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Genome-wide analysis reveals selection for Chinese Rongchang pigs

Lei CHEN, Shilin TIAN, Long JIN, Zongyi GUO, Dan ZHU, Lan JING, Tiandong CHE, Qianzi TANG, Siqing CHEN, Liang ZHANG, Tinghuan ZHANG, Zuohua LIU, Jinyong WANG, Mingzhou LI

《农业科学与工程前沿（英文）》 2017年第4卷第3期页码 319-326 doi: 10.15302/J-FASE-2017161

摘要： Livestock have undergone domestication and consequently strong selective pressure on genes or genomic regions that control desirable traits. To identify selection signatures in the genome of Chinese Rongchang pigs, we generated a total of about 170 Gb of DNA sequence data with about 6.4-fold coverage for each of six female individuals. By combining these data with the publically available genome data of 10 Asian wild boars, we identified 449 protein-coding genes with selection signatures in Rongchang pigs, which are mainly involved in growth and hormone binding, nervous system development, and drug metabolism. The accelerated evolution of these genes may contribute to the dramatic phenotypic differences between Rongchang pigs and Chinese wild boars. This study illustrated how domestication and subsequent artificial selection have shaped patterns of genetic variation in Rongchang pigs and provides valuable genetic resources that can enhance the use of pigs in agricultural production and biomedical studies.

关键词： domestication genome pig re-sequencing selection

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2014—2016年食品动物源RE-cmeABC阳性弯曲菌流行与耐药性现状 Article

刘德俊, 刘蔚雯, 李星, 姚红, 沈张奇, 汪洋, 沈建忠

《工程（英文）》 2020年第6卷第1期页码 34-39 doi: 10.1016/j.eng.2019.10.013

摘要：因此，本研究调查了2014—2016年连续三年间我国山东、上海和广东等三个重点养殖区食品动物源RE-cmeABC阳性弯曲菌的流行与耐药性现状。）结肠弯曲菌，空肠弯曲菌中RE-cmeABC的阳性率显著高于结肠弯曲菌。111株RE-cmeABC阳性空肠弯曲菌与46株RE-cmeABC阴性空肠弯曲菌相比在氟苯尼考、克林霉素和红霉素的耐药率上具有显著差异（P <然而，携带RE-cmeABC的菌株可以使环丙沙星与四环素对弯曲菌的MIC值分布趋于更高水平范围。本研究表明RE-cmeABC已在我国食品动物源弯曲菌中广泛流行，对公共卫生安全具有潜在威胁。

关键词： RE- cmeABC 弯曲菌环丙沙星氟苯尼考

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Development of small-molecule viral inhibitors targeting various stages of the life cycle of emerging and re-emerging

null

《医学前沿（英文）》 2017年第11卷第4期页码 449-461 doi: 10.1007/s11684-017-0589-5

摘要：

In recent years, unexpected outbreaks of infectious diseases caused by emerging and re-emerging viruses have become more frequent, which is possibly due to environmental changes. These outbreaks result in the loss of life and economic hardship. Vaccines and therapeutics should be developed for the prevention and treatment of infectious diseases. In this review, we summarize and discuss the latest progress in the development of small-molecule viral inhibitors against highly pathogenic coronaviruses, including severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, Ebola virus, and Zika virus. These viruses can interfere with the specific steps of viral life cycle by blocking the binding between virus and host cells, disrupting viral endocytosis, disturbing membrane fusion, and interrupting viral RNA replication and translation, thereby demonstrating potent therapeutic effect against various emerging and re-emerging viruses. We also discuss some general strategies for developing small-molecule viral inhibitors.

关键词： emerging and re-emerging viruses small-molecule inhibitor coronavirus Ebola virus Zika virus life cycle

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Exome sequencing greatly expedites the progressive research of Mendelian diseases

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《医学前沿（英文）》 2014年第8卷第1期页码 42-57 doi: 10.1007/s11684-014-0303-9

摘要：

The advent of whole-exome sequencing (WES) has facilitated the discovery of rare structure and functional genetic variants. Combining exome sequencing with linkage studies is one of the most efficient strategies in searching disease genes for Mendelian diseases. WES has achieved great success in the past three years for Mendelian disease genetics and has identified over 150 new Mendelian disease genes. We illustrate the workflow of exome capture and sequencing to highlight the advantages of WES. We also indicate the progress and limitations of WES that can potentially result in failure to identify disease-causing mutations in part of patients. With an affordable cost, WES is expected to become the most commonly used tool for Mendelian disease gene identification. The variants detected cumulatively from previous WES studies will be widely used in future clinical services.

关键词： genetics whole-exome sequencing Mendelian disease disease gene

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Responses to emerging and re-emerging infectious diseases: One world, One health

null

《医学前沿（英文）》 2018年第12卷第1期页码 1-2 doi: 10.1007/s11684-018-0619-y

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Accurate quantification of 3′-terminal 2′-O-methylated small RNAs by utilizing oxidative deep sequencing

《医学前沿（英文）》 2022年第16卷第2期页码 240-250 doi: 10.1007/s11684-021-0909-7

摘要： The continuing discoveries of novel classes of RNA modifications in various organisms have raised the need for improving sensitive, convenient, and reliable methods for quantifying RNA modifications. In particular, a subset of small RNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), are modified at their 3′-terminal nucleotides via 2′-O-methylation. However, quantifying the levels of these small RNAs is difficult because 2′-O-methylation at the RNA 3′-terminus inhibits the activity of polyadenylate polymerase and T4 RNA ligase. These two enzymes are indispensable for RNA labeling or ligation in conventional miRNA quantification assays. In this study, we profiled 3′-terminal 2′-O-methyl plant miRNAs in the livers of rice-fed mice by oxidative deep sequencing and detected increasing amounts of plant miRNAs with prolonged oxidation treatment. We further compared the efficiency of stem-loop and poly(A)-tailed RT-qPCR in quantifying plant miRNAs in animal tissues and identified stem-loop RT-qPCR as the only suitable approach. Likewise, stem-loop RT-qPCR was superior to poly(A)-tailed RT-qPCR in quantifying 3′-terminal 2′-O-methyl piRNAs in human seminal plasma. In summary, this study established a standard procedure for quantifying the levels of 3′-terminal 2′-O-methyl miRNAs in plants and piRNAs. Accurate measurement of the 3′-terminal 2′-O-methylation of small RNAs has profound implications for understanding their pathophysiologic roles in biological systems.

关键词： small RNAs 2′-O-methylation sequencing RT-qPCR

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TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

null

《医学前沿（英文）》 2015年第9卷第3期页码 322-330 doi: 10.1007/s11684-015-0408-9

摘要：

This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma (HCC) by comparing the global gene expression profiles between tumors and their corresponding non-tumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated (CENPF and FOXM1) and downregulated (CLEC4G, CRHBP, and CLEC1B) genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.

关键词： TCGA whole-transcriptome sequencing HCC liver cancer

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碳中和目标下我国再电气化研究

舒印彪 ,谢典 ,赵良 ,高亚静 ,赵勇 ,周朝阳

《中国工程科学》 2022年第24卷第3期页码 195-204 doi: 10.15302/J-SSCAE-2022.03.020

摘要：

我国将碳达峰、碳中和纳入生态文明建设总体布局，电力在引领绿色发展中将发挥更加重要的作用。实施再电气化，实现能源生产侧“清洁替代”和能源消费侧“电能替代”，对我国如期实现碳达峰、碳中和目标具有重要意义。本文剖析了再电气化的核心内涵，结合基本国情及资源禀赋，提出以再电气化助力我国实现低碳发展，按照“终端能源需求—能源转换系统—一次能源结构”的研究框架，综合考虑经济、技术、政策、环境等要素，分析了不同情景下我国能源电力演变趋势，提出再电气化发展前景。研究结果表明，实施再电气化将有力推动实现碳中和目标，2060 年非化石能源消费比重达80%以上、清洁能源发电量比重达90%、终端电能消费比重达70%。研究建议，一是统筹协调好各行业碳预算与减排路径，二是加快经济、产业结构调整，三是推动关键领域科技创新，四是完善电力市场、碳市场体系建设。

关键词：再电气化；碳中和；能源转型；电能替代

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Influence of increasing numbers of RE-inverters on the power quality in the distribution grids: A PQ

Przemyslaw JANIK, Grzegorz KOSOBUDZKI, Harald SCHWARZ

《能源前沿（英文）》 2017年第11卷第2期页码 155-167 doi: 10.1007/s11708-017-0469-3

摘要： This paper presents the selected power quality (PQ) indicia of a wind generator and a photovoltaic installation considered to be the representative of medium voltage and low voltage distribution grids. The analysis of measured values suggests that the decrease in PQ is a case of specific combination of distributed generation, grid parameters and load behaviour. Modern generators have a limited impact on PQ. On the other hand, fluctuations in power generation are regarded as an emerging PQ indicator. The growing number of distributed renewable installations causes stochastic, variable, and hardly predictable power flows in the distribution grid. The nature of fluctuations in wind and solar generation is different. In both cases, new indexes for the quantification of fluctuations are needed and are yet not standardised. Proper assessment of these fluctuations enables definition of useful fluctuation limits and rules for optimal storage system integration.

关键词： power quality harmonics sags photovoltaic(PV) system doubly feed induction generator (DFIG) inverters

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Exploring the cancer genome in the era of next-generation sequencing

null

《医学前沿（英文）》 2012年第6卷第1期页码 48-55 doi: 10.1007/s11684-012-0182-x

摘要：

The emergence of next-generation sequencing technologies has led to dramatic advances in cancer genome studies. The increased efficiency and resolution of next-generation sequencing greatly facilitate the detection of genetic, genomic, and epigenomic alterations, such as single nucleotide mutations, small insertions and deletions, chromosomal rearrangements, copy number variations, and DNA methylation. Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome sequencing has significantly improved the understanding of cancer biology, diagnosis, and therapy. The present study briefly reviews the recent pioneering studies on cancer genome sequencing and provides an unprecedented insight into the landscape of genomic alterations in human sporadic cancers.

关键词： next-generation sequencing cancer genome whole genome sequencing exome transcriptome

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Comparative study on microbial community in intermittently aerated sequencing batch reactors (SBR) and

Xiaolin Sheng, Rui Liu, Xiaoyan Song, Lujun Chen, Kawagishi Tomoki

《环境科学与工程前沿（英文）》 2017年第11卷第3期 doi: 10.1007/s11783-017-0929-3

摘要： A traditional sequencing batch reactor (SBR) and two intermittently aerated sequencing batch reactors (IASBRs) were parallelly operated for treating digested piggery wastewater. Their microbial communities were analyzed, and the nitrogen removal performance was compared during the long–term run. IASBRs demonstrated higher removal rates of total nitrogen (TN) and ammonium nitrogen (NH -N) than the SBR, and also demonstrated higher resistance against TN shock load. It was found that the more switch times between aerobic/anoxic in an IASBR, the higher the removal rates of TN and NH –N. All the reactors were predominated by , and , which were considered to be species of denitrifiers, ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB), respectively. However, the abundance and diversity was of great difference. Compared with SBR, IASBRs achieved higher abundance of denitrification–related bacteria. IASBR 1 with four aerobic/anoxic switch times was detected with 25.63% of , higher than that in IASBR 2 with two aerobic/anoxic switch times (11.57% of ), and much higher than that in the SBR (only 6.19% of ). IASBR 2 had the highest percentage of AOB, while IASBR 1 had the lowest percentage. The denitrifiers abundance was significantly positive correlated with the TN removal rate. However, the NH –N removal rate showed no significant correlation with the AOB abundance, but might relate to the AOB activity which was influenced by the average free ammonium (FA) concentration. was the only NOB genus detectable in all reactors, and were less than 0.03%.

关键词： Digested piggery wastewater Intermittent aeration Microbial community Partial nitrification–denitrification process Sequencing batch reactor (SBR)

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Landscape of emerging and re-emerging infectious diseases in China: impact of ecology, climate, and behavior

null

《医学前沿（英文）》 2018年第12卷第1期页码 3-22 doi: 10.1007/s11684-017-0605-9

摘要：

For the past several decades, the infectious disease profile in China has been shifting with rapid developments in social and economic aspects, environment, quality of food, water, housing, and public health infrastructure. Notably, 5 notifiable infectious diseases have been almost eradicated, and the incidence of 18 additional notifiable infectious diseases has been significantly reduced. Unexpectedly, the incidence of over 10 notifiable infectious diseases, including HIV, brucellosis, syphilis, and dengue fever, has been increasing. Nevertheless, frequent infectious disease outbreaks/events have been reported almost every year, and imported infectious diseases have increased since 2015. New pathogens and over 100 new genotypes or serotypes of known pathogens have been identified. Some infectious diseases seem to be exacerbated by various factors, including rapid urbanization, large numbers of migrant workers, changes in climate, ecology, and policies, such as returning farmland to forests. This review summarizes the current experiences and lessons from China in managing emerging and re-emerging infectious diseases, especially the effects of ecology, climate, and behavior, which should have merits in helping other countries to control and prevent infectious diseases.

关键词： infectious disease profile emerging infectious diseases influence factor

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Simultaneous denitrifying phosphorus accumulation in a sequencing batch reactor

YUAN Linjiang, HAN Wei, WANG Lei, YANG Yongzhe, WANG Zhiying

《环境科学与工程前沿（英文）》 2007年第1卷第1期页码 23-27 doi: 10.1007/s11783-007-0004-6

摘要： In order to achieve simultaneous nitrogen and phosphorus removal in the biological treatment process, denitrifying phosphorus accumulation (DNPA) and its affecting factors were studied in a sequencing batch reactor (SBR) with synthetic wastewater. The results showed that when acetate was used as the sole carbon resource in the influent, the sludge acclimatized under anaerobic/aerobic operation had good phosphorus removal ability. Denitrifying phosphorus accumulation was observed soon when fed with nitrate instead of aeration following the anaerobic stage, which is a vital premise to DNPA. If DNPA sludge is fed with nitrate prior to the anaerobic stage, the DNPA would weaken or even disappear. At the high concentration of nitrate fed in the anoxic stage, the longer anoxic time needed, the better the DNPA was. Induced DNPA did not disappear even though an aerobic stage followed the anoxic stage, but the shorter the aerobic stage lasted, the higher the proportions of phosphorus removal via DNPA to total removal.

关键词： SBR synthetic wastewater Induced DNPA resource removal ability

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Improvement of nitrification efficiency by bioaugmentation in sequencing batch reactors at low temperature

Di CUI,Ang LI,Tian QIU,Rui CAI,Changlong PANG,Jihua WANG,Jixian YANG,Fang MA,Nanqi REN

《环境科学与工程前沿（英文）》 2014年第8卷第6期页码 937-944 doi: 10.1007/s11783-014-0668-7

摘要： Bioaugmentation is an effective method of treating municipal wastewater with high ammonia concentration in sequencing batch reactors (SBRs) at low temperature (10°C). The cold-adapted ammonia- and nitrite- oxidizing bacteria were enriched and inoculated, respectively, in the bioaugmentation systems. In synthetic wastewater treatment systems, the average -N removal efficiency in the bioaugmented system (85%) was much higher than that in the unbioaugmented system. The effluent -N concentration of the bioaugmented system was stably below 8 mg·L after 20 d operation. In municipal wastewater systems with bioaugmentation, the effluent -N concentration was below 8 mg·L after 15 d operation. The average -N removal efficiency in unbioaugmentation system (about 82%) was lower compared with that in the bioaugmentation system. By inoculating the cold-adapted nitrite-oxidizing bacteria (NOB) into the SBRs after 10 d operation, the nitrite concentration decreased rapidly, reducing the -N accumulation effectively at low temperature. The functional microorganisms were identified by PCR-DGGE, including uncultured sp., uncultured sp., sp. and uncultured sp. The results suggested that the cold-adapted microbial agent of ammonia-oxidizing bacteria (AOB) and NOB could accelerate the start-up and promote achieving the stable operation of the low-temperature SBRs for nitrification.

关键词： nitrification sequencing batch reactors (SBRs) bioaugmentation low temperature

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METAGENOMICS COMBINED WITH HIGH-THROUGHPUT SEQUENCING REVEALS THE METHANOGENIC POTENTIAL OF FRESH CORN

《农业科学与工程前沿（英文）》 doi: 10.15302/J-FASE-2022471

摘要：

● Methane production from fresh straw was 7.50% higher than dry straw.

关键词： fresh corn straw high solid anaerobic digestion metagenomics microbial communities thermophilic

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标题作者时间类型操作

Genome-wide analysis reveals selection for Chinese Rongchang pigs

Lei CHEN, Shilin TIAN, Long JIN, Zongyi GUO, Dan ZHU, Lan JING, Tiandong CHE, Qianzi TANG, Siqing CHEN, Liang ZHANG, Tinghuan ZHANG, Zuohua LIU, Jinyong WANG, Mingzhou LI

期刊论文

2014—2016年食品动物源RE-cmeABC阳性弯曲菌流行与耐药性现状

刘德俊, 刘蔚雯, 李星, 姚红, 沈张奇, 汪洋, 沈建忠

期刊论文

Development of small-molecule viral inhibitors targeting various stages of the life cycle of emerging and re-emerging

null

期刊论文

Exome sequencing greatly expedites the progressive research of Mendelian diseases

null

期刊论文

Responses to emerging and re-emerging infectious diseases: One world, One health

null

期刊论文

Accurate quantification of 3′-terminal 2′-O-methylated small RNAs by utilizing oxidative deep sequencing

期刊论文

TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

null

期刊论文

碳中和目标下我国再电气化研究

舒印彪 ,谢典 ,赵良 ,高亚静 ,赵勇 ,周朝阳

期刊论文

Influence of increasing numbers of RE-inverters on the power quality in the distribution grids: A PQ

Przemyslaw JANIK, Grzegorz KOSOBUDZKI, Harald SCHWARZ

期刊论文

Exploring the cancer genome in the era of next-generation sequencing

null

期刊论文

Comparative study on microbial community in intermittently aerated sequencing batch reactors (SBR) and

Xiaolin Sheng, Rui Liu, Xiaoyan Song, Lujun Chen, Kawagishi Tomoki

期刊论文

Landscape of emerging and re-emerging infectious diseases in China: impact of ecology, climate, and behavior

null

期刊论文

Simultaneous denitrifying phosphorus accumulation in a sequencing batch reactor

YUAN Linjiang, HAN Wei, WANG Lei, YANG Yongzhe, WANG Zhiying

期刊论文

Improvement of nitrification efficiency by bioaugmentation in sequencing batch reactors at low temperature

Di CUI,Ang LI,Tian QIU,Rui CAI,Changlong PANG,Jihua WANG,Jixian YANG,Fang MA,Nanqi REN

期刊论文

METAGENOMICS COMBINED WITH HIGH-THROUGHPUT SEQUENCING REVEALS THE METHANOGENIC POTENTIAL OF FRESH CORN

期刊论文

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