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Pan-cancer analysis of RNA 5-methylcytosine reader (ALYREF)

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Oncology Research 2024年第3期32卷 503-515页

作者： XING YE ZHOUTING TUO KAI CHEN RUICHENG WU JIE WANG QINGXIN YU LUXIA YE AKIRA MIYAMOTO koo HAN YOO CHI ZHANG WURAN WEI DENGXIONG LI DECHAO FENG Samuel Oschin Comprehensive Cancer Institute Department of MedicineDepartment of Biomedical SciencesCedars-Sinai Medical CenterLos AngelesCA90048USA Department of Urology The Second Afiliated Hospital of Anhui Medical UniversityHefei230601China Department of Urology Institute of UrologyWest China HospitalSichuan UniversityChengdu610041China Department of Pathology Ningbo Diagnostic Pathology Center Ningbo315021China Department of Public Research Platfom Taizhou Hospital of Zhejiang Province Afliated to Wenzhou Medical UniversityLinhai317000China Department of Rehabilitation West Kyushu UniversityKanzaki shi842-8585Japan Department of Urology Kyung Hee UniversitySeoul446701South Korea Department of Rehabilitation The Afliated Hospital of Southwest Medical UniversityLuwzhou646000China

The incre asing interest in RNA modifications has signifcantly advanced epigenomic and epitranscriptomic *** study focuses on the immuno oncological impact of ALYREF in human cancer through a pan-cancer analysis,enhancing understanding of this gene's role in *** observed differential ALYREF expression between tumor and normal samples,correl ating strongly with prognosis in various cancers,particularly kidney renal papillary cell carcinoma(KIRP)and liver hepatocellular carcinoma(LIHC).ALYREF showed a negative correlation with most tumor-infitrating cells in lung squamous cell carcinoma(LUSC)and lymphoid neoplasm difuse large B-cell lymphoma(DLBC),while positive correlations were noted in IIHC,kidney chromophobe(KICH),mesothelioma(MESO),KIRP,pheochromocytoma and paraganglioma(PARD),and glioma(GBMLGG).Aditionally,ALYREF expression was closely associated with tumor heterogeneity,stemness indices,and a high mutation rate in TP53 across these *** conclusion,ALYREF may serve as an oncogenic biomarker in numerous cancers,meriting further research attention.

关键词： Pan-cancer RNA 5-methylcytosine ALYREF Immwno-oncological efects

Unraveling links between aging,circadian rhythm and cancer:Insights from evidence-based analysis

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Chinese Journal of Cancer Research 2024年第3期36卷 341-350页

作者： Dechao Feng Yuhan Xiao Jie Wang Ruicheng Wu Zhouting Tuo koo Han Yoo Wuran Wei Dilinaer Wusiman Zhipeng Wang Dengxiong Li Yubo Yang William C.Cho Mang Ke Department of Urology Institute of UrologyWest China HospitalSichuan UniversityChengdu 610041China Division of Surgery&Interventional Science University College LondonLondon W1W 7TSUK Department of Urology Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical UniversityTaizhou 317000China Department of Urology the Second Affiliated Hospital of Anhui Medical UniversityHefei 230601China Department of Urology Kyung Hee UniversitySeoul 130-701South Korea Department of Comparative Pathobiology College of Veterinary MedicinePurdue UniversityWest LafayetteIN47907USA Purdue Institute for Cancer Research Purdue UniversityWest LafayetteIN 47907USA Department of Urology Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengdu 610072China Department of Urology Three Gorges HospitalChongqing UniversityChongqing 404000China Department of Clinical Oncology Queen Elizabeth HospitalHong Kong SARChina

Aging and circadian rhythms have been connected for decades,but their molecular interaction has remained unknown,especially for *** this situation,we summarized the current research actuality and problems in this field using the bibliometric *** in the PubMed and Web of Science databases were ***,there is a rising trend in the publication volume regarding aging and circadian rhythms in the field of *** from USA,Germany,Italy,China and England have greater studies than *** three publication institutions are University of California System,UDICE-French Research Universities and University of Texas *** research hotspots include oxidative stress,breast cancer,melatonin,cell cycle,calorie restriction,prostate cancer and NF-κ*** conclusion,results generated by bibliometric analysis indicate that many approaches involve in the complex interactions between aging and circadian rhythm in *** established and emerging research directions guide our exploration of the regulatory mechanisms of aging and circadian rhythms in cancer and provide a reference for developing new research avenues.

关键词： Aging circadian rhythm human cancer bibliometric analysis oxidative stress

Lactic Acid Fermentation from Coffee Ground Waste Hydrolysate by Lactobacillus rhamnosus

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Journal of Renewable Materials 2019年第4期7卷 365-372页

作者： Ja-Ryong koo Hye Min Park Se kyung Kim Hyun Shik Yun Department of Biological Engineering Inha UniversityIncheon 22212Korea Institute of Industrial Biotechnology Inha University Research and Business FoundationIncheon 22212Korea

Lactic acid is an important organic acid that is widely used in the food,pharmaceutical,and cosmetic *** acid was produced from coffee ground waste which contains fermentable sugars and is increasingly generated from our daily dietary *** 114 strains of Lactobacillus species,Lactobacillus rhamnosus ATCC 10863 was selected for the production of lactic acid from coffee ground *** alkali pretreatment and saccharification,cellulose and hemicellulose in coffee ground waste were converted into fermentable *** experiments were conducted at various alkali solution,concentrations,and *** pretreatment with 35 g/L of KOH at 121oC for 60 min,the highest concentration of fermentable sugars was *** optimum concentration of Viscozyme L was 2%when saccharification was proceeded at 55oC for 7 *** productivity of lactic acid fermentation was the highest(0.59 g/L/h)at 100 g of coffee ground waste(1x concentration),whereas the lactic acid concentration was the highest at 600 g of coffee ground waste(6x concentration).As the concentration of coffee ground increased,the lactic acid concentration was also increased,however,the amount was not proportional to the coffee ground waste *** this study,it was found that coffee ground waste could be used as a culture medium for Lactobacillus rhamnosus ATCC 10863 through pretreatment and saccharification for the production of lactic acid.

关键词： Coffee ground waste Lactobacillus rhamnosus lactic acid fermentable sugars saccharification alkali pretreatment

High-Resolution Infrared-Vacuum Ultraviolet Photoion and Pulsed Field Ionization-Photoelectron Methods for Spectroscopic Studies of Neutrals and Cations

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Chinese Journal of Chemical Physics 2008年第3期21卷 193-201页

作者： Xi Xing Beth Reed Mi kyung Bahng Peng Wang Hin koo Woo Sun Jong Baek Chee Shing Lain Cheuk Yiu Ng Department of Chemistry University of California Davis Davis California 95616 USA

We show that by scanning the frequency of a single mode infrared （IR） optical parametric oscillator （IR- OPO） laser to excite the molecular species of interest and fixing the frequency of a vacuum ultraviolet （VUV） laser to photoionize the IR excited species, high-resolution IR spectra of polyatomic neutrals can be obtained with high sensitivity. The fact that this IR-VUV-photoion （IR-VUV-PI） method is based on VUV photoionization probe, and thus, allows the identification of the neutral IR absorber, makes it applicable for IR spectroscopy measurements of isotopemers, radicals, and clusters, which usually exist as impure samples. The highly resolved IR-VUV-PI measurements achieved using the single mode IR-OPO laser have made possible the selection of single rovibrational states of CH3X （X=Br and I）, C2H4, and C3H4 for VUV-pulsed field ionization-photoelectron （VUV-PFI-PE） measurements, resulting in rovibrationally resolved photoelectron spectra for these polyatomic molecules. These experiments show that the signal- to-noise ratios of the IR-VUV-PI and IR-VUV-PFI-PE spectra obtained by employing the high-resolution IR-OPO laser are significantly higher than those observed in previous IR-VUV-PI and IR-VUV-PFI-PE studies using a low-resolution IR-OPO laser. Further improvement in sensitivity of IR-VUV-PI and IR- VUV-PFI-PE measurements by using the collinear arrangement of IR-VUV lasers and molecular beam is discussed.

关键词： Vacuum ultraviolet Infrared Pulse-field photoelectron High resolution

Ethanol extract from Gynostemma pentaphyllum ameliorates dopaminergic neuronal cell death in transgenic mice expressing mutant A53T human alpha-synuclein

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Neural Regeneration Research 2020年第2期15卷 361-368页

作者： Hyun Jin Park Ting Ting Zhao Seung Hwan Kim Chong Kil Lee Bang Yeon Hwang kyung Eun Lee Myung koo Lee Department of Pharmacy College of PharmacyChungbuk National UniversityCheongjuRepublic of Korea 2Research Center for Bioresource and Health College of PharmacyChungbuk National UniversityCheongjuRepublic of Korea Department of Social Physical Education Songwon UniversityGwangjuRepublic of Korea

Gynostemma(G.) pentaphyllum(Cucurbitaceae) contains various bioactive gypenosides. Ethanol extract from G. pentaphyllum(GP-EX) has been shown to have ameliorative effects on the death of dopaminergic neurons in animal models of Parkinson’s disease(PD) induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-and 6-hydroxydopamine. PD patients exhibit multiple symptoms, so PD-related research should combine neurotoxin models with genetic models. In the present study, we investigated the ameliorative effects of GP-EX, including gypenosides, on the cell death of dopaminergic neurons in the midbrain of A53 T α-synuclein transgenic mouse models of PD(A53 T). Both GP-EX and gypenosides at 50 mg/kg per day were orally administered to the A53 T mice for 20 weeks.α-Synuclein-immunopositive cells and α-synuclein phosphorylation were increased in the midbrain of A53 T mice, which was reduced following treatment with GP-EX. Treatment with GP-EX modulated the reduced phosphorylation of tyrosine hydroxylase, extracellular signal-regulated kinase(ERK1/2), Bcl-2-associated death promoter(Bad) at Ser112, and c-Jun N-terminal kinase(JNK1/2) due to α-synuclein overexpression. In the A53 T group, GP-EX treatment prolonged the latency of the step-through passive avoidance test and shortened the transfer latency of the elevated plus maze test. Gypenosides treatment exhibited the effects and efficacy similar to those of GP-EX. Taken together, GP-EX, including gypenosides, has ameliorative effects on dopaminergic neuronal cell death due to the overexpression of α-synuclein by modulating ERK1/2, Bad at Ser112, and JNK1/2 signaling in the midbrain of A53 T mouse model of PD. Further studies are needed to investigate GP-EX as a treatment for neurodegenerative synucleinopathies, including PD. This study was approved by the Animal Ethics Committee of Chungbuk National University(approval No. CBNUA-956-16-01) on September 21, 2016.

关键词： A53T α-synuclein genetic mice ERK1/2 gynostemma pentaphyllum gypenosides Parkinson’s disease retention transfer latency time

Dynamic Friction Control Using Dynamic Structured RFNN and Friction Parameter Estimator

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Journal of Measurement Science and Instrumentation 2011年第2期2卷 191-194页

作者： Seong-ik HAN Kwon-soon LEE Dae-yeon YEO Sang-ok HAN kyung-wan koo Dept. of Electrical Engineering Dong-A Univsersity Busan 604-714 Korea Dept. of Electrical Engineering Chungnam National University Cheonan 305- 764 Korea Dept. of Defense Science of Technology Hoseo University Cheonan 330-713 Korea

A nonlinear dynamic friction control is dealt with using dynamic friction observer and intelligent cantrol. The adaptive dynamic friction obsrver based on the LuGre friction is proposed to estimate the friction parameters and a directly friction state variable The dynamic structured Fuzzy Neural Network （RFNN） is designed to give additional robustness to the cantrol system under the presence of the friction model uncertainty. A proposed composite cantrol scheme is applied to the position tracking control of the servo systen. The performances of the proposed friction observer and the friction controller are demonstrated by simulation.

关键词： LuGre friction model adaptive friction observer dynamic structured RFNN servo system control

Pathology and molecular characterization of recent Leucocytozoon caulleryi cases in layer flocks

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The Journal of Biomedical Research 2016年第6期30卷 517-524页

作者： Hae Rim Lee Bon-Sang koo Eun-ok Jeon Moo-Sung Han kyung-Cheol Min Seung Baek Lee Yeonji Bae In-Pil Mo Avian Disease Laboratory College of Veterinary MedicineChungbuk National University Division of Basic Research Bureau of Ecological ResearchNational Institute of Ecology

Leucocytozoonosis was found in three layer farms in chickens with suspected fatty liver or fatty liver hemorrhagic syndrome in Korea between 2009 and *** layer chicken flocks showed both mortality and decreased egg production for one or two weeks when they were between 59 and 82 weeks *** the necropsy,the most prominent gross lesions were found in the liver,which was enlarged,had a fragile texture,exhibited yellowish discolorations,and had various hemorrhagic *** reactions associated with megaloschizonts specific for Leucocytozoon caulleryi were prominent upon microscopic examination of the liver without significant *** addition,the ovaries and uterus were the most affected organs for Leucocytozoon caulleryi multiplication,which led to decreased egg *** studies with formalin-fixed,paraffin-embedded tissues were performed in search of a partial region of the cytochrome b gene for hemosporidian *** on these results,the causal agent was determined to be closely related to Leucocytozoon caulleryi reported in Japan and *** this study,we describe recently re-occurring leucocytozoonosis in layer chickens,which required histopathology for disease *** prevent outbreaks and maintain chicken health and egg production,layer chickens need to be monitored for symptoms of leucocytozoonosis.

关键词： chicken leucocytozoonosis Leucocytozoon caulleryi layer chicken flocks histopathology megaloschizont

Clinical significance of MET gene amplification in metastatic or locally advanced gastric cancer treated with first-line fluoropyrimidine and platinum combination chemotherapy

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Chinese Journal of Cancer Research 2019年第4期31卷 620-631页

作者： Seyoung Seo Min-Hee Ryu Baek-Yeol Ryoo Yangsoon Park Young Soo Park Young-Soon Na Chae-Won Lee Ju-kyung Lee Yoon-koo Kang Departments of Oncology Asan Medical CenterUniversity of Ulsan College of MedicineSeoul 05505Republic of Korea Department of Pathology Asan Medical CenterUniversity of Ulsan College of MedicineSeoul 05505Republic of Korea Asan Institute for Life Science Asan Medical CenterUniversity of Ulsan College of MedicineSeoul 05505Republic of Korea

Objective: To investigate the clinical significance of MET gene amplification in patients with gastric cancer in the palliative ***: MET amplification was assessed using fluorescence in situ hybridization(FISH) in 50 patients and quantitative polymerase chain reaction(qPCR) in 326 patients;259 patients treated with first-line fluoropyrimidine and platinum were included for survival ***: The results of FISH and qPCR indicated that the c-MET/CEP7 ratio was correlated with gene copy number. The optimal cutoff value for the copy number using qPCR to detect MET gene amplification with FISH was 5(κ=0.778, P5 detected by qPCR. MET-amplified gastric cancer was associated with an Eastern Cooperative Oncology Group(ECOG) performance status(PS) score of ≥2(33.3% vs. 10.5% P=0.007), peritoneal metastasis(76.2% vs. 46.2%, P=0.008), and elevated bilirubin levels(28.6% vs. 7.3%, P=0.006). The median overall survival(OS) and progression-free survival(PFS) were 11.9 and 5.6 months, respectively. MET-amplified gastric cancer was not associated with survival outcomes [hazard ratio(HR)=0.68, 95% confidence interval(95% CI): 0.35-1.32,P=0.254 for PFS;HR=0.68, 95% CI: 0.35-1.32, P=0.251 for OS].Conclusions: qPCR can be used to detect MET gene amplification. MET amplification was not a predictor of poor prognosis in patients with metastatic or unresectable gastric cancer.

关键词： MET amplification advanced gastric cancer prognosis quantitative real-time polymerase chain reaction

Ssu72 is a T-cell receptor-responsive modifier that is indispensable for regulatory T cells

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Cellular & Molecular Immunology 2021年第6期18卷 1395-1411页

作者： Jin-Kwan Lee Seo-Young koo Hye-Mi Nam Jee-Boong Lee Jiwon Ko kyung-Mo Kim Eun-Ji Park Tae Jin Kim Ho Lee Heounjeong Go Chang-Woo Lee Research Institute Curogen TechnologySuwonSouth Korea Department of Molecular Cell Biology Samsung Medical CenterSungkyunkwan University School of MedicineSuwonSouth Korea MOGAM Institute for Biomedical Research GyeonggiSouth Korea Department of Pathology Asan Medical CenterUniversity of Ulsan College of MedicineSeoulSouth Korea Asan Institute for Life Sciences Asan Medical CenterUniversity of Ulsan College of MedicineSeoulSouth Korea Department of Immunology Sungkyunkwan University School of MedicineSeoulSouth Korea Department of Cancer Biomedical Science Graduate School of Cancer Science and PolicyResearch InstituteNational Cancer CenterGyeonggiSouth Korea

The homeostatic balance between effector T cells and regulatory T cells(Tregs)is crucial for adaptive immunity;however,epigenetic programs that inhibit phosphorylation to regulate Treg development,peripheral expression,and suppressive activity are ***,we found that the Ssu72 phosphatase is activated by various T-cell receptor signaling pathways,including the T-cell receptor and IL-2R pathways,and localizes at the cell *** of Ssu72 in T cells disrupts CD4+T-cell differentiation into Tregs in the periphery via the production of high levels of the effector cytokines IL-2 and IFNγ,which induce CD4+T-cell activation and differentiation into effector cell *** also found a close correlation between downregulation of Ssu72 and severe defects in mucosal tolerance in ***,Ssu72 forms a complex with PLCγ1,which is an essential effector molecule for T-cell receptor signaling as well as Treg development and ***72 deficiency impairs PLCγ1 downstream signaling and results in failure of Foxp3 ***,our studies show that the Ssu72-mediated cytokine response coordinates the differentiation and function of Treg cells in the periphery.

关键词： Ssu72 Regulatory T cells FoxP3 T cell receptor Autoimmunity