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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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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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Effects of sulfur on variations in the chemical speciation of heavy metals from fly ash glass

《环境科学与工程前沿（英文）》 2023年 第17卷 第10期 doi: 10.1007/s11783-023-1728-7

摘要：

● A higher sulfur content reduced the curing rate of Cr in glass.

关键词： Dechlorinated fly ash     SO3     Heavy metal     Chemical speciation     Glass solidification    

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Seasonal and treatment-process variations in invertebrates in drinking water treatment plants

Zhiling Wu, Xianchun Tang, Hongbin Chen

《环境科学与工程前沿（英文）》 2021年 第15卷 第4期 doi: 10.1007/s11783-020-1354-6

摘要： Abstract • Seasonal and treatment-process variations in invertebrates in a DWTP were analyzed. • The propagation and leakage of invertebrates in BAC filter were the most serious. • Invertebrates can survive and reproduce in chlorine disinfected clear water tanks. • Proportions of endogenous invertebrates increased along the treatment process. Problems associated with excessive propagation and leakage of invertebrates in drinking water have received increasing attention in recent years. We performed a monthly survey of invertebrate abundance and taxa in the effluent of each treatment stage in a drinking water treatment plant between May 2015 and April 2016 and analyzed seasonal and treatment-process variations in invertebrates. The results showed that invertebrate abundances in raw water, effluent of the biological activated carbon (BAC) filter, and finished water significantly correlated with water temperature, whereas no correlation was observed between water temperature and invertebrate abundance in the effluents of the sedimentation tank and sand filter. The dominant taxa in the effluent of each treatment stage were rotifers, nematodes, and crustaceans. The sedimentation tank could efficiently remove invertebrates with an annual average removal rate of 92%. The propagation and leakage of invertebrates occurred in the sand and BAC filters but more seriously in the latter. The average reproduction rate in the BAC filter was 268.8% with rotifers as the taxon that leaked the most. Invertebrate survival and reproduction were also observed in the chlorine-disinfected clean water reservoir with an average reproduction rate of 41.9%. Owing to differences in chlorine resistance, the reproduction ability of the dominant taxa was in the order nematodes>crustaceans>rotifers. The proportion of endogenous invertebrates gradually increased along the treatment process. The average proportion of endogenous invertebrates in the finished water was higher than 79.0%. Our findings suggested that waterworks should pay more attention to endogenous invertebrate growth.

关键词： Invertebrates     Drinking water     Seasonal variations     Treatment process    

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Bioaerosol emissions variations in large-scale landfill region and their health risk impacts

《环境科学与工程前沿（英文）》 2022年 第16卷 第12期 doi: 10.1007/s11783-022-1593-9

摘要：

● The airborne bacteria in landfills were 4–50 times higher than fungi.

关键词： Microbial aerosols     Landfill sites     Health risk assessment     CALPUFF    

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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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Investigations on color variations of Morpho rhetenor butterfly wing scales

Guanglan LIAO, Haibo ZUO, Xuan JIANG, Xuefeng YANG, Tielin SHI

《机械工程前沿（英文）》 2012年 第7卷 第4期   页码 394-400 doi: 10.1007/s11465-012-0347-y

摘要：

Experiments and simulations are carried out to investigate the optical properties of butterfly wing scales. The upper surface of a male butterfly wing presents a single-layer of scales, the microstructures of which are responsible for the brilliant blue color. The color varies from cyan blue to yellow green and soon afterwards returns back to cyan blue when some ethanol is dropped on the upper surface. At the start of the ethanol volatilization process, the reflection spectrum remains stable. As the ethanol further volatilizes, the peak reflectance decreases slightly, then increases dramatically. Meanwhile, the peak wavelength keeps approximately constant, then decreases, and keeps almost stable at the end of the process. Therefore, the optical properties depend strongly on the varying ambient conditions, including the refractive index and the thickness of the packing medium. Moreover, the possible causes for the scales in dark green region after several dropping ethanol experiments are clarified. This research benefits our understanding of the color variation mechanisms of the wing scales, and provides inspiration for further studies and applications.

关键词： Morpho rhetenor     microstructures     color variations     ambient medium    

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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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Seasonal variations of transport pathways andpotential sources of PM

Yuan Chen, Shaodong Xie, Bin Luo

《环境科学与工程前沿（英文）》 2018年 第12卷 第1期 doi: 10.1007/s11783-018-1009-z

摘要： Seasonal pattern of transport pathways and potential sourcesof PM in Chengdu during 2012–2013were investigated based on hourly PM data,backward trajectories, clustering analysis, potential source contributionfunction (PSCF), and concentration-weighted trajectory (CWT) method.The annual hourly mean PM concentrationin Chengdu was 97.4 mg·m . 5, 5, 5 and 3 mean clusters were generatedin four seasons, respectively. Short-distance air masses, which travelledwithin the Sichuan Basin with no specific source direction and relativelyhigh PM loadings (>80 mg·m ) appearedas important pathways in all seasons. These short pathways indicatedthat emissions from both local and surrounding regions of Chengducontributed significantly to PM pollution.The cities in southern Chengdu were major potential sources with PSCF>0.6and CWT>90 mg·m . The northeastern pathway prevailed throughoutthe year with higher frequency in autumn and winter and lower frequencyin spring and summer. In spring, long-range transport from southernXinjiang was a representative dust invasion path to Chengdu, and theCWT values along the path were 30-60 mg·m . Long-range transportwas also observed in autumn from southeastern Xinjiang along a northwesterlypathway, and in winter from the Tibetan Plateau along a westerly pathway.In summer, the potential source regions of Chengdu were smaller thanthose in other seasons, and no long-range transport pathway was observed.Results of PSCF and CWT indicated that regions in Qinghai and Tibetcontributed to PM pollution in Chengdu aswell, and their CWT values increased to above 30 mg·m in winter.

关键词： Transport pathway     Backwardtrajectory     Clustering analysis     Potential source     Chengdu    

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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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Spatio-temporal variations of water quality in Yuqiao Reservoir Basin, North China

Yuan XU,Ruqin XIE,Yuqiu WANG,Jian SHA

《环境科学与工程前沿（英文）》 2015年 第9卷 第4期   页码 649-664 doi: 10.1007/s11783-014-0702-9

摘要： Fuzzy comprehensive assessment and multivariate statistical techniques including cluster analysis, discriminant analysis, principal component analysis, and factor analysis were applied to analyze the water quality status of Yuqiao Reservoir Basin, North China, for assessing its spatio-temporal variations and identifying potential pollution sources. In this paper, we considered data for 14 water quality parameters collected during 1990–2004 at 7 water quality monitoring sites. The results of fuzzy comprehensive assessment revealed that water quality in Yuqiao Reservoir Basin showed a downtrend from 1990 to 2001 with fluctuation, and a slowly upward trend after 2001. The major water quality belonged to Class III and IV. Besides, hierarchical cluster analysis divided 7 monitoring sites into two groups (Group A and B), and 12 months into three periods (low-flow (LF), normal-flow (NF), and high-flow (HF) period). Temp, pH, SS, T-har, DO, NO -N and TP were identified as significant variables affecting spatial variations, and Temp, pH and NO -N were identified as significant variables affecting temporal variations by discriminant analysis. Factor analysis identified four latent pollution sources for water quality variations: nutrient pollution, organic pollution, inorganic pollution, and natural pollution. Moreover, for Group A regions, pollution inputs mainly came from domestic wastewater and industrial sewage. For Group B regions, it is more likely that water pollution resulted from the combined effects of domestic wastewater, hospital wastewater, agriculture runoff, and fishpond discharge, as well as the incoming water from upstream.

关键词： Fuzzy comprehensive assessment     multivariate statistical analysis     water quality    

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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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Robust design approach to the minimization of functional performance variations of products and systems

J. ZHANG, H. DU, D. XUE, P. GU

《机械工程前沿（英文）》 2021年 第16卷 第2期   页码 379-392 doi: 10.1007/s11465-020-0607-1

摘要： Functional performance variations of products and systems are often used to measure the qualities of products and systems considering the changes in the design parameter values caused by uncertainties. A robust design approach has been developed in this research to minimize the functional performance variations considering the design parameter uncertainties by identifying the boundaries of the functional performance variations through optimization. In this work, a mathematical model is developed to describe the relationships among functional performance, design configurations and parameters, and design parameter uncertainties. A multi-level optimization model is established to identify: (1) The optimal design configuration, (2) the optimal values of design parameters, and (3) the boundaries of functional performance variations. Sensitivity analysis considering the impact of parameter uncertainties on functional performance variation boundaries has also been conducted. A case study on the design of a truss system has been conducted. Case study results show that the sensitivities of functional performance variation boundaries to the design parameter uncertainties can be reduced significantly using the new robust design approach.

关键词： product design     robust design     design optimization     uncertainties    

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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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标题 作者 时间 类型 操作

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

null

期刊论文

Statistical considerations for genomic selection

Huimin KANG, Lei ZHOU, Jianfeng LIU

期刊论文

Effects of sulfur on variations in the chemical speciation of heavy metals from fly ash glass

期刊论文

Seasonal and treatment-process variations in invertebrates in drinking water treatment plants

Zhiling Wu, Xianchun Tang, Hongbin Chen

期刊论文

Bioaerosol emissions variations in large-scale landfill region and their health risk impacts

期刊论文

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

期刊论文

Investigations on color variations of Morpho rhetenor butterfly wing scales

Guanglan LIAO, Haibo ZUO, Xuan JIANG, Xuefeng YANG, Tielin SHI

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

Seasonal variations of transport pathways andpotential sources of PM

Yuan Chen, Shaodong Xie, Bin Luo

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

Spatio-temporal variations of water quality in Yuqiao Reservoir Basin, North China

Yuan XU,Ruqin XIE,Yuqiu WANG,Jian SHA

期刊论文

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

期刊论文

Robust design approach to the minimization of functional performance variations of products and systems

J. ZHANG, H. DU, D. XUE, P. GU

期刊论文

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

null

期刊论文