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Metabologenomics and network pharmacology to understand the molecular mechanism of cancer research

World Journal of Clinical Cases 2024年第3期12卷 474-478页

作者： Yusuf Tutar Department of Basic Pharmaceutical Sciences Faculty of PharmacyDivision of BiochemistryUniversity of Health SciencesIstanbul 34668Turkey Health Sciences Faculty Recep Tayyip Erdogan UniversityRize 53350Turkey Molecular Oncology division Health Sciences InstitutesUniversity of Health SciencesIstanbul 34668Turkey Molecular Medicine division Health Sciences InstitutesUniversity of Health SciencesIstanbul 34668Turkey

In this editorial I comment on the article“Network pharmacological and molecular docking study of the effect of Liu-Wei-Bu-Qi capsule on lung cancer”published in the recent issue of the World Journal of Clinical Cases 2023 November 6;11(31):*** all living forms are able to manufacture particular chemicals-metabolites that enable them to differentiate themselves from one another and to overcome the unique obstacles they encounter in their natural *** methods for chemical warfare,communication,nutrition acquisition,and stress prevention are made possible by these specialized *** is a popular technique for collecting direct mea-surements of metabolic activity from many biological ***,con-fusing metabolite identification is a typical issue,and biochemical interpretation is frequently constrained by imprecise and erroneous genome-based estimates of enzyme *** annotation and gene integration uses a biochemical reaction network to obtain a metabolite-gene association so called *** network uses an approach that emphasizes metabolite-gene consensus via biochemical *** metabolomics and genomics data is ***,computer networking proposes that using meta-bolomics data may improve annotations in sequenced species and provide testable hypotheses for specific biochemical *** The genome and metabolites of biological organisms are not fully characterized with current ***,increasing high-throughput metabolomics and genomics data provide promising generation of paired data sets to understand the molecular mechanism of biochemical processes as well as determining targets for pharmaceutical drug *** network infrastructures to integrate omics analysis can provide molecular mechanism of biochemical ***,clinical data may be integrated to gene expression–metabolite expression by system genetics appr

关键词： Network pharmacology Metabologenomics Genome Pathways Cancer

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shinyTempSignal:an R shiny application for exploring temporal and other phylogenetic signals

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Journal of genetics and Genomics 2024年第7期51卷 762-768页

作者： Li Zhan Xiao Luo Wenqin Xie Xuan-An Zhu Zijing Xie Jianfeng Lin Lin Li Wenli Tang Rui Wang Lin Deng Yufan Liao Bingdong Liu Yantong Cai Qianwen Wang Shuangbin Xu Guangchuang Yu Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong 510515China Faculty of Computers Guangdong University of TechnologyGuangzhouGuangdong 510006China Ubigene Biosciences Co. Ltd.GuangzhouGuangdong 510530China State Key Laboratory of applied Microbiology Southern China Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Open Laboratory of Applied MicrobiologyGuangdong Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

The molecular clock model is fundamental for inferring species divergence times from molecular ***,its direct application may introduce significant biases due to sequencing errors,recombination events,and inaccurately labeled sampling *** accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous ***,while not all branches of a phylogenetic tree may exhibit a clear temporal signal,specific branches may still adhere to the assumptions,with varying evolutionary *** a relaxed molecular clock model better aligns with the complexities of *** root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic *** its utility,there remains a lack of corresponding software implementations for broader *** address this gap,we present shinyTempSignal,an interactive web application implemented with the shiny framework,available as an R package and publicly accessible at https://***/YuLab-SMU/*** tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed *** extending the root-to-tip regression method to diverse signals,shinyTempSignal helps in the detection of evolving features or traits,thereby laying the foundation for deeper insights and subsequent analyses.

关键词： Molecular clock Root-to-tip regression Temporal signal Phylogenetic signal

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Spirotetramat reduces fitness of the spotted-wing Drosophila,Drosophila suzukii

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Insect Science 2024年第4期31卷 1222-1230页

作者： Jing Yang Justin Flaven-Pouchon Yiwen Wang Bernard Moussian Section of Animal genetics Interfaculty Institute of Cell BiologyUniversity of TübingenTübingenGermany School of Pharmaceutical Science and Technology Tianjin UniversityTianjinChina INRAE CNRSUniversitéCôte d'AzurInstitut Sophia AgrobiotechSophia AntipolisFrance

With climate change,the spotted-wing Drosophila(SWD,Drosophila suzukii)invades a great number of fruit production regions worldwide.A plethora of insecticides are being applied for management of this *** expected,SWD develops resistance against some potent insecticides or is rather insensitive to some ***,there is an urgent need to identify and characterize alternative insecticides to control SWD ***,we have studied the effects of the orally applied inhibitor of the fatty acid synthesis pathway spirotetramat on SWD fitness with respect to fecundity and surface barrier function at different *** our experiments,we applied spirotetramat mixed with baker's yeast and showed that females and males were not repelled by effective concentrations of this *** found that spirotetramat,by trend,lowers egg numbers laid by fed *** eggs rapidly desiccate,and only a few larvae *** is lethal to larvae and reduces survival of adult flies under low-humidity *** together,based on our data,we propose to use yeast supplemented with spirotetramat and additional SWD-specific attractants in traps in non-crop areas in order to eradicate SWD populations before they infest crop production sites.

关键词： desiccation Drosophila suzuki insecticide lipids

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Phase structures and critical behavior of rational non-linear electrodynamics Anti de Sitter black holes in Rastall gravity

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Communications in Theoretical Physics 2024年第4期76卷 134-152页

作者： Yassine Sekhmani Dhruba Jyoti Gogoi Ratbay Myrzakulov Javlon Rayimbaev Ratbay Myrzakulov Eurasian International Centre for Theoretical Physics Astana 010009Kazakhstan L.N.Gumilyov Eurasian National University Astana 010008Kazakhstan Department of Physics Moran CollegeMoranhatCharaideo 785670AssamIndia Theoretical Physics division Centre for Atmospheric StudiesDibrugarh UniversityDibrugarh 786004AssamIndia New Uzbekistan University Movarounnahr Str.1Tashkent 100000Uzbekistan University of Tashkent for applied Sciences Gavhar Str.1Tashkent 100149Uzbekistan National University of Uzbekistan Tashkent 100174Uzbekistan

This research paper presents a black hole solution with a rational nonlinear electrodynamics source within the Rastall gravity *** paper analyzes the thermodynamic properties of the solution in normal phase space and explores its critical *** phase structure is examined using the extended first law of thermodynamics,with the cosmological constantΛserving as pressure *** isotherms exhibit van der Waals behavior at small values of horizon r_(+).The paper also investigates the Gibbs free energy behavior and finds two critical points with two pressures where the re-entrant phase transition occurs and *** also explore the prevalent microstructure of black holes in Ruppeiner geometry,uncovering significant deviations in the nature of particle interactions from conventional ***,the thermodynamic geometry is analyzed using the Ruppeiner formalism,with the normalized Ricci scalar indicating possible point-phase transitions of the heat capacity,and the normalized extrinsic curvature having the same sign as the normalized Ricci *** three-phase transitions of the heat capacity are those that we find for the normalized Ruppeiner ***,there is an absolute correspondence.

关键词： Rastall gravity biack hole Phase structures

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Genome-wide CRISPR screening identifies critical role of phosphatase and tensin homologous (PTEN) in sensitivity of acute myeloid leukemia to chemotherapy

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2024年第8期25卷 700-710页

作者： Liming LIN Jingjing TAO Ying MENG Yichao GAN Xin HE Shu LI Jiawei ZHANG Feiqiong GAO Dijia XIN Luyao WANG Yili FAN Boxiao CHEN Zhimin LU Yang XU Department of Hematology the Second Affiliated HospitalZhejiang University School of MedicineHangzhou 310009China Zhejiang Provincial Key Laboratory of Pancreatic Disease the First Affiliated Hospital and Institute of Translational MedicineCancer CenterZhejiang University School of MedicineHangzhou 310029China Institute of genetics Zhejiang UniversityHangzhou 310058China division of Hematopoietic Stem Cell&Leukemia Research Beckman Research Institute of City of HopeDuarteCA 91010USA Department of Hematology Shanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai 200025China

Although significant progress has been made in the development of novel targeted drugs for the treatment of acute myeloid leukemia(AML)in recent years,chemotherapy still remains the mainstay of treatment and the overall survival is poor in most ***,we demonstrated the antileukemia activity of a novel small molecular compound NL101,which is formed through the modification on bendamustine with a suberanilohydroxamic acid(SAHA)***101 suppresses the proliferation of myeloid malignancy cells and primary AML *** induces DNA damage and caspase 3-mediated apoptosis.A genome-wide clustered regularly interspaced short palindromic repeats(CRISPR)library screen revealed that phosphatase and tensin homologous(PTEN)gene is critical for the regulation of cell survival upon NL101 *** knockout or inhibition of PTEN significantly reduced NL101-induced apoptosis in AML and myelodysplastic syndrome(MDS)cells,accompanied by the activation of protein kinase B(AKT)signaling *** inhibition of mammalian target of rapamycin(mTOR)by rapamycin enhanced the sensitivity of AML cells to NL101-induced cell *** findings uncover PTEN protein expression as a major determinant of chemosensitivity to NL101 and provide a novel strategy to treat AML with the combination of NL101 and rapamycin.

关键词： Genome-wide clustered regularly interspaced short palindromic repeats(CRISPR)library Phosphatase and tensin homologous(PTEN) Rapamycin Acute myeloid leukemia(AML) Chemotherapy

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Self-supported VO_(2)on polydopamine-derived pyroprotein-based fibers for ultrastable and flexible aqueous zinc-ion batteries

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Carbon Energy 2024年第7期6卷 1-13页

作者： Jeong Seok Yeon Sul Ki Park Shinik Kim Santosh VMohite Won Il Kim Gun Jang Hyun-Seok Jang Jiyoung Bae Sang Moon Lee Won GHong Byung Hoon Kim Yeonho Kim Ho Seok Park School of Chemical Engineering College of EngineeringSungkyunkwan UniversityGyeonggi-doRepublic of Korea Department of Engineering University of CambridgeCambridgeUK Department of applied Chemistry Konkuk UniversityChungjuRepublic of Korea Department of Chemistry Ulsan National Institute of Science and Technology(UNIST)College of Natural SciencesUlsanRepublic of Korea Department of Physics Incheon National UniversityIncheonRepublic of Korea Intelligent Sensor Convergence Research Center Incheon National UniversityIncheonRepublic of Korea Institute of Basic Science Incheon National UniversityIncheonRepublic of Korea division of Material Analysis and Research Korea Basic Science InstituteDaejeonRepublic of Korea

A conventional electrode composite for rechargeable zinc-ion batteries(ZIBs)includes a binder for strong adhesion between the electrode material and the current ***,the introduction of a binder leads to electrochemical inactivity and low electrical conductivity,resulting in the decay of the capacity and a low rate *** present a binder-and conducting agent-free VO_(2)composite electrode using in situ polymerization of dopamine on a flexible current collector of pyroprotein-based *** as-fabricated composite electrode was used as a substrate for the direct growth of VO_(2)as a self-supported form on polydopamine-derived pyroprotein-based fibers(pp-fibers@VO_(2)(B)).It has a high conductivity and flexible nature as a current collector and moderate binding without conventional binders and conducting agents for the VO_(2)(B)*** addition,their electrochemical mechanism was *** energy storage is induced by Zn^(2+)/H^(+)coinsertion during discharging,which can be confirmed by the lattice expansion,the formation of by-products including Zn_(x)(OTf)_(y)(OH)_(2x−y)·nH_(2)O,and the reduction of V^(4+)to V^(3+).Furthermore,the assembled Zn//pp-fibers@VO_(2)(B)pouch cells have excellent flexibility and stable electrochemical performance under various bending states,showing application possibilities for portable and wearable power sources.

关键词： aqueous battery binder free conducting agent‐free flexible electrode zinc‐ion battery

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An improved interval model updating method via adaptive Kriging models

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applied Mathematics and Mechanics(English Edition) 2024年第3期45卷 497-514页

作者： Sha WEI Yifeng CHEN Hu DING Liqun CHEN Shanghai Key Laboratory of Mechanics in Energy Engineering Shanghai Frontier Science Center of MechanoinformaticsShanghai Institute of Applied Mathematics and MechanicsSchool of Mechanics and Engineering ScienceShanghai UniversityShanghai 200072China Shanghai Institute of Aircraft Mechanics and Control Shanghai 200092China

Interval model updating(IMU)methods have been widely used in uncertain model updating due to their low requirements for sample ***,the surrogate model in IMU methods mostly adopts the one-time construction *** makes the accuracy of the surrogate model highly dependent on the experience of users and affects the accuracy of IMU ***,an improved IMU method via the adaptive Kriging models is *** method transforms the objective function of the IMU problem into two deterministic global optimization problems about the upper bound and the interval diameter through universal grey *** optimization problems are addressed through the adaptive Kriging models and the particle swarm optimization(PSO)method to quantify the uncertain parameters,and the IMU is *** the construction of these adaptive Kriging models,the sample space is gridded according to sensitivity *** sampling is then performed in key subspaces based on the maximum mean square error(MMSE)*** interval division coefficient and random sampling coefficient are adaptively adjusted without human interference until the model meets accuracy *** effectiveness of the proposed method is demonstrated by a numerical example of a three-degree-of-freedom mass-spring system and an experimental example of a butted cylindrical *** results show that the updated results of the interval model are in good agreement with the experimental results.

关键词： interval model updating(IMU) non-probabilistic uncertainty adaptive Kriging model surrogate model grey number

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Brillouin Klein space and half-turn space in three-dimensional acoustic crystals

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Science Bulletin 2024年第13期69卷 2050-2058页

作者： Zhenxiao Zhu Linyun Yang Jien Wu Yan Meng Xiang Xi Bei Yan Jingming Chen Jiuyang Lu Xueqin Huang Weiyin Deng Ce Shang Perry Ping Shum Yihao Yang Hongsheng Chen Kexin Xiang Gui-Geng Liu Zhengyou Liu Zhen Gao State Key Laboratory of Optical Fiber and Cable Manufacture Technology Department of Electronic and Electrical EngineeringSouthern University of Science and TechnologyShenzhen 518055China School of Physics and Optoelectronics South China University of TechnologyGuangzhou 510640China Key Laboratory of Artificial Micro-and Nanostructures of Ministry of Education and School of Physics and Technology Wuhan UniversityWuhan 430072China King Abdullah University of Science and Technology(KAUST) Physical Science and Engineering Division(PSE)Thuwal 23955-6900Saudi Arabia Interdisciplinary Center for Quantum Information State Key Laboratory of Modern Optical InstrumentationZJU-Hangzhou Global Science and Technology Innovation CenterCollege of Information Science and Electronic EngineeringZJU-UIUC InstituteZhejiang UniversityHangzhou 310027China division of Physics and applied Physics School of Physical and Mathematical SciencesNanyang Technological UniversitySingapore 637371Singapore Institute for Advanced Studies Wuhan UniversityWuhan 430072China

The Bloch band theory and Brillouin zone(BZ)that characterize wave-like behaviors in periodic mediums are two cornerstones of contemporary physics,ranging from condensed matter to topological *** theoretical breakthrough revealed that,under the projective symmetry algebra enforced by artificial gauge fields,the usual two-dimensional(2D)BZ(orientable Brillouin two-torus)can be fundamentally modified to a non-orientable Brillouin Klein bottle with radically distinct manifold ***,the physical consequence of artificial gauge fields on the more general three-dimensional(3D)BZ(orientable Brillouin three-torus)was so far ***,we theoretically discovered and experimentally observed that the fundamental domain and topology of the usual 3D BZ can be reduced to a non-orientable Brillouin Klein space or an orientable Brillouin half-turn space in a 3D acoustic crystal with artificial gauge *** experimentally identify peculiar 3D momentum-space non-symmorphic screw rotation and glide reflection symmetries in the measured band ***,we experimentally demonstrate a novel stacked weak Klein bottle insulator featuring a nonzero Z2 topological invariant and self-collimated topological surface states at two opposite surfaces related by a nonlocal twist,radically distinct from all previous 3D topological *** discovery not only fundamentally modifies the fundamental domain and topology of 3D BZ,but also opens the door towards a wealth of previously overlooked momentum-space multidimensional manifold topologies and novel gaugesymmetry-enriched topological physics and robust acoustic wave manipulations beyond the existing paradigms.

关键词： Momentum-space non-symmorphic symmetry Brillouin Klein space and half-turn space Acoustic Klein bottle insulator Self-collimated topological surface states

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Somatic CDKN2A copy number variations are associated with the prognosis of esophageal squamous cell dysplasia

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Chinese Medical Journal 2024年第8期137卷 980-989页

作者： Zhiyuan Fan Jing Zhou Yuan Tian Yu Qin Zhaojun Liu Liankun Gu Sanford M.Dawsey Wenqiang Wei Dajun Deng National Central Cancer Registry National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021China Key Laboratory of Carcinogenesis and Translational Research(MOE/Beijing) Division of EtiologyPeking University Cancer Hospital and InstituteBeijing 100142China division of Cancer Epidemiology and genetics National Cancer InstituteBethesdaMDUSA Collaborative Innovation Center for Cancer Personalized Medicine Nanjing Medical UniversityNanjingJiangsu 211166China

Background:Somatic copy number variations(SCNVs)in the CDKN2A gene are among the most frequent events in the dysplasia-carcinoma sequence of esophageal squamous cell ***,whether CDKN2A SCNVs are useful biomarkers for the risk stratification and management of patients with esophageal squamous cell dysplasia(ESCdys)is *** study aimed to investigate the characteristics and prognostic value of CDKN2A SCNVs in patients with mild or moderate(m/M)***:This study conducted a prospective multicenter study of 205 patients with a baseline diagnosis of m/M ESCdys in five high-risk regions of China(Ci County,Hebei Province;Yanting,Sichuan Province;Linzhou,Henan Province;Yangzhong,Jiangsu Province;and Feicheng,Shandong Province)from 2005 to *** DNA was extracted from paraffin biopsy samples and paired peripheral white blood cells from patients,and a quantitative polymerase chain reaction assay,P16-Light,was used to detect CDKN2A copy *** cumulative regression and progression rates of ESCdys were evaluated using competing risk ***:A total of 205 patients with baseline m/M ESCdys were *** proportion of ESCdys regression was significantly lower in the CDKN2A deletion cohort than in the diploid and amplification cohorts(18.8%[13/69]vs.35.0%[28/80]vs.51.8%[29/56],P<0.001).In the univariable competing risk analysis,the cumulative regression rate was statistically significantly lower(P=0.008),while the cumulative progression rate was higher(P=0.017)in ESCdys patients with CDKN2A deletion than in those without CDKN2A ***2A deletion was also an independent predictor of prognosis in ESCdys(P=0.004)in the multivariable ***:The results indicated that CDKN2A SCNVs are associated with the prognosis of ESCdys and may serve as potential biomarkers for risk stratification.

关键词： Somatic copy number variations Esophageal squamous cell carcinoma Esophageal neoplasms Squamous intraepithelial lesions DNA copy number variations Prognosis Prospective study

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microRNA-2184 orchestrates Mauthner-cell axon regeneration in zebrafish via syt3 modulation

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Journal of genetics and Genomics 2024年第9期51卷 911-921页

作者： Xinghan Chen Yueru Shen Zheng Song Xinliang Wang Huaitong Yao Yuan Cai Zi-Ang Zhao Bing Hu Hefei National Research Center for Physical Sciences at the Microscale University of Science and Technology of ChinaHefeiAnhui 230026China The First Affiliated Hospital of USTC Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui 230026China Center for Advanced Interdisciplinary Science and Biomedicine of IHM Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui 230026China

MicroRNAs(miRNAs)play a significant role in axon regeneration following spinal cord ***,the functions of numerous miRNAs in axon regeneration within the central nervous system(CNS)remain largely ***,we elucidate the positive role of microRNA-2184(miR-2184)in axon regeneration within zebrafish Mauthner cells(M-cells).The upregulation of miR-2184 in a single M-cell can facilitate axon regeneration,while the specific sponge-induced silencing of miR-2184 leads to impeded *** show that syt3,a downstream target of miR-2184,negatively regulates axon regeneration,and the regeneration suppression modulated by syt3 depends on its binding to Ca2+.Furthermore,pharmacological stimulation of the cAMP/PKA pathway suggests that changes in the readily releasable pool may affect axon *** data indicate that miR-2184 promotes axon regeneration of M-cells within the CNS by modulating the downstream target syt3,providing valuable insights into potential therapeutic strategies.

关键词： Axon regeneration Axon ablation miR-2184 syt3 Readily releasable pool

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