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Mechanisms and impacts of chromosomal translocations in cancers

null

《医学前沿（英文）》 2012年 第6卷 第3期   页码 263-274 doi: 10.1007/s11684-012-0215-5

摘要：

Chromosomal aberrations have been associated with cancer development since their discovery more than a hundred years ago. Chromosomal translocations, a type of particular structural changes involving heterologous chromosomes, have made a critical impact on diagnosis, prognosis and treatment of cancers. For example, the discovery of translocation between chromosomes 9 and 22 and the subsequent success of targeting the fusion product BCR-ABL transformed the therapy for chronic myelogenous leukemia. In the past few decades, tremendous progress has been achieved towards elucidating the mechanism causing chromosomal translocations. This review focuses on the basic mechanisms underlying the generation of chromosomal translocations. In particular, the contribution of frequency of DNA double strand breaks and spatial proximity of translocating loci is discussed.

关键词： DNA double strand breaks     chromosomal translocations     genomic instability     spatial proximity     carcinogenesis    

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Tumor growth and metastasis can be inhibited by maintaining genomic stability in cancer cells

null

《医学前沿（英文）》 2015年 第9卷 第1期   页码 57-62 doi: 10.1007/s11684-015-0389-8

摘要：

The existence of cancer stem cells, stem-like cancer cells (SLCCs), or tumor-initiating cells is considered as the cause of tumor formation and recurrence, indicating the importance of studying novel therapy that targets SLCCs. The origin of SLCCs is controversial because of two competing hypotheses: SLCCs are either transformed from tissue adult stem cells or dedifferentiated from transformed progenitor cells. Our previous research demonstrates that SLCCs are inducible by increasing genomic instability in cancer cells. In this study, to block the emergence of SLCCs, aminoethyl isothiourea (AET), a compound that clears free radicals and is used to protect patients from radioactive exposure, was used as an agent that maintains genomic stability in combination with mitomycin C (MMC), a commonly used chemotherapeutic drug that damages DNA. Using a rabbit tumor model with VX2 hepatic carcinoma, we found that MMC alone increased lung metastases and disadvantaged survival outcome, but the combination of MMC and AET reversed this effect and even prolonged overall survival. Moreover, in a VX2 xenograft model by immunocompromised mice, MMC alone enriched tumor-initiating cells, but the administration of MMC in combination with AET eliminated tumor cells effectively. Furthermore, MMC alone enhanced genomic instability, but MMC combined with AET attenuated the extent of genomic instability in primary VX2 tumor tissue. Taken together, our data suggest that the genomic protector AET can inhibit the induction of SLCCs, and this combination treatment by AET and cytotoxic agents should be considered as a promising strategy for future clinical evaluation.

关键词： rabbit VX2 liver tumor     mitomycin C     AET     stem-like cancer cells     genomic instability    

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Generation and repair of AID-initiated DNA lesions in B lymphocytes

null

《医学前沿（英文）》 2014年 第8卷 第2期   页码 201-216 doi: 10.1007/s11684-014-0324-4

摘要：

Activation-induced deaminase (AID) initiates the secondary antibody diversification process in B lymphocytes. In mammalian B cells, this process includes somatic hypermutation (SHM) and class switch recombination (CSR), both of which require AID. AID induces U:G mismatch lesions in DNA that are subsequently converted into point mutations or DNA double stranded breaks during SHM/CSR. In a physiological context, AID targets immunoglobulin (Ig) loci to mediate SHM/CSR. However, recent studies reveal genome-wide access of AID to numerous non-Ig loci. Thus, AID poses a threat to the genome of B cells if AID-initiated DNA lesions cannot be properly repaired. In this review, we focus on the molecular mechanisms that regulate the specificity of AID targeting and the repair pathways responsible for processing AID-initiated DNA lesions.

关键词： class switch recombination     somatic hypermutation     activation-induced deaminase     DNA repair     genomic instability    

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Statistical considerations for genomic selection

Huimin KANG, Lei ZHOU, Jianfeng LIU

《农业科学与工程前沿（英文）》 2017年 第4卷 第3期   页码 268-278 doi: 10.15302/J-FASE-2017164

摘要： Genomic selection is becoming increasingly important in animal and plant breeding, and is attracting greater attention for human disease risk prediction. This review covers the most commonly used statistical methods and some extensions of them, i.e., ridge regression and genomic best linear unbiased prediction, Bayesian alphabet, and least absolute shrinkage and selection operator. Then it discusses the measurement of the performance of genomic selection and factors affecting the prediction of performance. Among the measurements of prediction performance, the most important and commonly used measurement is prediction accuracy. In simulation studies where true breeding values are available, accuracy of genomic estimated breeding value can be calculated directly. In real or industrial data studies, either training-testing approach or -fold cross-validation is commonly employed to validate methods. Factors influencing the accuracy of genomic selection include linkage disequilibrium between markers and quantitative trait loci, genetic architecture of the trait, and size and composition of the training population. Genomic selection has been implemented in the breeding programs of dairy cattle, beef cattle, pigs and poultry. Genomic selection in other species has also been intensively researched, and is likely to be implemented in the near future.

关键词： genomic estimated breeding value     genomic selection     linkage disequilibrium     statistical methods    

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Combustion instability detection using the wavelet detail of pressure fluctuations

JI Junjie, LUO Yonghao

《能源前沿（英文）》 2008年 第2卷 第1期   页码 116-120 doi: 10.1007/s11708-008-0019-0

摘要： A combustion instability detection method that uses the wavelet detail of combustion pressure fluctuations is put forward. To confirm this method, combustion pressure fluctuations in a stoker boiler are recorded at stable and unstable combustion with a pressure transducer. Daubechies one-order wavelet is chosen to obtain the wavelet details for comparison. It shows that the wavelet approximation indicates the general pressure change in the furnace, and the wavelet detail magnitude is consistent with the intensity of turbulence and combustion noise. The magnitude of the wavelet detail is nearly constant when the combustion is stable, however, it will fluctuate much when the combustion is unstable.

关键词： comparison     wavelet approximation     pressure transducer     general pressure     consistent    

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海底不稳定性研究进展及展望

高伟健,李伟

《中国工程科学》 2023年 第25卷 第3期   页码 109-121 doi: 10.15302/J-SSCAE-2023.03.010

摘要：

海底不稳定性及次生海底地质灾害广泛存在于海洋之中，对海岸港口设施、海洋钻井平台、海底管道光缆等海底基础建设颇具威胁。但目前对海底不稳定性的成因机制与主控因素仍知之甚少，为加深对海底不稳定性的认识，本文回顾了海底不稳定性研究进展，梳理了海底不稳定性及次生海底地质灾害的主要类别、全球分布情况和地球物理识别特征，归纳了目前海底不稳定性研究的定量分析方法，进一步分析了其成因机制、控制因素及工程地质灾害风险，探讨了海底陆坡失稳演化过程试验模拟技术的适用范畴与技术瓶颈。最后，从海底不稳定性的致灾机理研究、多源数据智能分析和海底失稳立体监测3 个维度提出了未来海底不稳定性研究的发展方向与对策建议，以期为海底不稳定性的模拟、预测和预警等工作提供指导性建议。

关键词： 海底不稳定性；海底地质灾害；成因机制；风险评估；不稳定性分析    

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GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

《农业科学与工程前沿（英文）》 2021年 第8卷 第2期

摘要：

Horticultural crops are a major source of high value nutritious food, and new improved cultivars developed through breeding are required for sustainable production in the face of abiotic and biotic stresses, and to deliver novel, premium products to consumers. However, grower confidence in the performance of new germplasm, particularly across environmental variability, is important for commercial adoption and germplasm-environment matching to optimize production.

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GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

Craig HARDNER, Satish KUMAR, Dorrie MAIN, Cameron PEACE

《农业科学与工程前沿（英文）》   页码 353-355 doi: 10.15302/J-FASE-2021387

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Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer

《医学前沿（英文）》 doi: 10.1007/s11684-023-1008-8

摘要： Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human cancer. However, knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely limited. Here, by taking advantage of in situ Hi-C, RNA-sequencing, and chromatin immunoprecipitation sequencing (ChIP-seq), we investigated structural reorganization and functional changes in chromosomal compartments, topologically associated domains (TADs), and CCCTC binding factor (CTCF)-mediated loops in gallbladder cancer (GBC) tissues and cell lines. We observed that the chromosomal compartment A/B switch was correlated with CTCF binding levels and gene expression changes. Increased inter-TAD interactions with weaker TAD boundaries were identified in cancer cell lines relative to normal controls. Furthermore, the chromatin short loops and cancer unique loops associated with chromatin remodeling and epithelial–mesenchymal transition activation were enriched in cancer compared with their control counterparts. Cancer-specific enhancer–promoter loops, which contain multiple transcription factor binding motifs, acted as a central element to regulate aberrant gene expression. Depletion of individual enhancers in each loop anchor that connects with promoters led to the inhibition of their corresponding gene expressions. Collectively, our data offer the landscape of hierarchical layers of cancer genome and functional alterations that contribute to the development of GBC.

关键词： 3D genome     cancer     TADs     loop     gene regulation    

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Detection of genomic signatures for pig hairlessness using high-density SNP data

Ying SU,Yi LONG,Xinjun LIAO,Huashui AI,Zhiyan ZHANG,Bin YANG,Shijun XIAO,Jianhong TANG,Wenshui XIN,Lusheng HUANG,Jun REN,Nengshui DING

《农业科学与工程前沿（英文）》 2014年 第1卷 第4期   页码 307-313 doi: 10.15302/J-FASE-2014039

摘要： Hair provides thermal regulation for mammals and protects the skin from wounds, bites and ultraviolet (UV) radiation, and is important in adaptation to volatile environments. Pigs in nature are divided into hairy and hairless, which provide a good model for deciphering the molecular mechanisms of hairlessness. We conducted a genomic scan for genetically differentiated regions between hairy and hairless pigs using 60K SNP data, with the aim to better understand the genetic basis for the hairless phenotype in pigs. A total of 38405 SNPs in 498 animals from 36 diverse breeds were used to detect genomic signatures for pig hairlessness by estimating between-population ( ) values. Seven diversifying signatures between Yucatan hairless pig and hairy pigs were identified on pig chromosomes (SSC) 1, 3, 7, 8, 10, 11 and 16, and the biological functions of two notable genes, and were revealed. When Mexican hairless pigs were contrasted with hairypigs, strong signatures were detected on SSC1 and SSC10, which harbor two functionally plausible genes, and . KEGG pathway analysis showed a subset of overrepresented genes involved in the T cell receptor signaling pathway, MAPK signaling pathway and the tight junction pathways. All of these pathways may be important in local adaptability of hairless pigs. The potential mechanisms underlying the hairless phenotype in pigs are reported for the first time. and are interesting candidate genes for the hairless phenotype in Yucatan hairless and Mexico hairless pigs, respectively. , , and as well as other genes involved in the MAPK and T cell receptor signaling pathways may be important in environmental adaption by improved tolerance to UV damage in hairless pigs. These findings improve our understanding of the genetic basis for inherited hairlessness in pigs.

关键词： hairlessness     pig     selective sweeping    

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表面张力作用下柱形胶体的弹性失稳

黄殿武,乔玲,汪时机

《中国工程科学》 2007年 第9卷 第4期   页码 50-54

摘要：

采用弹性理论研究了圆柱形胶体在表面张力作用下的弹性失稳问题；利用能量泛函变分的方法导出 了发生弹性失稳的非经典边界条件，得到了失稳的判据方程。分析判据方程发现，弹性失稳与圆柱体的半径、 内禀尺度和失稳波长相关。

关键词： 柱形胶体     弹性失稳     内禀尺度     表面效应    

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工程饱和介质中漩涡光的调制不稳定性 Review

D.G. Pires, N.M. Litchinitser

《工程（英文）》 2022年 第17卷 第10期   页码 31-43 doi: 10.1016/j.eng.2022.04.022

摘要：

光束在水下环境、雾、云或生物组织等混浊介质中的传播在科学和技术中有着越来越重要的应用，包括生物成像、水下和自由空间通信技术。虽然这些应用在传统上依赖于常规的线性偏振高斯光束，但光具有许多未被发掘的自由度，如自旋角动量（SAM）和轨道角动量（OAM）。本文提出了具有“旋转”自由度的复杂光束在工程化非线性胶体介质中的非线性光-物质相互作用。利用变分法和摄动法，我们考虑了非圆柱光学涡旋、椭圆光学涡旋和高阶贝塞尔光束在时间上的积分（HOBBIT），来预测这些光束演化的动力学行为和稳定性。这些结果可应用于许多强散射环境下涉及光透射的情况。

关键词： Optical vortex     Orbital angular momentum     Modulation instability     Turbid media    

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Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

《医学前沿（英文）》   页码 889-906 doi: 10.1007/s11684-023-0994-x

摘要： Primary central nervous system lymphoma (PCNSL) is an uncommon non-Hodgkin’s lymphoma with poor prognosis. This study aimed to depict the genetic landscape of Chinese PCNSLs. Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples, whose genomic characteristics and clinicopathologic features were also analyzed. Structural variations were identified in all patients with a mean of 349, which did not significantly influence prognosis. Copy loss occurred in all samples, while gains were detected in 77.9% of the samples. The high level of copy number variations was significantly associated with poor progression-free survival (PFS) and overall survival (OS). A total of 263 genes mutated in coding regions were identified, including 6 newly discovered genes (ROBO2, KMT2C, CXCR4, MYOM2, BCLAF1, and NRXN3) detected in ≥ 10% of the cases. CD79B mutation was significantly associated with lower PFS, TMSB4X mutation and high expression of TMSB4X protein was associated with lower OS. A prognostic risk scoring system was also established for PCNSL, which included Karnofsky performance status and six mutated genes (BRD4, EBF1, BTG1, CCND3, STAG2, and TMSB4X). Collectively, this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs, thereby enriching the present understanding of the genetic mechanisms of PCNSL.

关键词： primary central nervous system lymphoma     whole-genome sequencing     TMSB4X     copy number variation     gene mutation    

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Genomic variations in the counterpart normal controls of lung squamous cell carcinomas

null

《医学前沿（英文）》 2018年 第12卷 第3期   页码 280-288 doi: 10.1007/s11684-017-0580-1

摘要：

Lung squamous cell carcinoma (LUSC) causes approximately 400 000 deaths each year worldwide. The occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomic abnormalities. However, few studies have investigated the genomic variations that occur only in normal tissues that have been similarly exposed to tobacco smoke as tumor tissues. In this study, we sequenced the whole genomes of three normal lung tissue samples and their paired adjacent squamous cell carcinomas. We then called genomic variations specific to the normal lung tissues through filtering the genomic sequence of the normal lung tissues against that of the paired tumors, the reference human genome, the dbSNP138 common germline variants, and the variations derived from sequencing artifacts. To expand these observations, the whole exome sequences of 478 counterpart normal controls (CNCs) and paired LUSCs of The Cancer Genome Atlas (TCGA) dataset were analyzed. Sixteen genomic variations were called in the three normal lung tissues. These variations were confirmed by Sanger capillary sequencing. A mean of 0.5661 exonic variations/Mb and 7.7887 altered genes per sample were identified in the CNC genome sequences of TCGA. In these CNCs, C:G→T:A transitions, which are the genomic signatures of tobacco carcinogen N-methyl-N-nitro-N-nitrosoguanidine, were the predominant nucleotide changes. Twenty five genes in CNCs had a variation rate that exceeded 2%, including ARSD (18.62%), MUC4 (8.79%), and RBMX (7.11%). CNC variations in CTAGE5 and USP17L7 were associated with the poor prognosis of patients with LUSC. Our results uncovered previously unreported genomic variations in CNCs, rather than LUSCs, that may be involved in the development of LUSC.

关键词： lung cancer     counterpart normal control     genomic variations    

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Underlying mechanism of the hydrothermal instability of Cu

Nadeen Al-Janabi,Abdullatif Alfutimie,Flor R. Siperstein,Xiaolei Fan

《化学科学与工程前沿（英文）》 2016年 第10卷 第1期   页码 103-107 doi: 10.1007/s11705-015-1552-0

摘要： Water induced decomposition of Cu (BTC) (BTC= benzene-1,3,5-tricarboxylate) metal-organic framework (MOF) was studied using dynamic water vapour adsorption. Small-angle X-ray scattering, Fourier transform infrared spectroscopy and differential scanning calorimetry analyses revealed that the underlying mechanism of Cu (BTC) MOF decomposition under humid streams is the interpenetration of water molecules into Cu-BTC coordination to displace organic linkers (BTC) from Cu centres.

关键词： hydrothermal stability     metal-organic framework (MOF)     open metal sites (OMSs)     dynamic water vapour adsorption    

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标题 作者 时间 类型 操作

Mechanisms and impacts of chromosomal translocations in cancers

null

期刊论文

Tumor growth and metastasis can be inhibited by maintaining genomic stability in cancer cells

null

期刊论文

Generation and repair of AID-initiated DNA lesions in B lymphocytes

null

期刊论文

Statistical considerations for genomic selection

Huimin KANG, Lei ZHOU, Jianfeng LIU

期刊论文

Combustion instability detection using the wavelet detail of pressure fluctuations

JI Junjie, LUO Yonghao

期刊论文

海底不稳定性研究进展及展望

高伟健,李伟

期刊论文

GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

期刊论文

GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK

Craig HARDNER, Satish KUMAR, Dorrie MAIN, Cameron PEACE

期刊论文

Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer

期刊论文

Detection of genomic signatures for pig hairlessness using high-density SNP data

Ying SU,Yi LONG,Xinjun LIAO,Huashui AI,Zhiyan ZHANG,Bin YANG,Shijun XIAO,Jianhong TANG,Wenshui XIN,Lusheng HUANG,Jun REN,Nengshui DING

期刊论文

表面张力作用下柱形胶体的弹性失稳

黄殿武,乔玲,汪时机

期刊论文

工程饱和介质中漩涡光的调制不稳定性

D.G. Pires, N.M. Litchinitser

期刊论文

Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

期刊论文

Genomic variations in the counterpart normal controls of lung squamous cell carcinomas

null

期刊论文

Underlying mechanism of the hydrothermal instability of Cu

Nadeen Al-Janabi,Abdullatif Alfutimie,Flor R. Siperstein,Xiaolei Fan

期刊论文