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Molecular and quantum mechanical studies on the monomer recognition of a highly-regular β-helical antifreeze protein

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science China Chemistry 2004年第1期47卷 34-40页

作者： YANG Zuoyin, JIA Zongchao, LIU Ruozhuang & CHEN Guangjudepartment of Chemistry, Beijing Normal University, Beijing 1.0875, China Faculty of {1., Beijing University of Chemical Technology, Beijing 1.0029, China department of Biochemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada 1. department of Chemistry Beijing Normal University 100875 Beijing China 2. Faculty of science Beijing University of Chemical Technology 100029 Beijing China 3. department of Biochemistry Queen? University K7L 3N6 Kingston Ontario Canada

The possible interaction models for an antifreeze protein from Tenebrio molitar (TmAFP) have been systematically studied using the methods of molecular mechanics, molecular dynamics and quantum chemistry. It is hoped that these approaches would provide insights into the nature of interaction between protein monomers through sampling a number of interaction possibilities and evaluating their interaction energies between two monomers in the course of recognition. The results derived from the molecular mechanics indicate that monomer? β-sheets would be involved in interaction area and the side chains on two p-faces can match each other at the two-dimensional level. The results from molecular mechanics and ONIOM methods show that the strongest interaction energy could be gained through the formation of H-bonds when the twoβ-sheets are involved in the interaction model. Furthermore, the calculation of DFT and analysis of van der Waals bond charge density confirm further that recognition between the two TCTs mainly depends on inter-molecular hydroxyls. Therefore, our results demonstrate that during the course of interaction the most favorable association of TmAFPs is via their β-sheets.

关键词： antifreeze protein, recognition, dynamics simulation, molecular mechanics, quantum chemistry.

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Climatology of tropical cyclone tornadoes in China from 2006 to 201.

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science China Earth sciences 2020年第1期63卷 37-51页

作者： Lanqiang BAI Zhiyong MENG Kenta SUEKI Guixing CHEN Ruilin ZHOU School of atmospheric {1.s and Guangdong Province Key Laboratory for Climate Change and Natural Disaster StudiesSun Yat-sen UniversityGuangzhou 510275China Laboratory for Climate and Ocean-Atmosphere Studies Department of Atmospheric and Oceanic SciencesSchool of PhysicsPeking UniversityBeijing 100871China Southern Marine science and Engineering Guangdong Laboratory(Zhuhai) Zhuhai 519000China RIKEN Center for Computational science Kobe 650-0047Japan

We surveyed the occurrence of tropical cyclone(TC) tornadoes in China from 2006 to 201.. There were 64 cataloged TC tornadoes, with an average of five per year. About one-third of the landfalling TCs in China were tornadic. Consistent with previous studies, TC tornadoes preferentially formed in the afternoon shortly before and within about 36 h after landfall of the TCs. These tornadoes mainly occurred in coastal areas with relatively flat terrains. The maximum number of TC tornadoes occurred in Jiangsu and Guangdong provinces. Most of the TC tornadoes were spawned within 500 km of the TC center. Two notable characteristics were found:(1. TC tornadoes in China mainly occurred in the northeast quadrant(Earth-relative coordinates) rather than the right-front quadrant(TC motion-relative coordinates) of the parent TC circulation;and(2) most tornadoes were produced by TCs with a relatively weak intensity(tropical depressions/storms), in contrast with the United States where most tornadoes are associated with stronger TCs. Further analyses showed that TC tornadoes in China tend to be spawned in an environment with large low-level storm relative helicity and large convective available potential energy taking entrainment effects into account. TC tornadoes were particularly active in 201., with 24 reported tornadoes accounting for 37.5% of the total surveyed samples. The first recorded tornado outbreak in the modern history of China occurred in the envelope of TC Yagi(201.), in which 1. tornadoes were reported in association with significant midlevel intrusions of dry air and the interaction of Yagi with an approaching midlatitude midlevel trough.

关键词： Tornadoes Tropical cyclones Historical statistics China

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Plastic deformation behavior of Mg97Zn1.2 extruded alloys

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Transactions of Nonferrous Metals Society of China 2010年第7期20卷 1259-1268页

作者： K.HAGIHARA A.KINOSHITA Y.SUGINO M.YAMASAKI Y.KAWAMURA H.Y.YASUDA Y.UMAKOSHI Division of Materials and Manufacturing science Graduate School of EngineeringOsaka University2-1Yamada-okaSuitaOsaka 565-0871Japan department of Materials {1. Kumamoto University2-39-1KurokamiKumamoto 860-8555Japan National Institute for Materials science 1-2-1SengenTsukubaIbaraki 305-0047Japan

The mechanical properties of the Mg97ZnlY2 extruded alloy containing the long-period stacking ordered phase, the so-called LPSO-phase, with a volume fraction of 24%-25%, were examined by compression tests and cyclic tension-compression deformation tests. The plastic behavior of the extruded alloys with compositions of Mg99.2Zn0.2Y0.6 and Mg89Zn4Y7 （molar fraction, %）, which were almost the same compositions of Mg matrix phase and LPSO phase in Mg97Zn1.2 Mg/LPSO two-phase alloy, respectively, were also prepared. By comparing their mechanical properties, the strengthening mechanisms operating in the Mg97Zn1.Y2 extruded alloy were discussed. Existence of the LPSO-phase strongly enhanced the refinement of Mg matrix grain size during extrusion, which led to a large increment of the strength of alloy. In addition, the LPSO-phases, which were aligned along the extrusion direction in Mg97Zn1.2 extruded alloy, acted as hardening phases, just like reinforced fibers.

关键词： plastic deformation yield stress LPSO-phase dislocation twinning

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A reliable knowledge processing framework for combustion science using foundation models

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Energy and AI 2024年第2期16卷 396-416页

作者： Vansh Sharma Venkat Raman department of Aerospace Engineering University of MichiganAnn Arbor48109-2102MIUSA

This research explores the integration of large language models (LLMs) into scientific data assimilation, focusing on combustion science as a case study. Leveraging foundational models integrated with Retrieval-Augmented Generation (RAG) framework, the study introduces an approach to process diverse combustion research data, spanning experimental studies, simulations, and literature. The multifaceted nature of combustion research emphasizes the critical role of knowledge processing in navigating and extracting valuable information from a vast and diverse pool of sources. The developed approach minimizes computational and economic expenses while optimizing data privacy and accuracy. It incorporates prompt engineering and offline open-source LLMs, offering user autonomy in selecting base models. The study provides a thorough examination of text segmentation strategies, conducts comparative studies between LLMs, and explores various optimized prompts to demonstrate the effectiveness of the framework. By incorporating an external vector database, the framework outperforms a conventional LLM in generating accurate responses and constructing robust arguments. Additionally, the study delves into the investigation of optimized prompt templates for the purpose of efficient extraction of scientific literature. Furthermore, we present a targeted scaling study to quantify the algorithmic performance of the framework as the number of prompt tokens increases. The research addresses concerns related to hallucinations and false research articles by introducing a custom workflow developed with a detection algorithm to filter out inaccuracies. Despite identified areas for improvement, the framework consistently delivers accurate domain-specific responses with minimal human oversight. The prompt-agnostic approach introduced holds promise for future improvements. The study underscores the significance of integrating LLMs and knowledge processing techniques in scientific research, provi

关键词： Large language models(LLM) Foundation models Combustion Knowledge processing Retrieval-augmented generation(RAG)

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MicroRNA-329-3p inhibits the Wnt/β-catenin pathway and proliferation of osteosarcoma cells by targeting transcription factor 7-like 1

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Oncology Research 2024年第3期32卷 463-476页

作者： Hur SUN MASANORI KAWANO TATSUYA IWASAKI ICHRO ITONAGA YUTA KUBOTA HROSHI TSUMURA KAZUHRO TANAKA department of Orthopaedic Surgery Faculty of MedicineOita UniversityOita879-5503Japan

An important factor in the emergence and progre sion of osteosarcoma(OS)is the dysregulated expression of microRNAs(miRNAs).Transcription factor 7-like 1.TCF7LI),a member of the T cell factor/lymphoid enhancer factor(TCF/LEF)transcription factor family,interacts with the Wnt signaling pathway regulator β-catenin and acts as a DNA-specific binding *** study sought to elucidate the impact of the interaction between miR 3293p and TCF7L1.*** growth and apoptosis of OS and analyze the regulatory expression relationship between miRNA and mRNA in osteosarcoma cells using a variety of ***329-3p was significantly downregulated,while TCF7L1.was considerably up-regulated in all examined OS cell ***,a clinical comparison study was performed using the TCGA ***,the regulatory relationship between miR-329-3p and TCF7L1.on the proliferation and apoptosis of OS cells was verified through in vitro and in vivo *** miR 329-3p was transfected into the OS cell line,the expression of TCF7L1.decreased,the proliferation of OS cells was inhibited,the cytoskeleton disintegrated,and the nucleus condensed to fom apoptotic *** expression of proteins that indicate apoptosis increased *** cell cycle was arrested in the G0/G1.phase,and the G1.S transition was *** introduction of miR 3293p also inhibited downstream Cyclin D1.of the Wnt *** experiments indicated that the overexpression of miR-329-3p signi ficanly inhibited the growth of OS xenografts in nude mice,and the expression of TCF7L1.and C-Myc in tumor tssues *** 329-3p was significantly reduced in OS cells and played a suppressive role in tumorigenesis and proliferation by targeting TCF7L1.both in vitro and in *** cell cycle arrest and pathway inhibition were observed upon the regulation of TCF7LI by miR *** these results,it can be inferred that miR.3293p exerts anticancer efects in osteosarcom

关键词： MiR-329-3p TCF7L1 Wnt/β-catenin pathway Osteosarcoma Proliferation

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Direct somatic embryogenesis and related gene expression networks in leaf explants of Hippeastrum ‘Bangkok Rose’

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Horticultural Plant Journal 2024年第2期10卷 556-572页

作者： Jingjue Zeng Yi Deng Shahid Iqbal Jiarui Zhang Kunlin Wu Guohua Ma Lin Li Guangyi Dai Rufang Deng Lin Fang Songjun Zeng Guangdong Provincial Key Laboratory of Applied Botany South China Botanical GardenChinese Academy of SciencesGuangzhouGuangdong 510650China University of the Chinese Academy of sciences Beijing 100049China South China National Botanical Garden GuangzhouGuangdong 510650China Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural science and Technology ZhaoqingGuangdong 526000China Horticultural science {1. North Florida Research and Education CenterUniversity of Florida/IFASQuincyFL 32351USA Public Laboratory of South China Botanical Garden Chinese Academy of SciencesGuangzhouGuangdong 510650China Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement South China Botanical GardenChinese Academy of SciencesGuangzhouGuangdong 510650China

Hippeastrum, a highly diverse genus in the Amaryllidaceae family, is a valuable ornamental bulbous flowering plant. Somatic embryogenesis(SE) is an efficient method for mass production of Hippeastrum plantlets. Previous studies have been devoted to the in vitro propagation of Hippeastrum, but the SE and its regulatory networks are rarely reported. In this study, we established a direct SE method of Hippeastrum Bangkok Rose' using leaf bases as explants. MS supplemented with 1.00 mg·L^(-1.NAA +1.00 mg·L^(-1.KT + 0.25 mg·L^(-1.TDZ was the optimal medium for SE. Histological observations showed that the bipolar somatic embryo originated from the epidermal cell layer and underwent initiation,globular, scutellar and coleoptile stages. During SE, endogenous hormones of IAA, CTK, ABA, and SA were highly accumulated. Transcriptomic analysis revealed the genes encoding auxin biosynthesis/metabolic enzymes and efflux carriers were induced, while the auxin receptor of TIR1.and ARF transcriptional repressor of Aux/IAA were down-regulated and up-regulated, respectively, leading to suppression of auxin signaling. In contrast, cytokine signaling was promoted at the early stage of SE, as biosynthesis, transport, and signaling components were *** stress-related genes were up-regulated at the early or late stages of SE. Chromatin remodeling could also be dynamically regulated via distinct expression enzymes that control histone methylation and acetylation during SE. Moreover, key SE regulators, including WOXs and SERKs were highly expressed along with SE. Overall, the present study provides insights into the SE regulatory mechanisms of the Hippeastrum.

关键词： Hippeastrum Tissue culture Somatic embryogenesis Gene regulation

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A Review of Type 1.and Type 2 Intraductal Papillary Neoplasms of the Bile Duct

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Current Medical science 2024年第3期44卷 485-493页

作者： Xia-hui HUANG Tian-xiang CHEN Hong-liang LIU Ming-wen HUANG department of General Surgery The Second Affiliated Hospital of Nanchang UniversityNanchang330006China

Intraductal papillary neoplasm of the bile duct(IPNB)is a heterogeneous disease similar to intraductal papillary mucinous neoplasm of the *** lesions have been recognized as one of the three major precancerous lesions in the biliary tract since *** 201.,Japanese and Korean pathologists reached a consensus,classifying IPNBs into type l and type 2 *** are more prevalent in male patients in East Asia and are closely related to diseases such as cholelithiasis and *** a molecular genetic perspective,IPNBs exhibit early genetic variations,and different molecular pathways may be involved in the tumorigenesis of type 1.and type 2 *** histological subtypes of IPNBs include gastric,intestinal,pancreaticobiliary,or oncocytic subtypes,but type 1.IPNBs typically exhibit more regular and well-organized histological features than type 2 IPNBs and are more commonly found in the intrahepatic bile ducts with abundant *** to the rarity of these lesions and the absence of specific clinical and laboratory features,imaging is crucial for the preoperative diagnosis of IPNB,with local bile duct dilation and growth along the bile ducts being the main imaging *** resection remains the optimal treatment for IPNBs,but negative bile duct margins and the removal of lymph nodes in the hepatic hilum significantly improve the postoperative survival rates for patients with IPNBs.

关键词： intraductal papillary neoplasm of the bile duct subclassification neoplasms precancerous tissue prognosis

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Synthesis of three-dimensional hierarchical cobalt hydroxide microstructures

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science China Chemistry 2010年第4期53卷 841-845页

作者： SONG XuChun1. ZHAO Yang2, ZHENG YiFan3, YANG E1.& LIU ZhiSheng1.1.nstitute of Physical Chemistry, department of Chemistry, Fujian Normal University, Fuzhou 350007, China 2department of Chemistry, Henan Normal University, Xinxiang 453007, China 3College of Chemical Engineering & Materials science, Zhejiang University of Technology, Hangzhou 31.01., China 1. Institute of Physical Chemistry Department of Chemistry Fujian Normal University Fuzhou 350007 China2. Department of Chemistry Henan Normal University Xinxiang 453007 China3. College of Chemical Engineering & Materials Science Zhejiang University of Technology Hangzhou 310014 China

β-Co(OH)2 with three-dimensional (3-D) structures was prepared by a simple hydrothermal method. It was found that the amount of cetyltrimethylammonium bromide (CTAB), the pH value, and the reaction time all had an important influence on the formation of this morphology. The products were characterized by X-ray diffraction, energy-dispersive X-ray analysis, and scanning electron microscopy. A possible mechanism of the formation of the 3-D microstructures of β-Co(OH)2 was proposed.

关键词： cobalt hydroxide microstructures hydrothermal

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Pachymic acid exerts antitumor activities by modulating the Wnt/β-catenin signaling pathway via targeting PTP1.

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Asian Pacific Journal of Tropical Biomedicine 2024年第4期14卷 170-180页

作者： Hao Zhang Kun Zhu Xue-Feng Zhang Yi-Hui Ding Bing Zhu Wen Meng Qing-Song Ding Fan Zhang department of Emergency Affiliated Hangzhou First People’s HospitalZhejiang University School of MedicineHangzhou 310006ZhejiangChina department of Cardiothoracic Surgery The Third Affiliated Hospital of Qiqihar Medical CollegeQiqihar 161000HeilongjiangChina department of Cardiothoracic Surgery The Affiliated Heilongjiang Provincial Hospital of Harbin Institute of TechnologyHarbin 150036HeilongjiangChina

Objective:To determine the inhibitory effects of pachymic acid on lung adenocarcinoma(LUAD)cells and elucidate its underlying ***:CCK-8,wound healing,Transwell,Western blot,tube formation,and immunofluorescence assays were carried out to measure the effects of various concentrations of pachymic acid on LUAD cell proliferation,metastasis,angiogenesis as well as ***,molecular docking technology was used to detect the potential targeted binding association between pachymic acid and protein tyrosine phosphatase 1.(PTP1.).Moreover,PTP1. was overexpressed in A549 cells to detect the specific mechanisms of pachymic ***:Pachymic acid suppressed LUAD cell viability,metastasis as well as angiogenesis while inducing cell *** also targeted PTP1. and lowered PTP1. ***,PTP1. overexpression reversed the effects of pachymic acid on metastasis,angiogenesis,and autophagy as well as the expression of Wnt3a andβ-catenin in LUAD ***:Pachymic acid inhibits metastasis and angiogenesis,and promotes autophagy in LUAD cells by modulating the Wnt/β-catenin signaling pathway via targeting PTP1..

关键词： Pachymic acid Lung adenocarcinoma Protein tyrosine phosphatase 1. Wnt/β-catenin signaling pathway Metastasis Angiogenesis Autophagy

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Influence of Intraseasonal Oscillation on the Asymmetric Decays of El Ni?o and La Ni?a

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Advances in atmospheric {1.s 2019年第8期36卷 779-792页

作者： Xiaomeng SONG Renhe ZHANG Xinyao RONG State Key Laboratory of Severe Weather Chinese Academy of Meteorological SciencesBeijing 100081China department of {1. and Oceanic sciences and Institute of {1. sciences Fudan UniversityShanghai 200433China

Warm and cold phases of El Nino–Southern Oscillation (ENSO) exhibit a significant asymmetry in their decay speed. To explore the physical mechanism responsible for this asymmetric decay speed, the asymmetric features of anomalous sea surface temperature (SST) and atmospheric circulation over the tropical Western Pacific (WP) in El Nino and La Nina mature-to-decay phases are analyzed. It is found that the interannual standard deviations of outgoing longwave radiation and 850 hPa zonal wind anomalies over the equatorial WP during El Nino (La Nina) mature-to-decay phases are much stronger (weaker) than the intraseasonal standard deviations. It seems that the weakened (enhanced) intraseasonal oscillation during El Nino (La Nina) tends to favor a stronger (weaker) interannual variation of the atmospheric wind, resulting in asymmetric equatorial WP zonal wind anomalies in El Nino and La Nina decay phases. Numerical experiments demonstrate that such asymmetric zonal wind stress anomalies during El Nino and La Nina decay phases can lead to an asymmetric decay speed of SST anomalies in the central-eastern equatorial Pacific through stimulating di erent equatorial Kelvin waves. The largest negative anomaly over the Nino3 region caused by the zonal wind stress anomalies during El Nino can be threefold greater than the positive Nino3 SSTA anomalies during La Nina, indicating that the stronger zonal wind stress anomalies over the equatorial WP play an important role in the faster decay speed during El Nino.

关键词： ENSO asymmetry ENSO decay intraseasonal oscillation OGCM

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