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Hierarchical learning of gastric cancer molecular subtypes by integrating multi-modal DNA-level omics data and clinical stratification

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Quantitative Biology 2024年第2期12卷 182-196页

作者： Binyu Yang Siying Liu Jiemin Xie Xi Tang Pan Guan Yifan Zhu Xuemei Liu Yunhui Xiong Zuli Yang Weiyao Li Yonghua Wang Wen chen Qingjiao Li Li c.xia Department of Statistics and Financial Mathematics School of MathematicsSouth China University of TechnologyGuangzhouChina School of Physics and Optoelectronics South China University of TechnologyGuangzhouChina Department of Pathology The Sixth Affiliated HospitalSun Yat-sen UniversityGuangzhouChina School of Food Science and Engineering South China University of TechnologyGuangzhouChina Department of Laboratory Medicine the Eighth Affiliated HospitalSun Yat-sen UniversityShenzhenChina

Molecular subtyping of gastric cancer(Gc)aims to comprehend its genetic ***,the efficacy of current subtyping methods is hampered by their mixed use of molecular features,a lack of strategy optimization,and the limited availability of public Gc *** is a pressing need for a precise and easily adoptable subtyping approach for early DNA-based screening and *** on TcGA subtypes,we developed a novel DNA-based hierarchical classifier for gastric cancer molecular subtyping(HcG),which employs gene mutations,copy number aberrations,and methylation patterns as *** incorporating the closely related esophageal adenocarcinomas dataset,we expanded the TcGA Gc dataset for the training and testing of HcG(n=453).The optimization of HcG was achieved through three hierarchical strategies using Lasso-Logistic regression,evaluated by their overall the area under receiver operating characteristic curve(auROc),accuracy,F1 score,the area under precision-recall curve(auPRc)and their capability for clinical stratification using multivariate survival ***-specific DNA alteration biomarkers were discerned through difference tests based on HcG defined *** HcG classifier demonstrated superior performance in terms of overall auROc(0.95),accuracy(0.88),F1 score(0.87)and auPRc(0.86),significantly improving the clinical stratification of patients(overall p-value=0.032).Difference tests identified 25 subtype-specific DNA alterations,including a high mutation rate in the SYNE1,ITGB4,and cOL22A1 genes for the MSI subtype,and hypermethylation of ALS2cL,KIAA0406,and RPRD1B genes for the EBV *** is an accurate and robust classifier for DNA-based Gc molecular subtyping with highly predictive clinical stratification *** training and test datasets,along with the analysis programs of HcG,are accessible on the GitHub website(***/LabxScUT).

关键词： DNA alterations gastric cancer hierarchical classification molecular subtyping multi-omics

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The statistical power of k-mer based aggregative statistics for alignment-free detection of horizontal gene transfer

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Synthetic and Systems Biotechnology 2019年第3期4卷 150-156页

作者： Guan-Da Huang Xue-Mei Liu Tian-Lai Huang Li-c.xia School of Physics and Optoelectronics South China University of TechnologyGuangzhou510640China Department of Medicine Stanford University School of MedicineStanfordCA94305USA

Alignment-based database search and sequence comparison are commonly used to detect horizontal gene transfer(HGT).However,with the rapid increase of sequencing depth,hundreds of thousands of contigs are routinely assembled from metagenomics studies,which challenges alignment-based HGT analysis by overwhelming the known reference *** HGT by k-mer statistics thus becomes an attractive *** alignment-free statistics have been demonstrated in high performance and efficiency in wholegenome and transcriptome *** adapt k-mer statistics for HGT detection,we developed two aggregative statistics T^(S)_(sum ) and T^(*)_(sum),which subsample metagenome contigs by their representative regions,and summarize the regional D^(S) _(2) and D^(*)_(2)metrics by their upper *** systematically studied the aggregative statistics’power at different k-mer size using *** analysis showed that,in general,the power of T^(S)_(sum) and T^(*)_(sum) increases with sequencing coverage,and reaches a maximum power>80%at k=6,with 5%Type-I error and the coverage ratio>*** statistical power ofT^(S)_(sum) and T^(*)_(sum) was evaluated with realistic simulations of HGT mechanism,sequencing depth,read length,and base *** expect these statistics to be useful distance metrics for identifying HGT in metagenomic studies.

关键词： Alignment-free sequence comparison k-mer Horizontal gene transfer Statistical power

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用经验格林函数方法模拟汶川M_W7.9地震的强地震动

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世界地震译丛 2018年第1期49卷 35-52页

作者： c.xia B.M.Zhao M.Horike T.Kagawa 高楠(译) 王超(译) 朱玉萍(校) 中国地震台网中心中国地震局地球物理研究所不详

汶川M_W7.9地震的发生震惊了中国乃至全世界,不仅仅因为该地震震级巨大,还因为其可怕的伤亡。评估汶川M_W7.9地震的复杂性及破坏力需对其地震特征进行研究。本文运用经验格林函数方法(EGF)模拟了地震的强地震动。首先,选取了4个震级为M_... 详细信息

汶川M_W7.9地震的发生震惊了中国乃至全世界,不仅仅因为该地震震级巨大,还因为其可怕的伤亡。评估汶川M_W7.9地震的复杂性及破坏力需对其地震特征进行研究。本文运用经验格林函数方法(EGF)模拟了地震的强地震动。首先,选取了4个震级为M_W4.9和M_W5.0的余震,对这些余震的运动利用格林函数进行了模拟。通过模拟,可以估算出包括断层规模和应力降在内的余震震源参数。然后,通过试错法正演模拟得出M_W7.9地震凹凸体(强震动生成区)的震源模型。为验证该震源模型的准确性,运用经验格林函数方法模拟合成了9个台站的强地震动。将模拟得出的强地震动与观测记录到的加速度波形、速度波形和拟加速度反应谱相比较。尽管有一些差异,但在大部分台站,合成的强地震动与观测记录结果相吻合。在模拟得出的震源模型中,断层面上3个凹凸体的应力降约为10MPa,而凹凸体面积与破裂面积比为0.24,接近经验关系式得出的结果0.22。

关键词：经验格林函数强地震动加速度反应谱格林函数方法模拟合成震源模型地震震级观测记录

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Minimum mass-entransy dissipation profile for one-way isothermal diffusive mass-transfer process with mass-resistance and massleakage

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Science china(Technological Sciences) 2024年第8期67卷 2427-2435页

作者： cHEN LinGen xia ShaoJun Institute of Thermal Science and Power Engineering Wuhan Institute of TechnologyWuhan 430205China School of Mechanical Electrical EngineeringWuhan Institute of TechnologyWuhan 430205China School of Power Engineering Naval University of EngineeringWuhan 430033China

As a new concept,mass-entransy is one of the twins in the core of entransy *** can describe mass-transfer ability for masstransfer processes(MTPes),just as thermal-entransy for describing heat-transfer ***,mass-entransy dissipation can be utilized to evaluate the loss of mass-transfer *** mass-entransy dissipation(MMED) is utilized to optimize one-way isothermal diffusive MTPes with mass-leakage and mass-transfer law(g ∝ Δ(c),where c means concentration).For a given net amount of mass-transferred key components at the low-concentration side,optimality-condition for the MMED of isothermal diffusive MTPes is obtained by using the *** of the amount of mass-transferred and mass-leakage on optimal results are analyzed,and the obtained optimization profiles are compared with those for MTP profiles of constant-concentration-difference(c_1-c_2=const) and constant-concentration-ratio(c_1/c_2=const).The product of square of key-component-concentration(Kcc) difference between high-and low-concentration sides and inert component concentration at high-concentration side for the MMED of the MTP with no mass-leakage is a constant,and the optimal relationship of the Kccs between high-and low-concentration sides with mass-leakage is significantly different from the *** mass-leakage is relatively small,the MTP with c_1-c_2=const strategy is superior to that with c_1/c_2=const strategy,and the latter is superior to the former with an increase in mass-leakage.A combination of mass-entransy concept,finite-time thermodynamics,and averaged-optimization-method is a meaningful tool for optimizing MTPes.

关键词： diffusive mass-transfer-law mass-leakage one-way isothermal mass-transfer minimum mass-entransy dissipation finite-time thermodynamics averaged-optimization-method

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Asperuloside Promotes Apoptosis of cervical cancer cells through Endoplasmic Reticulum Stress-Mitochondrial Pathway

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chinese Journal of Integrative Medicine 2024年第1期30卷 34-41页

作者： QI Zhi-min WANG xia LIU xia ZHAO Juan Medical Examination center Hebei Province Hospital of Chinese MedicineShijiazhuang(050011)China Department of Gynaecology and Obstetrics Hebei Province Hospital of Chinese MedicineShijiazhuang(050011)China Experimental center for Teaching Hebei Medical UniversityShijiazhuang(050017)China

Objective: To investigate the effects of asperuloside on cervical cancer based on endoplasmic reticulum(ER) stress and mitochondrial pathway. Methods: Different doses(12.5–800 μg/mL) of asperuloside were used to treat cervical cancer cell lines Hela and caSki to calculate the half maximal inhibitory concentration(Ic_(50)) of asperuloside. The cell proliferation was analyzed by clone formation assay. cell apoptosis, intracellular reactive oxygen species(ROS) and mitochondrial membrane potential were determined by flow cytometry. The protein expressions of cleaved-caspase-3, Bcl-2, Bax, cyt-c, cleaved-caspase-4 and glucose-regulated protein 78(GRP78) were analyzed by Western blot. And the inhibitor of ER stress, 4-phenyl butyric acid(4-PBA) was used to treat cervical cancer cells to further verify the role of ER stress in the apoptosis of cervical cancer cells induced by asperuloside. Results: Asperuloside of 325, 650, and 1300 μg/mL significantly inhibited the proliferation and promoted apoptosis of Hela and caSki cells(Pcantly increased intracellular ROS levels, reduced mitochondrial membrane potential, significantly reduced Bcl-2 protein expression level, and increased Bax, cyt-c, GRP78 and cleaved-caspase-4 expressions(Pcantly promoted cell proliferation and reduced apoptosis(Pcould reverse 4-PBA-induced increased cell proliferation, decreased apoptosis and cleaved-caspase-3,-4 and GRP78 protein expressions(Pconclusion: Our study revealed the role of asperuloside in cervical cancer, suggesting that asperuloside promotes apoptosis of cervical cancer cells through ER stress-mitochondrial pathway.

关键词： asperuloside chinese medicine cervical cancer endoplasmic reticulum stress mitochondrial damage apoptosis

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Synergy effect of regulated Li-plating and functional solid electrolyte interphase on graphite anodes

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Nano Research 2024年第9期17卷 8077-8085页

作者： Panpan Wang Baojia xia Jianling Li State Key Laboratory of Advanced Metallurgy University of Science and Technology BeijingBeijing 100083China Shanghai Institute of Microsystem and Information Technology Chinese Academy of SciencesShanghai 201800China

The growth of Li dendrites poses potential safety hazard to lithium-ion batteries(LIBs),and eliminating Li dendrites thoroughly stills face tough difficulties ***,regulating Li-plating is a critical optimization-direction to address the ***,a“graphite-Li hybrid”anode with high reversibility is realized under the constant-capacity lithiation(ccL).Within ccL,the uniform distribution of Li-plating on the graphite surface is successfully *** evolution in different states of solid electrolyte interphase(SEI)is investigated in detail to study the interaction between the potentials and impedance during the process of Liintercalation and *** the potential below 0 V and the state of charge(SOc)of 110%relative to the theoretical capacity,the F-rich SEI with high stability is constructed to hinder the emergency of Li dendrites and maintain the intact structure of graphite anode under long *** cell presents more than 100%coulombic efficiency(cE)with the 900 cycles,demonstrating the reversible Li-plating and the utilization of *** the ccL half-cell provides a good cycling performance and specific capacity of 900 cycles at 0.5 c,it is attributed to the synergy effect of stable inorganic-rich SEI and regulated active Li-plating.

关键词： "graphite-Li hybrid"anode Li-plating reversibility solid electrolyte interphase(SEI)

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Three-dimensional topological crystalline insulator without spin-orbit coupling in nonsymmorphic photonic metacrystal

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chinese Physics B 2024年第10期33卷 282-286页

作者： Zhide Yu Lingbo xia School of Physics and Electronics Hunan UniversityChangsha 410082China

By including certain point group symmetry in the classification of band topology,Fu proposed a class of threedimensionaltopological crystalline insulators(TcIs)without spin-orbit coupling in *** Fu’s model,surface states(ifpresent)doubly degenerate atГandM when time-reversal and c4 symmetries are *** analogs of Fu’s modelwith surface states quadratically degenerate atM are widely studied,while surface states with quadratic degeneracy atГare rarely *** this study,we propose a three-dimensional TcI without spin-orbit coupling in a judiciously designednonsymmorphic photonic *** surface states of photonic TcIs exhibit quadratic band degeneracy in the(001)surface Brillouin zone(BZ)center(Гpoint).The gapless surface states and their quadratic dispersion are protected by c4and time-reversal symmetries,which correspond to the nontrivial band topology characterized by Z_(2)topological ***,the surface states along lines fromГto the(001)surface BZ boundary exhibit zigzag feature,which is interpretedfrom symmetry perspective by building composite operators constructed by the product of glide symmetries with *** metacrystal array surrounded with air possesses high order hinge states with electric fields highlylocalized at the hinge that may apply to optical *** gapless surface states and hinge states reside in a cleanfrequency *** topological surface states emerge at the boundary of the metacrystal and perfect electric conductor(PEc),which provide a pathway for topologically manipulating light propagation in photonic devices.

关键词： topological crystalline insulator nonsymmorphic photonic metacrystal

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Recent advances in transition-metal catalyzed nitrene transfer reactions with carbamates

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chinese chemical Letters 2024年第3期35卷 76-86页

作者： Yanshu Luo Xinyu Zhang Yuanzhi xia college of chemistry and Materials Engineering Wenzhou UniversityWenzhou 325035China

Nitrene transfer reactions are powerful tools in synthetic organic *** recent years,transitionmetal catalyzed nitrene transfer reactions with carbamates as the nitrene precursors have been widely *** species undergoes facile c-H amination,aziridination,and bifunctionalization of alkenes under the catalysis of different transition metals including Rh,Fe,Ru and others,enabling the efficient construction of various nitrogen-containing *** this review,the recent developments in nitrene transfer reactions with carbamates via N-O bond cleavage were introduced based on different types of reaction,and the key mechanistic information and synthetic applications of the methodologies were discussed.

关键词： Transition-metal catalysis Nitrene transfer carbamate c—H amination Aziridination Bifunctionalization

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Eigenfrequency analysis of bridges using a smartphone and a novel low-cost accelerometer prototype

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Frontiers of Structural and civil Engineering 2024年第2期18卷 202-215页

作者： Seyedmilad KOMARIZADEHASL Ye xia Mahyad KOMARY Fidel LOZANO Department of civil and Environment Engineering Universitat Politècnica de CatalunyaBarcelona 08034Spain Department of Bridge Engineering Tongji UniversityShanghai 200092China Department of civil Engineering Universidad de Castilla-La ManchaCiudad Real 13071Spain

Researchers are paying increasing attention to the development of low-cost and microcontroller-based accelerometers,in order to make structural health monitoring feasible for conventional bridges with limited monitoring *** with the low-cost sensor development,the use of the embedded accelerometers of smartphones for eigenfrequency analysis of bridges is becoming popular in the civil engineering *** paper,for the first time in the literature,studies these two promising technologies by comparing the noise density and eigenfrequency analysis of a self-developed,validated and calibrated low-cost Internet of things based accelerometer LARA(low cost adaptable reliable accelerometer)with those of a state of the art smartphone(iPhone XR).The eigenfrequency analysis of a footbridge in San Sebastian,Spain,showed that the embedded accelerometer of the iPhone XR can measure the natural frequencies of the under study bridge.

关键词： smartphone modal analysis eigenfrequency analysis low-cost accelerometers Arduino Raspberry Internet of things

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Nickel/Photoredox Dual catalytic chan-Lam coupling of Aryl Azides and Arylboric Acids

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chinese Journal of chemistry 2024年第18期42卷 2228-2234页

作者： xia Ge Haojie Ji Hongjian Lu Schoolof chemistry and chemical Engineering Nanjing UniversityNanjingJiangsu 210093China

Unsymmetrical diarylamines are crucial components in many pharmaceuticals and functional *** this study,we introduce an efficient chan-Lam cross-coupling method that utilizes phenylboronic acids and aryl azides as coupling agents in a redox-neutral environment,enabled by a synergistic nickel/photoredox catalytic *** approach leverages a proton-coupled electron transfer mechanism to bypass the typical nitrene pathway associated with aryl azides,which is prone to intramolecular rearrangement,c-H amination,and reductive ***,our method exhibits broad compatibility with a variety of functional groups,including those derived from pharmaceuticals,demonstrating its versatile potential in organic synthesis and drug modification.

关键词： Azides chan-Lam reaction Nickel Iridium Redox-neutral Photochemistry

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