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Identification of Proteins and Genes Associated with Hedgehog Signaling Pathway Involved in Neoplasm Formation Using Text-Mining Approach

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Big Data Mining and Analytics 2024年第1期7卷 107-130页

作者： Nadezhda yu.Biziukova Sergey M.ivanov Oga A.Tarasova Department of Bioinformatics Institute of Biomedical ChemistryMoscow 119121Russia Department of Bioinformatics Pirogov Russian National Research Medical UniversityMoscow 117997Russia

Analysis of molecular mechanisms that lead to the development of various types of tumors is essential for biology and medicine,because it may help to find new therapeutic opportunities for cancer treatment and cure including personalized treatment *** of the pathways known to be important for the development of neoplastic diseases and pathological processes is the Hedgehog signaling pathway that normally controls human embryonic *** accumulation of various types of biological data,including interactions between proteins,regulation of genes transcription,proteomics,and metabolomics experiments results,allows the application of computational analysis of these big data for identification of key molecular mechanisms of certain diseases and pathologies and promising therapeutic *** aim of this study is to develop a computational approach for revealing associations between human proteins and genes interacting with the Hedgehog pathway components,as well as for identifying their roles in the development of various types of *** automatically collect sets of abstract texts from the NCBI PubMed bibliographic *** recognition of the Hedgehog pathway proteins and genes and neoplastic diseases we use a dictionary-based named entity recognition approach,while for all other proteins and genes machine learning method is *** association extraction,we develop a set of semantic *** complete the results of the text analysis with the gene set enrichment *** identified key pathways that may influence the Hedgehog pathway and their roles in tumor development are then verified using the information in the literature.

关键词： text-mining data mining Hedgehog pathway neoplastic processes enrichment analysis pathology molecularmechanisms

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STCF conceptual design report (Volume 1): Physics & detector

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Frontiers of physics 2024年第1期19卷 1-154页

作者： M.Achasov X.C.Ai L.P.An R.Aliberti Q.An X.Z.Bai y.Bai O.Bakina A.Barnyakov V.Blinov V.Bobrovnikov D.Bodrov A.Bogomyagkov A.Bondar I.Boyko Z.H.Bu F.M.Cai H.Cai J.J.Cao Q.H.Cao X.Cao Z.Cao Q.Chang K.T.Chao D.y.Chen H.Chen H.X.Chen J.F.Chen K.Chen L.L.Chen P.Chen S.L.Chen S.M.Chen S.Chen S.P.Chen W.Chen X.Chen X.F.Chen X.R.Chen y.Chen y.Q.Chen H.y.Cheng J.Cheng S.Cheng T.G.Cheng J.P.Dai L.y.Dai X.C.Dai D.Dedovich A.Denig I.Denisenko J.M.Dias D.Z.Ding L.y.Dong W.H.Dong V.Druzhinin D.S.Du y.J.Du Z.G.Du L.M.Duan D.Epifanov y.L.Fan S.S.Fang Z.J.Fang G.Fedotovich C.Q.Feng X.Feng y.T.Feng J.L.Fu J.Gao y.N.Gao P.S.Ge C.Q.Geng L.S.Geng A.Gilman L.Gong T.Gong B.Gou W.Gradl J.L.Gu A.Guevara L.C.Gui A.Q.Guo F.K.Guo J.C.Guo J.Guo y.P.Guo Z.H.Guo A.Guskov K.L.Han L.Han M.Han X.Q.Hao J.B.He S.Q.He X.G.He y.L.He Z.B.He Z.X.Heng B.L.Hou T.J.Hou y.R.Hou C.y.Hu H.M.Hu K.Hu R.J.Hu W.H.Hu X.H.Hu y.C.Hu J.Hua G.S.Huang J.S.Huang M.Huang Q.y.Huang W.Q.Huang X.T.Huang X.J.Huang y.B.Huang y.S.Huang N.Hüsken V.ivanov Q.P.Ji J.J.Jia S.Jia Z.K.Jia H.B.Jiang J.Jiang S.Z.Jiang J.B.Jiao Z.Jiao H.J.Jing X.L.Kang X.S.Kang B.C.Ke M.Kenzie A.Khoukaz I.Koop E.Kravchenko A.Kuzmin y.Lei E.Levichev C.H.Li C.Li D.y.Li F.Li G.Li G.Li H.B.Li H.Li H.N.Li H.J.Li H.L.Li J.M.Li J.Li L.Li L.Li L.y.Li N.Li P.R.Li R.H.Li S.Li T.Li W.J.Li X.Li X.H.Li X.Q.Li X.H.Li y.Li y.y.Li Z.J.Li H.Liang J.H.Liang y.T.Liang G.R.Liao L.Z.Liao y.Liao C.X.Lin D.X.Lin X.S.Lin B.J.Liu C.W.Liu D.Liu F.Liu G.M.Liu H.B.Liu J.Liu J.J.Liu J.B.Liu K.Liu K.y.Liu K.Liu L.Liu Q.Liu S.B.Liu T.Liu X.Liu y.W.Liu y.Liu y.L.Liu Z.Q.Liu Z.y.Liu Z.W.Liu I.Logashenko y.Long C.G.Lu J.X.Lu N.Lu Q.F.Lü y.Lu y.Lu Z.Lu P.Lukin F.J.Luo T.Luo X.F.Luo y.H.Luo H.J.Lyu X.R.Lyu J.P.Ma P.Ma y.Ma y.M.Ma F.Maas S.Malde D.Matvienko Z.X.Meng R.Mitchell A.Nefediev y.Nefedov S.L.Olsen Q.Ouyang P.Pakhlov G.Pakhlova X.Pan y.Pan E.Passemar y.P.Pei H.P.Peng L.Peng X.y.Peng X.J.Peng K.Peters S.Pivovarov E.Pyata B.B.Qi y.Q.Qi W.B.Qian y.Qian C.F.Qiao J.J.Qin J.J.Qin L.Q.Qin X.S.Qin T.L.Qiu J.Rademacker C.F.Redmer H.y.Sang Anhui University Hefei 230039China Beihang University Beijing 100191China Budker Institute of Nuclear Physics Novosibirsk 630090Russia CAS Key Laboratory of Theoretical Physics Institute of Theoretical PhysicsChinese Academy of SciencesBeijing 100190China Cavendish Laboratory University of CambridgeJJ Thomson AveCambridge CB30HEUnited Kingdom Central China Normal University Wuhan 430079China Central South University Changsha 410083China China University of Geosciences Wuhan 430074China China University of Mining and Technology Xuzhou 221116China École Polytechnique Fédérale de Lausanne(EPFL) LausanneSwitzerland Fudan University Shanghai 200433China Goethe University Frankfurt D-60325 Frankfurt am MainGermany Guangxi Normal University Guilin 541004China Guangxi Uninversity Nanning 530004China Hangzhou Institute for Advanced Study UCASHangzhou 310024China Hebei Normal University Shijiazhuang 050024China Hebei University Baoding 071002China Hefei University of Technology Hefei 230601China Helmholtz Institute Mainz Staudinger Weg 18D-55099 MainzGermany Henan Normal University Xinxiang 453007China Henan University Kaifeng 475004China High Energy Physics Center Chung-Ang UniversitySeoul 06974Korea Higher School of Economy 11 Pokrovsky Bulvar Moscow 109028Russia Huangshan University Huangshan 245000China Hubei University of Automotive Technology Shiyan 442002China Hunan Normal University Changsha 410081China Hunan University of Science and Technology Xiangtan 411201China Hunan University Changsha 410082China Indiana University BloomingtonIndiana 47405USA Inner Mongolia University Hohhot 010021China Institute of Advanced Science Facilities Shenzhen 518107China Institute of High Energy Physics Chinese Academy of SciencesBeijing 100049China Institute of Modern Physics Chinese Academy of SciencesLanzhou 730000China Institute of Physics Academia SinicaTaipeiTaiwan 11529China Institute of Theoretical Physics Chinese Academy of SciencesBeijing 100190China Jilin University Changch

The superτ-charm facility(STCF)is an electron–positron collider proposed by the Chinese particle physics *** is designed to operate in a center-of-mass energy range from 2 to 7 GeV with a peak luminosity of 0.5×10^(35) cm^(–2)·s^(–1) or *** STCF will produce a data sample about a factor of 100 larger than that of the presentτ-charm factory—the BEPCII,providing a unique platform for exploring the asymmetry of matter-antimatter(charge-parity violation),in-depth studies of the internal structure of hadrons and the nature of non-perturbative strong interactions,as well as searching for exotic hadrons and physics beyond the Standard *** STCF project in China is under development with an extensive R&D *** document presents the physics opportunities at the STCF,describes conceptual designs of the STCF detector system,and discusses future plans for detector R&D and physics case studies.

关键词： electron–positron collider tau-charm region high luminosity STCF detector conceptual design

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Dirac operator on the sphere with attached wires

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Chinese Physics B 2016年第4期25卷 335-338页

作者： E N Grishanov D A Eremin D A ivanov I yu Popov Ogarev Mordovia State University Bolshevistskaya Str. 68 Saransk Russia ITMO University Kroverkskiy pr. 49 St. Petersburg 197101 Russia

An explicitly solvable model for tunnelling of relativistic spinless particles through a sphere is suggested. The model operator is constructed by an operator extensions theory method from the orthogonal sum of the Dirac operators on a semi- axis and on the sphere. The transmission coefficient is obtained. The dependence of the transmission coefficient on the particle energy has a resonant character. One observes pairs of the Breit-Wigner and the Fano resonances. It correlates with the corresponding results for a non-relativistic particle.

关键词： Dirac operator nanostructure tunnelling solvable model

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Highly transparent ytterbium doped yttrium lanthanum oxide ceramics

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Journal of Rare Earths 2014年第3期32卷 254-258页

作者： M.ivanov yu.Kopylov V.Kravchenko 李江 A.Medvedev 潘裕柏 Institute of Electrophysics UrB of RAS 106Amundsena 620016 Ekaterinburg Russia Institute of Radioengineering and Electronics named after V.A. Kotelnikov RAS Vvedensky Sq. 1 Fryazino Moscow region 141120 Russia Shanghai Institute of Ceramics Chinese Academy of Science Ural Federal University 19 Mira 620002 Ekaterinburg Russia

To prepare ytterbium doped lanthania yttria nanopowder a method of laser evaporation of mixed oxides was used. After calcinations of the powder at 1200 ℃ a pure single-phase solid solution yb3＋：（Laxy1-x）2O3 was formed in the nanoparticles. Influence of lanthanum oxide as an isovalent additive on the yttria structure was investigated. The lanthanium ions were proved to be a good aid to sinter yttria ceramics doped with yb3＋ at moderate temperatures about 1650 ℃. The ceramics with relative density higher than 99.99% and grain size about 40 μm were fabricated. Full transmittance of 1.8 mm thick yb0.11 La0.23y1.66O3 ceramics reached 82.5% at 800 nm. This material could be a good gain medium for ytterbium high power pulse lasers.

关键词： RE-doped ceramics nanopowders ytterbium oxide transparency

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Influence of Features of Interphase Boundaries on Mechanical Properties and Fracture Pattern in Metal-Ceramic Composites

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Journal of Materials Science & Technology 2013年第11期29卷 1025-1034页

作者： Sergey Psakhie Vladimir Ovcharenko Baohai yu Evgeny Shilko Sergey Astafurov yu.y ivanov Alexey Byeli Alexey Mokhovikov Institute of Strength Physics and Materials Science Siberian Branch of the Russian Academy of Sciences Institute of High Technology Physics Tomsk Polytechnic University Shenyang National Laboratory for Materials Science Institute of High Current Electronics Siberian Branch of the Russian Academy of Sciences Physical-Technical Institute yurga Technological Institute Tomsk Polytechnic University

The results of a theoretical study on the influence of strength of interphase boundaries in metal-ceramic composite on macroscopical characteristics of composite response such as strength, deformation capacity, fracture energy and fracture pattern are presented. The study was conducted by means of computer-aided simulation by means of movable cellular automaton method taking account of a developed ＂mesoscopical＂ structural model of particle-reinforced composite. The strength of interphase boundaries is found to be a key structural factor determining not only the strength properties of metal-ceramic composite, but also the pattern and rate of fracture. The principles for achievement of the high-strength values of particle/binder interfaces in the metal-ceramic composition due to the formation of the wide transition zones （areas of variable chemical composition） at the interphase boundaries are discussed. Simulation results confirm that such transition zones provide a change in fracture mechanism and make the achievement of a high-strength and a high deformation capacity of metal-ceramic composite possible.

关键词： Metal--ceramic composites Particle-reinforced composite Interphase boundaries Discrete element based analysis Strength and fracture energy Fracture pattern

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Effect of Surface Layer Structural-Phase Modification on Tribological and Strength Properties of a TiC–(Ni–Cr) Metal Ceramic Alloy

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Acta Metallurgica Sinica(English Letters) 2018年第5期31卷 547-551页

作者： Bao-Hai yu V.E.Ovcharenko K.V.ivanov A.A.Mokhovikov yan-Hui Zhao Institute of Metal Research Chinese Academy of Sciences Shenyang 110016 China Tomsk Polytechnic University Tomsk 634050 Russia Institute of Strength Physics and Materials Science Siberian Branch of the Russian Academy of Sciences Tomsk 634021Russia

This paper reports TiC–（Ni–Cr） metal ceramic alloy（ratio of components 50：50） with nanoscaled components formed in the surface layer and smoothly transformed into the initial inner structure throughout the material under pulsed electron irradiation of the alloy surface. Principal changes in the surface layer are ascribed to the formation of gradient structure leading to the increase in wear resistance of the surface layer, drop of friction coefficient and improvement of specimen bending resistance when stressing on the irradiated surface side. The above changes of tribological and strength properties in the surface layer under pulsed electron irradiation become more apparent with increasing atomic mass of a plasma-forming inert gas.

关键词： Metal ceramic alloy Particle-reinforced composite Interphase boundaries Tribological behavior Bending strength Electron beam treatment

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Stages and Fracture Mechanisms of Lamellar Pearlite of 100-m-Long Differentially Hardened Rails Under Long-Term Operation Conditions

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Acta Metallurgica Sinica(English Letters) 2018年第12期31卷 1356-1360页

作者： A.A.yuriev V.E.Gromov V.A.Grishunin yu.F.ivanov R.S.Qin A.P.Semin LTD Evraz-Integrated West Siberian MetallurgicalCombine NovokuznetskRussia Siberian State Industrial University NovokuznetskRussia National Research Tomsk Polytechnic University TomskRussia Institute of High Current Electronics SD RAS TomskRussia School of Engineering and Innovation The Open UniversityWalton HallMilton Keynes MK 7 6AAUK

Using the methods of transmission electron microscopy, the carbide phase evolution in surface layers of the differentiallyquenched rails is studied after the passed tonnage of 691.8 million tons at the depth up to 10 mm along the central axis andfillet of rail head. The action of two mutual supplement mechanisms of steel carbide phase transformation in surface layersat rail operation is established：（1） cutting mechanism of cementite particles with the following departure in the volume offerrite grains or plates （in pearlite structure）; （2） cutting mechanism and following dissolution of cementite particles,transfer of carbon atoms on dislocations （in Cottrell atmospheres and dislocation cores）, transfer of carbon atoms bymoving dislocations into ferrite grains volume （or plates） with the following repeated formation of nanosized cementiteparticles. The first mechanism is accompanied by the change in linear sizes and morphology of carbide particles. Cementiteelement composition change is not essential. Carbide structure change can take place during the second mechanism.

关键词： Cementite Pearlite Fracture Rails Mechanisms Operation

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High-voltage Nanosecond Pulse Generators of the ＂PROTEUS＂ Line for Discharge with Runaway Electrons Applications

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高电压技术 2013年第10期39卷 2506-2513页

作者： Anatoly N. Maltsev Maxim V. Martynov Alexey V. Mikov Viktor G. Podkovyrov Leonid L. Zhukov Alexander yu. ivanov Institute of Atmospheric Optics Russian Academy of Sciences Tomsk 634021 Russia Electrodynamic Systems & Technologies LLC Tomsk 634021 Russia Institute of High-current Electronics Russian Academy of Sciences Tomsk 634021 Russia

Many applications of gas discharge with runaway electrons (DRE) require high-voltage pulse generators (HVPG) with very high increasing rate of output voltage (up to 100 kV/ns), long operation life and low cost. Such HVPGs have to be controlled by external computer for working in combination with other modern equipment. In this paper, some HVPGs development for DRE application in industry and medicine are described. The functional structure and operation principles are discussed for the HVPG of "PROTEUS' line. It is shown that on different loads, the "PROTEUS" generators can produce high-voltage nanosecond pulse with energy up to 1 J, output voltage amplitude from zero to 150 kV, and pulse repetition frequency from zero to 2 000 Hz. Four models of the "PROTEUS" generators are described. The output voltage leading front duration is 150 ns for the "PROTEUS-I" model, 10-20 ns for the "PROTEUS-II", 2 ns for the "PROTEUS-IH" and 0.5 ns for the "PROTEUS-IV". DRE parameters obtained by using "PROTEUS" HVPGs are demonstrated. Some results of DRE application in solid-state surface modification of natural textile and polymer films are shown as well.

关键词： PROTEUS 纳秒脉冲发生器电子应用气体放电高压失控输出电压脉冲重复频率

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Copper-induced liver fibrosis affects the behavior of bone marrow cells in primary culture

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Frontiers in Biology 2017年第4期12卷 271-279页

作者： Anatoliy I. Bozhkov Eugeniy G. ivanov yuliya A. Kuznetsova Svetlana L. Ohiienko Anastasiya yu. Bondar 1. Research Institute of Biology of V.N. Karazin Kharkov National University sq. Svobody 4 61022 Kharkov Ukraine

BACKGROUND： The present study investigated the effects （LMCC）, which were administered per os, on the differentiation, of rats in primary culture. of low-molecular-weight components of bovine colostrum growth, and survival of cells obtained from the bone marrow METHODS： Bone marrow cells （BMCs） were obtained from both the rat femurs and were cultured in medium 199 supplemented with antibiotics （8% streptomycin and 8% gentamycin） and 20% inactivated fetal calf serum. In addition, the number of BMCs was counted and their morphotypes were determined. RESULTS： Animals were treated with copper （Cu） sulfate to induce liver fibrosis. Subsequent treatment with LMCC eliminated growth inhibition and normalized the bodyweight and temperature of animals with Cu-induced liver fibrosis. The number of lymphocytes in the bone marrow of animals with Cu-induced liver fibrosis was significantly higher than that in the bone marrow of control animals. The number ofneutrophils in untreated animals with liver fibrosis and LMCC-treated animals with liver fibrosis was lower than that in control animals. Neutrophils obtained from untreated animals with liver fibrosis and LMCC-treated animals with liver fibrosis underwent two-times faster degradation in vitro than neutrophils obtained from control animals. CONCLUSIONS： Our results indicate that LMCC affects the distribution of different morphological types of BMCs but does not prevent their degradation in vitro, which was two-times faster than that of BMCs obtained from control animals.

关键词： bone marrow cells bone marrow colostntm liver fibrosis

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基于XeF(C-A)放大器的混合(固态/气态)超高功率飞秒激光系统(英文)

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光学精密工程 2011年第2期19卷 252-259页

作者： LOSEV V ALEKSEEV S ivanov N KOVALCHUK B MIKHEEVL MESyATS G PANCHENKO yu PUCHIKIN A RATAKHIN N yASTREMSKy A Institute of High Current Electronics of Siberian Branch of Russian Academy of Sciences aveAkademichesky 2/3Tomsk 634055Russia Lebedev Physical Institute of Russian Academy of Sciences Leninsky Prospekt53119991 Russia

提出了基于前端发生器和终端放大器,使用光泵浦XeF（C-A）激活介质的太瓦级混合激光器（THL-100）系统。前端发生器由长532 nm的连续激光泵浦的钛宝石飞秒脉冲振荡器,脉冲展宽机构,532 nm的脉冲激光泵浦的再生多通道放大器,衍射光栅压... 详细信息

提出了基于前端发生器和终端放大器,使用光泵浦XeF（C-A）激活介质的太瓦级混合激光器（THL-100）系统。前端发生器由长532 nm的连续激光泵浦的钛宝石飞秒脉冲振荡器,脉冲展宽机构,532 nm的脉冲激光泵浦的再生多通道放大器,衍射光栅压缩器和二次谐波发生器（KDP）组成。其光束输出参数为：脉冲持续时间50 fs,二次谐波（475 nm）辐射能量5 mJ。前端发生器以10 Hz的单脉冲模式工作。XeF（C-A）放大器由双高压脉冲发生器（线性变压器）,爆炸式阴极发射真空二极管,电子束注入系统,充满Xe的气室转换器和激光单元组成。高压发生器包括12个变压器,每个变压器有8个电容（40 nF）和火花隙,电容可以充电至100 kV。真空二极管中的电子束参数为：总电流300 kA,峰值电压550kV,脉冲持续时间约150 ns。穿透金属箔片到达Xe转换器的6个100 cm×12 cm电子束的总能量为67 kJ。激光系统通过泵浦能量的级联处理导致Xe2＊的快速形成,并在（172±5）nm连续辐射。真空紫外辐射通过CaF2窗口辐射到含有XeF2蒸汽和氮气缓冲气体的激光单元中,使XeF2光解,形成XeF＊准分子。由真空紫外辐射泵浦的放大器激活介质长110 cm,直径为24 cm。文中通过数值模拟给出了输出参数和第一实验结果,根据XeF（C-A）放大器参数模型和增益测量结果,得到的输出能量高达23 J,这意味着50 fs脉冲的峰值功率高达4060 TW。

关键词：混合激光器 XeF(C—A)放大器飞秒脉冲宽度电子束紫外转换器

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