, Catanzani E, Chang J, Chen DY, Chen JL, Chen ZF, Cui MY, Cui TS, Cui YX, Dai HT, D'Amone A, De Benedittis A, De Mitri I, de Palma F, Deliyergiyev M, Di Santo M, Dong TK, Dong ZX, Donvito G, Droz D, Duan JL, Duan KK, D'Urso D, Fan RR, Fan YZ, Fang K, Fang F, Feng CQ, Feng L, Fusco P, Gao M, Gargano F, Gong K, Gong YZ, Guo DY, Guo JH, Guo XL, Han SX, Hu YM, Huang GS, Huang XY, Huang YY, Ionica M, Jiang W, Kong J, Kotenko A, Kyratzis D, Lei SJ, Li S, Li WL, Li X, Li XQ, Liang YM, Liu CM, Liu H, Liu J, Liu SB, Liu WQ, Liu Y, Loparco F, Luo CN, Ma M, Ma PX, Ma T, Ma XY, Marsella G, Mazziotta MN, Mo D, Niu XY, Pan X, Parenti A, Peng WX, Peng XY, Perrina C, Qiao R, Rao JN, Ruina A, Salinas MM, Shang GZ, Shen WH, Shen ZQ, Shen ZT, Silveri L, Song JX, Stolpovskiy M, Su H, Su M, Sun ZY, Surdo A, Teng XJ, Tykhonov A, Wang H, Wang JZ, Wang LG, Wang S, Wang XL, Wang Y, Wang YF, Wang YZ, Wang ZM, Wei DM, Wei JJ, Wei YF, Wen SC, Wu D, Wu J, Wu LB, Wu SS, Wu X, Xia ZQ, Xu HT, Xu ZH, Xu ZL, Xu ZZ, Xue GF, Yang HB, Yang P, Yang YQ, Yao HJ, Yu YH, Yuan GW, Yuan Q, Yue C, Zang JJ, Zhang F, Zhang SX, Zhang WZ, Zhang Y, Zhang YJ, Zhang YL, Zhang YP, Zhang YQ, Zhang Z, Zhang ZY, Zhao C, Zhao HY, Zhao XF, Zhou CY, Zhu Y. Measurement of the Cosmic Ray Helium Energy Spectrum from 70 GeV to 80 TeV with the DAMPE Space Mission. PHYSICAL REVIEW LETTERS 2021; 126:201102. [PMID: 34110215 DOI: 10.1103/physrevlett.126.201102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/25/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The measurement of the energy spectrum of cosmic ray helium nuclei from 70 GeV to 80 TeV using 4.5 years of data recorded by the Dark Matter Particle Explorer (DAMPE) is reported in this work. A hardening of the spectrum is observed at an energy of about 1.3 TeV, similar to previous observations. In addition, a spectral softening at about 34 TeV is revealed for the first time with large statistics and well controlled systematic uncertainties, with an overall significance of 4.3σ. The DAMPE spectral measurements of both cosmic protons and helium nuclei suggest a particle charge dependent softening energy, although with current uncertainties a dependence on the number of nucleons cannot be ruled out.
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Yu ZM, Hou ZH, Zong Z, Jiang ZP, Zhou TC, Ma N, Chen JL, Chen S. [Combined minimally invasive treatment of chronic giant inguinal hernia]. ZHONGHUA WEI CHANG WAI KE ZA ZHI = CHINESE JOURNAL OF GASTROINTESTINAL SURGERY 2021; 23:1216-1219. [PMID: 33353282 DOI: 10.3760/cma.j.cn.441530-20190903-00336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ursu A, Wang KW, Bush JA, Choudhary S, Chen JL, Baisden JT, Zhang YJ, Gendron TF, Petrucelli L, Yildirim I, Disney MD. Structural Features of Small Molecules Targeting the RNA Repeat Expansion That Causes Genetically Defined ALS/FTD. ACS Chem Biol 2020; 15:3112-3123. [PMID: 33196168 DOI: 10.1021/acschembio.0c00049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genetically defined amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), collectively named c9ALS/FTD, are triggered by hexanucleotide GGGGCC repeat expansions [r(G4C2)exp] within the C9orf72 gene. In these diseases, neuronal loss occurs through an interplay of deleterious phenotypes, including r(G4C2)exp RNA gain-of-function mechanisms. Herein, we identified a benzimidazole derivative, CB096, that specifically binds to a repeating 1 × 1 GG internal loop structure, 5'CGG/3'GGC, that is formed when r(G4C2)exp folds. Structure-activity relationship (SAR) studies and molecular dynamics (MD) simulations were used to define the molecular interactions formed between CB096 and r(G4C2)exp that results in the rescue of disease-associated pathways. Overall, this study reveals a unique structural feature within r(G4C2)exp that can be exploited for the development of lead medicines and chemical probes.
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Liang WL, Li HG, Zhong G, Wang BS, Ma JD, Chen JL, Mao HW, Yu-Lung YL, Lee PH. [Targeted therapy of pyogenic sterile arthritis, pyoderma gangrenosum, and acne syndrome (PAPA): a case report and literature review]. ZHONGHUA ER KE ZA ZHI = CHINESE JOURNAL OF PEDIATRICS 2020; 58:977-981. [PMID: 33256319 DOI: 10.3760/cma.j.cn112140-20200430-00456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Objective: To analyze the clinical course and targeted therapy of pyogenic sterile arthritis, pyoderma gangrenosum, and acne (PAPA) syndrome. Methods: The clinical history of a 6-year-old boy with PAPA syndrome, who was admitted to Hong Kong University Shenzhen Hospital in September 2017, was reviewed. His genetic diagnosis was confirmed by whole exome sequencing. The response to targeted therapy was evaluated by comparing the inflammatory markers (erythrocyte sedimentation rate (ESR) and C reactive protein (CRP) and serum cytokines (interleukin (IL)-1, IL-6 and tumor necrosis factor-α (TNF-α)) before and after biological agents treatment. For literature review, "PAPA syndrome" and"PSTPIP1 gene"were used as keywords to retrieve papers published from January 1997 to December 2019 from Pubmed, Wanfang and CNKI database. Results: The patient was a 6-year-old boy, admitted to the hospital due to recurrent joint swelling and pain for more than 4 years. Before treatment, the CRP (256 mg/L), ESR (105 mm/1 h) and cytokines including serum TNF-α (7.43 ng/L), IL-1 (<5 ng/L), IL-6 (301 ng/L) were significantly elevated. Culture of the joint effusion was negative, but the IL-6 level was above 1 000 ng/L. MRI showed osteomyelitis at the lower end of the right femur. Gene detection found a heterozygous variation of PSTPIP1 gene (c.748G>A, p.E250K). Arthralgia once alleviated after the initiation of tocilizumab and infliximab, but recurred after 1 year of treatment. Thereafter, the anti-IL-1 receptor antagonist (Anakinra) was commenced, followed by a significant improvement of the arthralgia, and a complete remission during the follow-up. Besides, the level of CRP, ESR, serum TNF-α, IL-1 and IL-6 were all decreased to normal on the last followed up in December 2019. Literature review found 29 articles and 87 patients in total. The initial symptoms included those of arthritis (n=58), pyoderma gangrenosum (n=33), and acne (n=24). Among all the cases, 13 genotypes were confirmed, and 47 variations involved amino acid p.E250. Steroid and/or biological agents were used in most patients. Conclusions: PAPA syndrome should be suspected in children with recurrent pyogenic sterile arthritis, and an early diagnosis could be achieved by genetic test. Targeted treatment with biological agent may control the symptoms effectively. Biological agents can control symptoms of this disorder effectively.
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Angelbello AJ, Benhamou RI, Rzuczek SG, Choudhary S, Tang Z, Chen JL, Roy M, Wang KW, Yildirim I, Jun AS, Thornton CA, Disney MD. A Small Molecule that Binds an RNA Repeat Expansion Stimulates Its Decay via the Exosome Complex. Cell Chem Biol 2020; 28:34-45.e6. [PMID: 33157036 DOI: 10.1016/j.chembiol.2020.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/08/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022]
Abstract
Many diseases are caused by toxic RNA repeats. Herein, we designed a lead small molecule that binds the structure of the r(CUG) repeat expansion [r(CUG)exp] that causes myotonic dystrophy type 1 (DM1) and Fuchs endothelial corneal dystrophy (FECD) and rescues disease biology in patient-derived cells and in vivo. Interestingly, the compound's downstream effects are different in the two diseases, owing to the location of the repeat expansion. In DM1, r(CUG)exp is harbored in the 3' untranslated region, and the compound has no effect on the mRNA's abundance. In FECD, however, r(CUG)exp is located in an intron, and the small molecule facilitates excision of the intron, which is then degraded by the RNA exosome complex. Thus, structure-specific, RNA-targeting small molecules can act disease specifically to affect biology, either by disabling the gain-of-function mechanism (DM1) or by stimulating quality control pathways to rid a disease-affected cell of a toxic RNA (FECD).
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Haniff H, Tong Y, Liu X, Chen JL, Suresh BM, Andrews RJ, Peterson JM, O’Leary CA, Benhamou RI, Moss WN, Disney MD. Targeting the SARS-CoV-2 RNA Genome with Small Molecule Binders and Ribonuclease Targeting Chimera (RIBOTAC) Degraders. ACS CENTRAL SCIENCE 2020; 6:1713-1721. [PMID: 33140033 PMCID: PMC7553039 DOI: 10.1021/acscentsci.0c00984] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Indexed: 05/07/2023]
Abstract
COVID-19 is a global pandemic, thus requiring multiple strategies to develop modalities against it. Herein, we designed multiple bioactive small molecules that target a functional structure within the SARS-CoV-2's RNA genome, the causative agent of COVID-19. An analysis to characterize the structure of the RNA genome provided a revised model of the SARS-CoV-2 frameshifting element, in particular its attenuator hairpin. By studying an RNA-focused small molecule collection, we identified a drug-like small molecule (C5) that avidly binds to the revised attenuator hairpin structure with a K d of 11 nM. The compound stabilizes the hairpin's folded state and impairs frameshifting in cells. The ligand was further elaborated into a ribonuclease targeting chimera (RIBOTAC) to recruit a cellular ribonuclease to destroy the viral genome (C5-RIBOTAC) and into a covalent molecule (C5-Chem-CLIP) that validated direct target engagement and demonstrated its specificity for the viral RNA, as compared to highly expressed host mRNAs. The RIBOTAC lead optimization strategy improved the bioactivity of the compound at least 10-fold. Collectively, these studies demonstrate that the SARS-CoV-2 RNA genome should be considered druggable.
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Xu JJ, Jiang L, Song Y, Yao Y, Jia SD, Liu Y, Yuan DS, Li TY, Chen J, Wu Y, Zhang J, Chen JL, Yang YJ, Gao RL, Qiao SB, Xu B, Yuan JQ. [Related factors and the long-term outcome after percutaneous coronary intervention of premature acute myocardial infarction]. ZHONGHUA XIN XUE GUAN BING ZA ZHI 2020; 48:655-660. [PMID: 32847321 DOI: 10.3760/cma.j.cn112148-20191208-00738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the related factors of premature acute myocardial infarction(AMI), and to compare the the long-term outcomes in patients with and without premature AMI after percutaneous coronary intervention (PCI). Methods: This study was a prospective cohort study.From January 2013 to December 2013, 10 724 consecutive patients with coronary heart disease undergoing PCI in Fuwai Hospital were enrolled. Among them 1 920 patients with the diagnosis of AMI were divided into two groups: premature AMI (man≤50 years old, woman≤60 years old) and non-premature AMI. The baseline characteristics were collected, and multivariate logistic regression was uesed to analysis the related factors of premature AMI. The clinical outcomes, including the major adverse cardiovascular and cerebrovascular events(MACCE) which was the composite of cardiac death, myocardial infarction, revascularization, stroke and stent thrombosis, as well as bleeding events, during hospitalization, at 2 years and 5 years follow-up were analyzed. Results: A total of 1 920 AMI patiens were included(age was (56.5±11.3) years old),with 1 612(84.0%) males. There were statistically significant differences between the two groups in gender, body mass index, blood lipid, complications, inflammatory markers, etc (all P<0.05). Multivariate logistic regression analysis showed body mass index(OR=1.06, 95%CI 1.01-1.10, P<0.01), triglyceride(OR=1.47, 95%CI 1.14-1.90, P<0.01), serum uric acid level(OR=1.02, 95%CI 1.01-1.04, P<0.01), high density lipoprotein cholesterol level(OR=0.33, 95%CI 0.14-0.78, P=0.01) and history of hypertension(OR=0.72, 95%CI 0.56-0.93, P=0.01) were independent related factors of premature AMI. The incidence of all-cause death and cardiac death were lower during hospitalization, at 2 years and 5 years follow-up in the premature AMI group than in non-premature AMI group(all P<0.05). In the premature AMI group, the incidence of MACCE and stroke was lower, with more bleeding events in 5 years follow-up(all P<0.05). Conclusions: Metabolic abnormalities, including high BMI, high triglyceride level and high serum uric acid, low high-density lipoprotein cholesterol level are the related factor of premature AMI. The incidence of ischemic events in patients with premature AMI is lower, while the incidence of bleeding events is higher than non-premature AMI patients.
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Haniff HS, Knerr L, Chen JL, Disney MD, Lightfoot HL. Target-Directed Approaches for Screening Small Molecules against RNA Targets. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:869-894. [PMID: 32419578 PMCID: PMC7442623 DOI: 10.1177/2472555220922802] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA molecules have a variety of cellular functions that can drive disease pathologies. They are without a doubt one of the most intriguing yet controversial small-molecule drug targets. The ability to widely target RNA with small molecules could be revolutionary, once the right tools, assays, and targets are selected, thereby defining which biomolecules are targetable and what constitutes drug-like small molecules. Indeed, approaches developed over the past 5-10 years have changed the face of small molecule-RNA targeting by addressing historic concerns regarding affinity, selectivity, and structural dynamics. Presently, selective RNA-protein complex stabilizing drugs such as branaplam and risdiplam are in clinical trials for the modulation of SMN2 splicing, compounds identified from phenotypic screens with serendipitous outcomes. Fully developing RNA as a druggable target will require a target engagement-driven approach, and evolving chemical collections will be important for the industrial development of this class of target. In this review we discuss target-directed approaches that can be used to identify RNA-binding compounds and the chemical knowledge we have today of small-molecule RNA binders.
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Angelbello AJ, Chen JL, Disney MD. Small molecule targeting of RNA structures in neurological disorders. Ann N Y Acad Sci 2020; 1471:57-71. [PMID: 30964958 PMCID: PMC6785366 DOI: 10.1111/nyas.14051] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
Aberrant RNA structure and function operate in neurological disease progression and severity. As RNA contributes to disease pathology in a complex fashion, that is, via various mechanisms, it has become an attractive therapeutic target for small molecules and oligonucleotides. In this review, we discuss the identification of RNA structures that cause or contribute to neurological diseases as well as recent progress toward the development of small molecules that target them, including small molecule modulators of pre-mRNA splicing and RNA repeat expansions that cause microsatellite disorders such as Huntington's disease and amyotrophic lateral sclerosis. The use of oligonucleotide-based modalities is also discussed. There are key differences between small molecule and oligonucleotide targeting of RNA. The former targets RNA structure, while the latter prefers unstructured regions. Thus, some targets will be preferentially targeted by oligonucleotides and others by small molecules.
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Zhang Y, Peng J, Ding R, Xie H, Mu L, Chen JL. Development of a quartz crystal microbalance diagnostic for measuring material erosion and deposition on the first wall in EAST. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:076101. [PMID: 32752797 DOI: 10.1063/5.0012210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
A quartz crystal microbalance (QMB) diagnostic system has been established in Experimental Advanced Superconducting Tokamak (EAST) for real-time and in situ measurements of erosion and deposition rates of plasma-facing materials at the first wall. A ∼70 nm aluminum (Al) film has been coated on the QMB crystal surface to measure the erosion rate by charge exchange neutral particles. Dual sensors of the QMB system have been used with a closed sensor for reference. The stability and light sensitivity of the QMB system have been tested in the lab, demonstrating its feasibility on the application of EAST experiments. The QMB system with cooling water has been successfully applied in the 2018 EAST campaign. The net erosion thickness measured by the QMB has been well validated by thickness measurements using the Rutherford backscattering spectrometry. The developed QMB systems can help us to understand the physics processes of material erosion and deposition at main chamber walls for long pulse operations in EAST.
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Bao HR, Chen JL, Li F, Zeng XL, Liu XJ. Relationship between PI3K/mTOR/RhoA pathway-regulated cytoskeletal rearrangements and phagocytic capacity of macrophages. ACTA ACUST UNITED AC 2020; 53:e9207. [PMID: 32520207 PMCID: PMC7279697 DOI: 10.1590/1414-431x20209207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 03/26/2020] [Indexed: 12/02/2022]
Abstract
The objective of this study was to investigate the relationship between PI3K/mTOR/RhoA signaling regulated cytoskeletal rearrangements and phagocytic capacity of macrophages. RAW264.7 macrophages were divided into four groups; blank control, negative control, PI3K-RNAi, and mTOR-RNAi. The cytoskeletal changes in the macrophages were observed. Furthermore, the phagocytic capacity of macrophages against Escherichia coli is reported as mean fluorescence intensity (MFI) and percent phagocytosis. Transfection yielded 82.1 and 81.5% gene-silencing efficiencies against PI3K and mTOR, respectively. The PI3K-RNAi group had lower mRNA and protein expression levels of PI3K, mTOR, and RhoA than the blank and negative control groups (Р<0.01). The mTOR-RNAi group had lower mRNA and protein levels of mTOR and RhoA than the blank and the negative control groups (Р<0.01). Macrophages in the PI3K-RNAi group exhibited stiff and inflexible morphology with short, disorganized filopodia and reduced number of stress fibers. Macrophages in the mTOR-RNAi group displayed pronounced cellular deformations with long, dense filopodia and an increased number of stress fibers. The PI3K-RNAi group exhibited lower MFI and percent phagocytosis than blank and negative control groups, whereas the mTOR-RNAi group displayed higher MFI and percent phagocytosis than the blank and negative controls (Р<0.01). Before and after transfection, the mRNA and protein levels of PI3K were both positively correlated with mTOR and RhoA (Р<0.05), but the mRNA and protein levels of mTOR were negatively correlated with those of RhoA (Р<0.05). Changes in the phagocytic capacity of macrophages were associated with cytoskeletal rearrangements and were regulated by the PI3K/mTOR/RhoA signaling pathway.
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Chen JL, Zhang P, Abe M, Aikawa H, Zhang L, Frank AJ, Zembryski T, Hubbs C, Park H, Withka J, Steppan C, Rogers L, Cabral S, Pettersson M, Wager TT, Fountain MA, Rumbaugh G, Childs-Disney JL, Disney MD. Design, Optimization, and Study of Small Molecules That Target Tau Pre-mRNA and Affect Splicing. J Am Chem Soc 2020; 142:8706-8727. [PMID: 32364710 PMCID: PMC7357857 DOI: 10.1021/jacs.0c00768] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Approximately 95% of human genes are alternatively spliced, and aberrant splicing events can cause disease. One pre-mRNA that is alternatively spliced and linked to neurodegenerative diseases is tau (microtubule-associated protein tau), which can cause frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17) and can contribute to Alzheimer's disease. Here, we describe the design of structure-specific lead small molecules that directly target tau pre-mRNA from sequence. This was followed by hit expansion and analogue synthesis to further improve upon these initial lead molecules. The emergent compounds were assessed for functional activity in a battery of assays, including binding assays and an assay that mimics molecular recognition of tau pre-mRNA by a U1 small nuclear ribonucleoprotein (snRNP) splicing factor. Compounds that emerged from these studies had enhanced potency and selectivity for the target RNA relative to the initial hits, while also having significantly improved drug-like properties. The compounds are shown to directly target tau pre-mRNA in cells, via chemical cross-linking and isolation by pull-down target profiling, and to rescue disease-relevant splicing of tau pre-mRNA in a variety of cellular systems, including primary neurons. More broadly, this study shows that lead, structure-specific compounds can be designed from sequence and then further optimized for their physicochemical properties while at the same time enhancing their activity.
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Yu ZM, Ma N, Chen JL, Jiang ZP, Li YR, Hou ZH, Gan WC, Zhou TC, Chen S. [Intestinal obstruction caused by broad ligament hernia: a case report]. ZHONGHUA WEI CHANG WAI KE ZA ZHI = CHINESE JOURNAL OF GASTROINTESTINAL SURGERY 2020; 23:319-320. [PMID: 32192315 DOI: 10.3760/cma.j.cn.441530-20200306-00128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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Alkaid Albqoor M, Chen JL, Weiss S, Waters C, Choi J. Self-rated health of Middle Eastern immigrants in the US: a national study. Public Health 2019; 180:64-73. [PMID: 31855621 DOI: 10.1016/j.puhe.2019.10.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/02/2019] [Accepted: 10/30/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVES The aim of the study was to examine self-rated health (SRH) of Middle Eastern immigrants in the US compared with US-born non-Hispanic whites and to examine factors associated with fair/poor SRH among Middle Eastern immigrants in the US. STUDY DESIGN We used a cross-sectional design to analyze the National Health Interview Survey from 2001 to 2015. METHODS Secondary survey analysis procedures were conducted using the SAS program, with a total of 3,966 Middle Eastern and 731,285 US-born non-Hispanic whites. Descriptive statistics and regression analyses were used. RESULTS Middle Eastern immigrants had significantly higher rates of fair/poor SRH than US-born whites across the three survey waves. Reporting symptoms of serious psychological distress, older age (60+ years), current alcohol-drinking status, and having a family member with disability were the factors associated significantly with higher odds of reporting fair/poor SRH in Middle Eastern immigrants, whereas education was a protecting factor of fair/poor SRH. CONCLUSIONS This study indicates that Middle Eastern immigrants are one of the US immigrant populations that report poor health status, which reveals the need for health policy attention to reduce health disparities.
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Zou JY, Zhao WH, Chen JL, Du XK, Hu XW, Ye ZY. [The role of EBUS-TBNA in the systematic evaluation of lymph node staging and resectability analysis in non-small cell lung cancer]. ZHONGHUA ZHONG LIU ZA ZHI [CHINESE JOURNAL OF ONCOLOGY] 2019; 41:792-795. [PMID: 31648504 DOI: 10.3760/cma.j.issn.0253-3766.2019.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To evaluate the role of endobronchial ultrasound guided transbronchial needle aspiration (EBUS-TBNA) in lymph node staging and resectability assessment of patients with non-small cell lung cancer (NSCLC). Methods: The clinical data of 154 patients with NSCLC who underwent EBUS-TBNA from March 2015 to December 2018 were collected. All accessible mediastinal and hilar lymph nodes were systematically explored and punctured using EBUS-TBNA. EBUS-TBNA and CT were used for preoperative staging and resectability evaluation. Results: The sensitivity, specificity and accuracy of EBUS-TBNA were 94.2%, 100.0% and 96.0%, respectively, while those of CT were 89.9%, 31.8% and 72.0%, respectively. The differences were statistically significant (P<0.05). The sensitivity, specificity and accuracy of EBUS-TBNA in lymph nodes with short diameter less than 15 mm were 92.4%, 100.0% and 96.0%, respectively, while those of CT were 80.7%, 34.8% and 60.1%, respectively, with statistical differences (P<0.05). The staging of 62 patients was changed, 27 cases were up-regulated and 35 cases were down-regulated. Among them, 32 cases had been changed to resectable. The evaluating resectability of EBUS-TBNA showed excellent consistency with that of pathological results (Kappa=0.95). The sensitivity and specificity were 100.0% and 97.2%, respectively. Conclusion: EBUS-TBNA can systemically evaluate the metastatic status of NSCLC patients and improve the accuracy of preoperative lymph node staging and resectability assessment.
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Spasic A, Berger KD, Chen JL, Seetin MG, Turner DH, Mathews DH. Improving RNA nearest neighbor parameters for helices by going beyond the two-state model. Nucleic Acids Res 2019; 46:4883-4892. [PMID: 29718397 PMCID: PMC6007268 DOI: 10.1093/nar/gky270] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/22/2018] [Indexed: 12/31/2022] Open
Abstract
RNA folding free energy change nearest neighbor parameters are widely used to predict folding stabilities of secondary structures. They were determined by linear regression to datasets of optical melting experiments on small model systems. Traditionally, the optical melting experiments are analyzed assuming a two-state model, i.e. a structure is either complete or denatured. Experimental evidence, however, shows that structures exist in an ensemble of conformations. Partition functions calculated with existing nearest neighbor parameters predict that secondary structures can be partially denatured, which also directly conflicts with the two-state model. Here, a new approach for determining RNA nearest neighbor parameters is presented. Available optical melting data for 34 Watson–Crick helices were fit directly to a partition function model that allows an ensemble of conformations. Fitting parameters were the enthalpy and entropy changes for helix initiation, terminal AU pairs, stacks of Watson–Crick pairs and disordered internal loops. The resulting set of nearest neighbor parameters shows a 38.5% improvement in the sum of residuals in fitting the experimental melting curves compared to the current literature set.
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Chen JL, Moss WN, Spencer A, Zhang P, Childs-Disney JL, Disney MD. The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology. PLoS One 2019; 14:e0219210. [PMID: 31291322 PMCID: PMC6619747 DOI: 10.1371/journal.pone.0219210] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/18/2019] [Indexed: 12/31/2022] Open
Abstract
Tauopathies are neurodegenerative diseases that affect millions of people worldwide including those with Alzheimer’s disease. While many efforts have focused on understanding the role of tau protein in neurodegeneration, there has been little done to systematically analyze and study the structures within tau’s encoding RNA and their connection to disease pathology. Knowledge of RNA structure can provide insights into disease mechanisms and how to affect protein production for therapeutic benefit. Using computational methods based on thermodynamic stability and evolutionary conservation, we identified structures throughout the tau pre-mRNA, especially at exon-intron junctions and within the 5′ and 3′ untranslated regions (UTRs). In particular, structures were identified at twenty exon-intron junctions. The 5′ UTR contains one structured region, which lies within a known internal ribosome entry site. The 3′ UTR contains eight structured regions, including one that contains a polyadenylation signal. A series of functional experiments were carried out to assess the effects of mutations associated with mis-regulation of alternative splicing of exon 10 and to identify regions of the 3′ UTR that contain cis-regulatory elements. These studies defined novel structural regions within the mRNA that affect stability and pre-mRNA splicing and may lead to new therapeutic targets for treating tau-associated diseases.
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O’Leary CA, Andrews RJ, Tompkins VS, Chen JL, Childs-Disney JL, Disney MD, Moss WN. RNA structural analysis of the MYC mRNA reveals conserved motifs that affect gene expression. PLoS One 2019; 14:e0213758. [PMID: 31206539 PMCID: PMC6576772 DOI: 10.1371/journal.pone.0213758] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/30/2019] [Indexed: 12/15/2022] Open
Abstract
The MYC gene encodes a human transcription factor and proto-oncogene that is dysregulated in over half of all known cancers. To better understand potential post-transcriptional regulatory features affecting MYC expression, we analyzed secondary structures in the MYC mRNA using a program that is optimized for finding small locally-folded motifs with a high propensity for function. This was accomplished by calculating folding metrics across the MYC sequence using a sliding analysis window and generating unique consensus base pairing models weighted by their lower-than-random predicted folding energy. A series of 30 motifs were identified, primarily in the 5' and 3' untranslated regions, which show evidence of structural conservation and compensating mutations across vertebrate MYC homologs. This analysis was able to recapitulate known elements found within an internal ribosomal entry site, as well as discover a novel element in the 3' UTR that is unusually stable and conserved. This novel motif was shown to affect MYC expression, potentially via the modulation of miRNA target accessibility or other trans-regulatory factors. In addition to providing basic insights into mechanisms that regulate MYC expression, this study provides numerous, potentially druggable RNA targets for the MYC gene, which is considered “undruggable” at the protein level.
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