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CpG Island Definition and Methylation Mapping of the T2T-YAO Genome

GENOMICS PROTEOMICS & BIOINFORMATICS 2024年第2期22卷 qzae009页

作者： xiao, Ming wei, Rui yu, Jun Gao, Chujie Yang, Fengyi Zhang, Le Sichuan Univ Coll Comp Sci Chengdu 610065 Peoples R China Univ Chinese Acad Sci Hangzhou Inst Adv Study Sch Life Sci Key Lab Syst Hlth Sci Zhejiang Prov Hangzhou 310024 Peoples R China Chinese Acad Sci Beijing Inst Genom CAS Key Lab Genome Sci & Informat Beijing 100101 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China

Precisely defining and mapping all cytosine (C) positions and their clusters, known as CpG islands (CGIs), as well as their methylation status, are pivotal for genome-wide epigenetic studies, especially when population-centric reference genomes are ready for timely application. Here, we first align the two high-quality reference genomes, T2T-YAO and T2T-CHM13, from different ethnic backgrounds in a base-by-base fashion and compute their genome-wide density-defined and position-defined CGIs. Second, by mapping some representative genome-wide methylation data from selected organs onto the two genomes, we find that there are about 4.7%-5.8% sequence divergency of variable categories depending on quality cutoffs. Genes among the divergent sequences are mostly associated with neurological functions. Moreover, CGIs associated with the divergent sequences are significantly different with respect to CpG density and observed CpG/expected CpG (O/E) ratio between the two genomes. Finally, we find that the T2T-YAO genome not only has a greater CpG coverage than that of the T2T-CHM13 genome when whole-genome bisulfite sequencing (WGBS) data from the European and American populations are mapped to each reference, but also shows more hyper-methylated CpG sites as compared to the T2T-CHM13 genome. Our study suggests that future genome-wide epigenetic studies of the Chinese populations rely on both acquisition of high-quality methylation data and subsequent precision CGI mapping based on the Chinese T2T reference.

关键词： T2T-YAO Position-defined CpG island Density-defined CpG island DNA methylation Genome analysis DNA METHYLATION SURVIVAL DATABASE GENES

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Pituitary metastasis from lung adenocarcinoma:A case report

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World Journal of Clinical Cases 2024年第15期12卷 2597-2605页

作者： Qing Wang xiao-wei Liu Ke-yu Chen Department of Critical Care Medicine Chengdu First People’s HospitalChengdu 610000Sichuan ProvinceChina Department of Neurosurgery Chengdu Second People's HospitalChengdu 610017Sichuan ProvinceChina Department of the First Clinical Medical College Lanzhou UniversityLanzhou 730000Gansu ProvinceChina Evidence Based Medicine Center School of Basic Medical SciencesLanzhou UniversityLanzhou 730000Gansu ProvinceChina

BACKGROUND Pituitary gland metastasis is an unusual event,and pituitary metastasis from lung adenocarcinoma is extremely rare and associated with poor *** date,approximately 15 cases have been *** SUMMARY Here,we present the case of a 64-year-old woman with pituitary metastasis derived from lung adenocarcinoma,which was difficult to distinguish from other sellar *** patient presented to the neurosurgery clinic with blurred vision and intermittent *** hospitalization,brain computed tomography(CT)and magnetic resonance imaging revealed a pituitary *** CT revealed irregular nodules in the basal segment of the lower lobe of the left lung,which were likely lung *** emission tomography-CT revealed a carbohydrate metabolism tumor in the lungs and sellar region,which was considered *** pathological examination of the sellar tumor revealed lung *** Excision of pituitary metastases combined with radiotherapy and chemotherapy should be a priority treatment for patients with pituitary metastasis.

关键词： Pituitary metastasis Lung adenocarcinoma Prolactin Sellar region tumors Case report

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Identification and functional analysis of CG3526 in spermatogenesis of Drosophila melanogaster

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Insect Science 2024年第1期31卷 79-90页

作者： Qihao Hu Yanhong xiao Runnan wei Ting Tang Liang Wen yuzhen Lu xiao-Qiang yu Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology Guangzhou Key Laboratory of Insect Development Regulation and Application ResearchInstitute of Insect Science and TechnologySchool of Life SciencesSouth China Normal UniversityGuangzhou510631 China

Spermatogenesis is a critical part of reproduction in insects;however,its molecular mechanism is still largely *** this study,we identified a testis-specific gene CG3526 in Drosophila *** analysis showed that CG3526 contains a zinc binding domain and 2 C2H2 type zinc fingers,and it is clustered to the vertebrate really interesting new gene(RING)family E3 ubiquitin-protein *** CG3526 was knocked down by RNA interference(RNAi),the testis became much smaller in size,and the apical tip exhibited a sharp and thin end instead of the blunt and round shape in the control *** importantly,compared to the control flies,only a few mature sperm were present in the seminal vesicle of C587-Gal4>CG3526 RNAi *** staining of the testis from CG3526 RNAi flies showed that the homeostasis of testis stem cell niche was disrupted,cell distribution in the apical tip was scattered,and the process of spermatogenesis was not ***,we found that the phenotype of CG3526 RNAi flies’testis was similar to that of testis of Stat92E RNAi flies,the expression level of CG3526 was significantly downregulated in the Stat92EF06346 mutant flies,and the promoter activity of CG3526 was upregulated by *** together,our results indicated that CG3526 is a downstream effector gene in the JAK-STAT signaling pathway that plays a key role in the spermatogenesis of Drosophila.

关键词： CG3526 JAK-STAT spermatogenesis STAT92E testis

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Physics of cavitation near particles

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Journal of Hydrodynamics 2024年第1期36卷 102-118页

作者： Jia-xin yu xiao-yu Wang Jun-wei Shen Jin-sen Hu Xiang-qing Zhang Da-qing He yu-ning Zhang Key Laboratory of Power Station Energy Transfer Conversion and System(Ministry of Education) School of Energy Power and Mechanical EngineeringNorth China Electric Power UniversityBeijing102206China

The combined effect of cavitation and silt abrasion presents a great challenge and threat to secure the operation and the efficiency of hydraulic machineries working in sediment-laden *** present paper critically reviews the current research progress on the interaction mechanisms of the bubbles and the ***,the analytical models including boundary treatment methods for predicting the jet dynamics of the bubble collapse near particles are ***,the bubble collapsing dynamics,jet dynamics and shock wave characteristics near particles are revealed both experimentally and ***,the bubble-particle-wall system is investigated with a focus on microjets.

关键词： Cavitation bubble particle jet shock wave

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Evaluating effectiveness and safety of combined percutaneous transhepatic gallbladder drainage and laparoscopic cholecystectomy in acute cholecystitis patients:Meta-analysis

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World Journal of Gastrointestinal Surgery 2024年第5期16卷 1407-1419页

作者： yu Li wei-Ke xiao xiao-Jun Li Hui-yuan Dong Department of General Surgery No.942 Hospital of PLAYinchuan 750004Ningxia Hui Autonomous RegionChina

BACKGROUND Acute cholecystitis(AC)is a common disease in general *** cholecystectomy(LC)is widely recognized as the"gold standard"surgical procedure for treating *** low-risk patients without complications,LC is the recommended treatment plan,but there is still controversy regarding the treatment strategy for moderate AC patients,which relies more on the surgeon's experience and the medical platform of the visiting *** transhepatic gallbladder puncture drainage(PTGBD)can effectively alleviate gallbladder inflammation,reduce gallbladder wall edema and adhesion around the gallbladder,and create a"time window"for elective *** To compare the clinical efficacy and safety of LC or PTGBD combined with LC for treating AC patients,providing a theoretical basis for choosing reasonable surgical methods for AC *** In this study,we conducted a clinical investigation regarding the combined use of PTGBD tubes for the treatment of gastric cancer patients with *** performed searches in the following databases:PubMed,Web of Science,EMBASE,Cochrane Library,China National Knowledge Infrastructure,and Wanfang *** search encompassed literature published from the inception of these databases to the ***,relevant data were extracted,and a meta-analysis was conducted using RevMan 5.3 *** A comprehensive analysis was conducted,encompassing 24 studies involving a total of 2564 *** patients were categorized into two groups:1371 in the LC group and 1193 in the PTGBD+LC *** outcomes of the meta-analysis revealed noteworthy disparities between the PTGBD+LC group and the LC group in multiple dimensions:(1)Operative time:Mean difference(MD)=17.51,95%CI:9.53-25.49,P<0.01;(2)Conversion to open surgery rate:Odds ratio(OR)=2.95,95%CI:1.90-4.58,P<0.01;(3)Intraoperative bleeding loss:MD=32.27,95%CI:23.03-41.50,P<0.01;(4)Postoperative hospital stay:MD=1.44,95%CI:0.14-2.73,P=0.03;(5)Overall posto

关键词： Acute cholecystitis Laparoscopic cholecystectomy Percutaneous transhepatic gallbladder drainage Metaanalysis Efficacy

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Sensing properties and mechanisms of LaF_(3)-Co_(3)O_(4) nanorods for low-concentration methanol detection

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Rare Metals 2024年第5期43卷 2193-2204页

作者： xiao-Xi He Hong-Feng Chai Yi-Wen Zhou Ke-wei Liu Ze-Xin yu Chao Zhang College of Mechanical Engineering Yangzhou UniversityYangzhou225127China Institutefor Manufacturing Technologies of Ceramic Components and Composites(IMTCCC) University of Stuttgart70569 StuttgartGermany

Methanol is one of the characteristic gases that distinguish between healthy individuals and lung cancer(LC)lesions in exhaled human *** concentration in exhaled breath is generally below one part per million(1×10^(-6)).The second-phase composite is widely regarded as one of the methods to improve the gas-sensing perfor-mance of metal oxide semiconductor(MOS)*** this study,LaF_(3)-Co_(3)O_(4) was synthesized by a simple hydrothermal method to enhance its low-concentration methanol gas-sensing performance.5 at%LaF_(3)-Co_(3)O_(4) nanorods exhibited excellent methanol detection performance,including a wider linear detection concentration range(0.2×10^(-6)~5×10^(-6)),a response value exceeding 4.0 for 1×10^(-6)methanol at 275°C and 75%relative humidity(RH),long-term stability(maximum deviation within 15%over 2 weeks),and excellent *** mechanism of performance enhancement was studied using various techniques,and density functional *** special spinel structure of Co_(3)O_(4),the high ionic migration of F-in LaF_(3),the larger specific surface area of 5 at%LaF_(3)-Co_(3)O_(4) nanorods,and the generated crystal defects all explain the excellentmethanol gas-sensing *** work provides a novel route to prepare MOS composite materials for low-concentration methanol gas detection.

关键词： Gas sensor LaF_(3) Co_(3)O_(4) Methanol Lung cancer

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A Bregman-Style Improved ADMM and its Linearized Version in the Nonconvex Setting:Convergence and Rate Analyses

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Journal of the Operations Research Society of China 2024年第2期12卷 298-340页

作者： Peng-Jie Liu Jin-Bao Jian Hu Shao xiao-Quan Wang Jia-wei Xu xiao-yu Wu School of Mathematics Jiangsu Center for Applied MathematicsChina University of Mining and TechnologyXuzhou 221116JiangsuChina School of Mathematics and Physics Center for Applied Mathematics of GuangxiGuangxi Minzu UniversityNanning 530006GuangxiChina Department of Civil and Environmental Engineering The Hong Kong Polytechnic UniversityHong KongChina School of Mathematics and Computational Science Xiangtan UniversityXiangtan 411105HunanChina

This work explores a family of two-block nonconvex optimization problems subject to linear *** first introduce a simple but universal Bregman-style improved alternating direction method of multipliers(ADMM)based on the iteration framework of ADMM and the Bregman ***,we utilize the smooth performance of one of the components to develop a linearized version of *** to the traditional ADMM,both proposed methods integrate a convex combination strategy into the multiplier update *** each proposed method,we demonstrate the convergence of the entire iteration sequence to a unique critical point of the augmented Lagrangian function utilizing the powerful Kurdyka–Łojasiewicz property,and we also derive convergence rates for both the sequence of merit function values and the iteration ***,some numerical results show that the proposed methods are effective and encouraging for the Lasso model.

关键词： Nonconvex optimization Alternating direction method of multipliers Kurdyka-Lojasiewicz property Convergence rate

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Elaborating strengthen mechanism of Pt-Ir solid solution superalloy at finite temperature

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Rare Metals 2024年第3期43卷 1243-1256页

作者： wei yu xiao-yu Chong yun-Xuan Zhou Meng-Di Gan Ying-Xue Liang Yan wei Ai-Min Zhang Chang-Yi Hu Xing-yu Gao Li Chen Hai-Feng Song Jing Feng Faculty of Materials Science and Engineering Kunming University of Science and TechnologyKunming650093China yunnan Precious Metals Laboratory Co.LTD Kunming650106China Laboratory of Computational Physics Institute of Applied Physics and Computational MathematicsBeijing100088China

Pt-Ir alloy is potential superalloys used above 1300℃because of their high strength and creep ***,the ductility of Pt-Ir alloy has rapidly deteriorated with the increase of Ir,resulting in poor *** work quantitatively evaluated the solid solution strengthening(SSS)and grain refinement strengthening(GRS)of Pt-Ir alloy using first-principles calculations combined with experimental ***,the stretching force constants in the second nearest neighbor region(SFC^(2nd))of pure Ir(193.7 eV·nm^(-2))are 3.40 times that of pure Pt(57.0 eV·nm^(-2)),i.e.,the interatomic interaction is greatly enhanced with the increase of Ir content,which leads to the decrease of ductility,and modulus misfit plays a dominant role in ***,the physical mechanisms responsible for the hardness(H_(V))of Pt-Ir alloy,using the power-law-scaled function of electron work function coupled SSS and GRS,are attributed to the electron redistribution caused by different Ir ***,a thorough assessment of the thermodynamic characteristics of Pt-Ir binary alloy was conducted,culminating in development of a mapping model that effectively relates enmposition,temperature and *** results revealed that the compressive strength incrcases with the Ir content,and the highest strength was observed in Pt_(0.25)Ir_(0.75).This study provides valuable insights into the Pt-Ir alloy system.

关键词： Elastic properties Phonon Solid solution strengthen Force constants CALPHAD

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Colonoscopy plays an important role in detecting colorectal neoplasms in patients with gastric neoplasms

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World Journal of Gastrointestinal Oncology 2024年第1期16卷 133-143页

作者： Xu-Rui Liu Ze-Lin Wen Fei Liu Zi-wei Li xiao-yu Liu wei Zhang Dong Peng Department of Gastrointestinal Surgery The First Affiliated Hospital of Chongqing Medical UniversityChongqing 400016China Department of Gastrointestinal Surgery Yongchuan Hospital of Chongqing Medical UniversityChongqing 402160China

BACKGROUND Gastric cancer(GC)and colorectal cancer(CRC)are the fifth and third most common cancer worldwide,***,GC is reported to have a potential predictive value for CRC,especially for advanced *** To evaluate the necessity of colonoscopy for gastric neoplasm(GN)*** Four databases,including PubMed,EMBASE,the Cochrane Library,and Ovid,were used to perform the search strategy on May 2,*** prevalence of colorectal neoplasms(CRN)and baseline characteristics were compared between the neoplasm group and the control *** variables are expressed as the mean difference and standard *** of categorical variables in the two groups are expressed as odds ratios(OR)and 95%confidence intervals(95%CIs).Subgroup analysis according to different kinds of GNs was conducted for more in-depth *** results of this study are represented by forest *** bias was evaluated by a funnel *** data analyses were performed by STATA SE 16.0 *** A total of 3018 patients with GNs and 3905 healthy controls(age and sex matched)were enrolled for *** comparing the prevalence of CRNs between the two groups,CRNs were detected significantly more frequently in GN patients than in controls(OR=1.69,95%CI=1.28 to 2.23,I^(2)=85.12%,P=0.00),especially in patients with GC(OR=1.80,95%CI=1.49 to 2.18,I^(2)=25.55%,P<0.1).Moreover,other risk factors including age(OR=1.08,95%CI=1.00 to 1.17,I^(2)=90.13%,P=0.00)and male sex(OR=2.31,95%CI=1.26 to 4.22,I^(2)=87.35%,P=0.00),were related to the prevalence of *** patients in the GN group,body mass index(BMI,OR=0.88,95%CI=0.80 to 0.98,I^(2)=0.00%,P=0.92)and smoking(OR=1.03,95%CI=1.01 to 1.05,I^(2)=0.00%,P=0.57)were protective and risk factors for CRNs,*** Patients are recommended to undergo colonoscopy when diagnosed with GNs,especially GC patients with a low BMI and a history of smoking.

关键词： Gastric neoplasm Gastric cancer Colorectal neoplasm Colonoscopy

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Dissolution kinetics and reaction mechanism of Al_(2)O_(3) in molten CaF_(2)-CaO-Al_(2)O_(3) slag

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Journal of Iron and Steel Research International 2024年第4期31卷 861-869页

作者： Yao-xin Du Yan-wu Dong Zhou-hua Jiang Ganna Stovpchenko yu-shuo Li Jun Huang Xin-wei Wang yu-xiao Liu School of Metallurgy Northeastern UniversityShenyang 110819LiaoningChina Key Laboratory of Ecological Metallurgy of Multimetallic Mineral Northeastern UniversityShenyang 110819LiaoningChina State Key Laboratory of Rolling and Automation Northeastern UniversityShenyang 110819LiaoningChina E.O.Paton Electric Welding Institute of the National Academy of Science of Ukraine Kiev 03115Ukraine

The dissolution behavior of Al_(2)O_(3) in molten CaF_(2)-CaO-Al_(2)O_(3) slag,a basic slag system of electroslag remelting process,was investigated by rotating cylinder method using corundum rods to simulate Al_(2)O_(3) inclusions in *** experimental results show that the dissolution rate of Al_(2)O_(3);rods in CaF_(2)-CaO-Al_(2)O_(3) slag increases with the increase in rotating speed and temperature,and the rate-controlling step is the mass transfer in the *** dissolution rate of Al_(2)O,in CaF_(2)-CaO-Al_(2)O_(3) slag increases with the increase in the ratio of CaO to Al_(2)O_(3),which is due to the increase in dissolution driving force and the decrease in slag *** apparent activation energy of the mass transfer of AlOs in slag C is calculated to be 222.86 kJ mol^(-1).During the dissolution of Al_(2)0,inclusions in the slag,it reacts with F in liquid slag at first,then reacts with CaO to form the intermediate compounds of xCaO-yAl_(2)O_(3) system,and finally dissolves in molten *** dissolution rate of Al_(2)O_(3) inclusions in CaF_(2)-CaO-Al_(2)O_(3) slag for electroslag remelting is positively correlated with the ratio of the dissolution driving force and slag viscosity,and the correlation coeficient is 2.487×10^(-11).

关键词： Inclusion Electroslag remelting Mass transfer:Dissolution rate-Dissolution driving force

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