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A post-GWAS replication study confirming the association of

Shaohua YANG,Chao QI,Yan XIE,Xiaogang CUI,Yahui GAO,Jianping JIANG,Li JIANG,Shengli ZHANG,Qin ZHANG,Dongxiao SUN

《农业科学与工程前沿（英文）》 2014年 第1卷 第4期   页码 321-330 doi: 10.15302/J-FASE-2014037

摘要： Genome-wide association studies with an Illumina Bovine50K chip have detected 105 SNPs associated with one or multiple milk production traits in the Chinese Holstein population. Of these, 38 significant SNPs detected with high confidence by both L1-TDT and MMRA methods were selected to further mine potential key genes affecting milk yield and milk composition. By blasting the flanking sequences of these 38 SNPs with the bovine genome sequence combined with comparative genomics analysis, 26 genes were found to contain or be near to such SNPs. Among them, the gene is merely 87 bp away from the significant SNP, Hapmap30383-BTC-005848. Hence, we report herein genotype-phenotype associations to further validate the genetic effects of the gene. By pooled DNA sequencing of 14 unrelated Holstein sires, a total of 18 with seven novel SNPs were identified. Among them, nine SNPs were in the 5′ regulatory region, one in exon 6 and the other in the 3′ UTR and 3′ regulatory region. A total of nine of these identified SNPs were successfully genotyped and analyzed by mass spectrometry for association with five milk production traits in an independent resource population. The results showed that these SNPs were statistically significant for more than two traits [ <(0.0001-0.0267)]. In addition, mRNA expression analyses revealed that was ubiquitous in eight different tissues, with a relatively higher expression level in the mammary gland than in other tissues. These findings, therefore, provide strong evidence for association of variants with milk yield and milk composition traits and may be applied in Chinese Holstein breeding programs.

关键词： GWAS     functional annotation     Chinese Holstein     milk production traits     C14H8orf33 gene     single nucleotide polymorphisms     association study    

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Profiling and annotation combined method formultimedia application specificMPSoCperformance estimation

Kai HUANG,Xiao-xu ZHANG,Si-wen XIU,Dan-dan ZHENG,Min YU,De MA,Kai HUANG,Gang CHEN,Xiao-lang YAN

《信息与电子工程前沿（英文）》 2015年 第16卷 第2期   页码 135-151 doi: 10.1631/FITEE.1400239

摘要： Accurate and fast performance estimation is necessary to drive design space exploration and thus support important design decisions. Current techniques are either time consuming or not accurate enough. In this paper, we solve these problems by presenting a hybrid method for multimedia multiprocessor system-on-chip (MPSoC) performance estimation. A general coverage analysis tool GNU gcov is employed to profile the execution statistics during the native simulation. To tackle the complexity and keep the analysis and simulation manageable, the orthogonalization of communication and computation parts is adopted. The estimation result of the computation part is annotated to a transaction accurate model for further analysis, by which a gradual refinement of MPSoC performance estimation is supported. The implementation and its experimental results prove the feasibility and efficiency of the proposed method.

关键词： MPSoC     Gradual refinement     Native simulation     Performance estimation     Profiling     Annotation     Gcov    

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Annotation and validation of genes involved in photosynthesis and starch synthesis from a

Yang ZHANG,Xin CHEN,Haiyan WANG,Zhiqiang XIA,Peng LING,Wenquan WANG

《农业科学与工程前沿（英文）》 2016年 第3卷 第4期   页码 308-320 doi: 10.15302/J-FASE-2016113

摘要： A full-length cDNA library from leaf and root tissues of cassava ( ) Arg7 and one accession of its wild ancestor W14 ( ssp. ) has been constructed. The library is comprised of four sub-libraries, containing 32640 recombinant clones, 6028 cDNA clones from their 5′ ends, and 128 clones from the 3′ ends were sequenced. In total, 5013 high-quality expressed sequence tags (ESTs) and 1259 unigenes were obtained. Of these, 746 unigenes were identified by their sequence homologies to ESTs from model plants, and 323 unigenes were mapped onto 114 different KEGG pathways. From these, 24 differentially expressed genes involved in starch metabolism and photosynthesis were identified and five of them were selected to compare their expression level between Arg7 and W14. Notably, Arg7 has a higher net photosynthesis rate in leaves, higher ribulose-1,5-bisphosphate carboxy-lase oxygenase activities in leaves, and higher AGPase activity in roots. This resource is the first EST collection from wild cassava and should be of value for gene discovery, genome annotation and studies of evolution.

关键词： Manihot esculenta     expressed sequence tag     unigene     pathway     expression pattern    

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Comprehensive functional annotation of susceptibility variants identifies genetic heterogeneity between

Na Qin, Yuancheng Li, Cheng Wang, Meng Zhu, Juncheng Dai, Tongtong Hong, Demetrius Albanes, Stephen Lam, Adonina Tardon, Chu Chen, Gary Goodman, Stig E. Bojesen, Maria Teresa Landi, Mattias Johansson, Angela Risch, H-Erich Wichmann, Heike Bickeboller, Gadi Rennert, Susanne Arnold, Paul Brennan, John K. Field, Sanjay Shete, Loic Le Marchand, Olle Melander, Hans Brunnstrom, Geoffrey Liu, Rayjean J. Hung, Angeline Andrew, Lambertus A. Kiemeney, Shan Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil Caporaso, Penella Woll, Philip Lazarus, Matthew B. Schabath, Melinda C. Aldrich, Victoria L. Stevens, Guangfu Jin, David C. Christiani, Zhibin Hu, Christopher I. Amos, Hongxia Ma, Hongbing Shen

《医学前沿（英文）》 2021年 第15卷 第2期   页码 275-291 doi: 10.1007/s11684-020-0779-4

摘要： Although genome-wide association studies have identified more than eighty genetic variants associated with non-small cell lung cancer (NSCLC) risk, biological mechanisms of these variants remain largely unknown. By integrating a large-scale genotype data of 15 581 lung adenocarcinoma (AD) cases, 8350 squamous cell carcinoma (SqCC) cases, and 27 355 controls, as well as multiple transcriptome and epigenomic databases, we conducted histology-specific meta-analyses and functional annotations of both reported and novel susceptibility variants. We identified 3064 credible risk variants for NSCLC, which were overrepresented in enhancer-like and promoter-like histone modification peaks as well as DNase I hypersensitive sites. Transcription factor enrichment analysis revealed that USF1 was AD-specific while CREB1 was SqCC-specific. Functional annotation and gene-based analysis implicated 894 target genes, including 274 specifics for AD and 123 for SqCC, which were overrepresented in somatic driver genes (ER=1.95, =0.005). Pathway enrichment analysis and Gene-Set Enrichment Analysis revealed that AD genes were primarily involved in immune-related pathways, while SqCC genes were homologous recombination deficiency related. Our results illustrate the molecular basis of both well-studied and new susceptibility loci of NSCLC, providing not only novel insights into the genetic heterogeneity between AD and SqCC but also a set of plausible gene targets for post-GWAS functional experiments.

关键词： lung cancer     genome-wide association study     function annotation     immune     homologous recombination repair deficiency     genetic heterogeneity    

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Development and applications of functional gene microarrays in the analysis of the functional diversity

Zhili HE, Joy D. VAN NOSTRAND, Ye DENG, Jizhong ZHOU

《环境科学与工程前沿（英文）》 2011年 第5卷 第1期   页码 1-20 doi: 10.1007/s11783-011-0301-y

摘要： Functional gene arrays (FGAs) are a special type of microarrays containing probes for key genes involved in microbial functional processes, such as biogeochemical cycling of carbon, nitrogen, sulfur, phosphorus, and metals, biodegradation of environmental contaminants, energy processing, and stress responses. GeoChips are considered as the most comprehensive FGAs. Experimentally established probe design criteria and a computational pipeline integrating sequence retrieval, probe design and verification, array construction, data analysis, and automatic update are used to develop the GeoChip technology. GeoChip has been systematically evaluated and demonstrated to be a powerful tool for rapid, specific, sensitive, and quantitative analysis of microbial communities in a high-throughput manner. Several generations of GeoChip have been developed and applied to investigate the functional diversity, composition, structure, function, and dynamics of a variety of microbial communities from different habitats, such as water, soil, marine, bioreactor, human microbiome, and extreme ecosystems. GeoChip is able to address fundamental questions related to global change, bioenergy, bioremediation, agricultural operation, land use, human health, environmental restoration, and ecological theories and to link the microbial community structure to environmental factors and ecosystem functioning.

关键词： functional gene arrays (FGAs)     GeoChip     microbial communities     functional diversity/composition/structure     environmental factor     ecosystem functioning    

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Fluorescent probes and functional materials for biomedical applications

《化学科学与工程前沿（英文）》 2022年 第16卷 第10期   页码 1425-1437 doi: 10.1007/s11705-022-2163-1

摘要： Due to their simplicity in preparation, sensitivity and selectivity, fluorescent probes have become the analytical tool of choice in a wide range of research and industrial fields, facilitating the rapid detection of chemical substances of interest as well as the study of important physiological and pathological processes at the cellular level. In addition, many long-wavelength fluorescent probes developed have also proven applicable for in vivo biomedical applications including fluorescence-guided disease diagnosis and theranostics (e.g., fluorogenic prodrugs). Impressive progresses have been made in the development of sensing agents and materials for the detection of ions, organic small molecules, and biomacromolecules including enzymes, DNAs/RNAs, lipids, and carbohydrates that play crucial roles in biological and disease-relevant events. Here, we highlight examples of fluorescent probes and functional materials for biological applications selected from the special issues “Fluorescent Probes” and “Molecular Sensors and Logic Gates” recently published in this journal, offering insights into the future development of powerful fluorescence-based chemical tools for basic biological studies and clinical translation.

关键词： fluorescent probes     imaging     cell     biomedicine     biomolecules    

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Temporal dimension and water quality control in an emission trading scheme based on water environmental functional

Zhaoxing HAN, Zhenyao SHEN, Yongwei GONG, Qian HONG

《环境科学与工程前沿（英文）》 2011年 第5卷 第1期   页码 119-129 doi: 10.1007/s11783-011-0272-z

摘要： Emission trading is one of the most effective alternatives to controlling water pollution. Water environmental functional zone (WEFZ) is used to determine the water quality standard and identify the zone boundary for each river or reach. In this study, a new emission trading scheme was addressed based on WEFZ, accounting for both the temporal dimension and water quality control. A temporal factor of emission trading was proposed based on variations in the environmental capacity within a year by dividing the year into three periods, including high, normal, and low periods of environmental capacity. During each period, emission trading was implemented exclusively. A water quality-control scheme was suggested based on the water quality requirement in the water functional zone, in which the water quality at the downstream boundary of the zone was required to meet the water standard following auto-purification in the stream. Two methods of calculating water quality control are addressed for point-source pollution and non-point-source pollution. The calculated temporal dimension and water quality control were located in Dongxi River of the Daning Watershed in the Three Gorges Watershed. The high period was during June, July, and August, the normal period was during April, May, September, and October, and the low period was during January, February, March, November, and December. The results from the water quality calculation demonstrated that the discharge of point-source and non-point-source pollutions led to an excess of common contaminants at the downstream boundary of WEFZ. The temporal and spatial factors above should be incorporated into the emission trading scheme based on WEFZ.

关键词： emission trading     water functional zone     water quality control    

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A Study of the Functional Mechanism of Petrochemical Engineering Construction Project Management

Ji-ming Wang

《工程管理前沿（英文）》 2014年 第1卷 第2期   页码 129-139 doi: 10.15302/J-FEM-2014020

摘要： This paper, proceeding from the project construction process, the management mode and the implementation way, makes an in-depth study of the environmental characteristics and the managerial elements of petrochemical engineering construction project, revealing the inherent laws, establishing a theoretical model, and proposing a theory of the mechanisms of construction project management; and presents profound revelations found for construction project management in petrochemical engineering in seven aspects, which can play a guiding role in improving the managerial performance of petrochemical construction project. The theory established proposes that: The construction project management in petrochemical engineering is a complex systematic process, formed of 5 phases and 55 sub-processes of management, and exposed to many factors of influence; the environmental characteristics and managerial elements exercise positive impacts on managerial performance, but different factors have different impacts and act in different ways on managerial performance; the managerial elements of petrochemical engineering construction project are tiered, transferable, systematic and quantifiable, and the role of managerial elements in the managerial performance can be systematically integrated, quantitatively explained and transferred in a multi-level way.

关键词： petrochemical engineering     construction project     project management     functional mechanism    

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Effects of functional groups for CO

Chenkai Gu, Yang Liu, Weizhou Wang, Jing Liu, Jianbo Hu

《化学科学与工程前沿（英文）》 2021年 第15卷 第2期   页码 437-449 doi: 10.1007/s11705-020-1961-6

摘要： Metal organic frameworks (MOFs) are promising adsorbents for CO capture. Functional groups on organic linkers of MOFs play important roles in improving the CO capture ability by enhancing the CO sorption affinity. In this work, the functionalization effects on CO adsorption were systematically investigated by rationally incorporating various functional groups including –SO H, –COOH, –NH , –OH, –CN, –CH and –F into a MOF-177 template using computational methods. Asymmetries of electron density on the functionalized linkers were intensified, introducing significant enhancements of the CO adsorption ability of the modified MOF-177. In addition, three kinds of molecular interactions between CO and functional groups were analyzed and summarized in this work. Especially, our results reveal that –SO H is the best-performing functional group for CO capture in MOFs, better than the widely used –NH or –F groups. The current study provides a novel route for future MOF modification toward CO capture.

关键词： metal-organic frameworks     functional groups     CO2 capture     GCMC     DFT    

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Microbial community and functional genes in the rhizosphere of alfalfa in crude oil-contaminated soil

Yi ZHONG, Jian WANG, Yizhi SONG, Yuting LIANG, Guanghe LI

《环境科学与工程前沿（英文）》 2012年 第6卷 第6期   页码 797-805 doi: 10.1007/s11783-012-0405-z

摘要： A rhizobox system constructed with crude oil-contaminated soil was vegetated with alfalfa ( L.) to evaluate the rhizosphere effects on the soil microbial population and functional structure, and to explore the potential mechanisms by which plants enhance the removal of crude oil in soil. During the 80-day experiment, 31.6% of oil was removed from the adjacent rhizosphere (AR); this value was 27% and 53% higher than the percentage of oil removed from the far rhizosphere (FR) and from the non-rhizosphere (NR), respectively. The populations of heterotrophic bacteria and hydrocarbon-degrading bacteria were higher in the AR and FR than in the NR. However, the removal rate of crude oil was positively correlated with the proportion of hydrocarbon-degrading bacteria in the rhizosphere. In total, 796, 731, and 379 functional genes were detected by microarray in the AR, FR, and NR, respectively. Higher proportions of functional genes related to carbon degradation and organic remediation, were found in rhizosphere soil compared with NR soil, suggesting that the rhizosphere selectively increased the abundance of these specific functional genes. The increase in water-holding capacity and decrease in pH as well as salinity of the soil all followed the order of AR>FR>NR. Canonical component analysis showed that salinity was the most important environmental factor influencing the microbial functional structure in the rhizosphere and that salinity was negatively correlated with the abundance of carbon and organic degradation genes.

关键词： crude oil-contaminated soil     phytoremediation     rhizosphere effects     rhizobox     functional genes    

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Behavioral methods for the functional assessment of hair cells in zebrafish

null

《医学前沿（英文）》 2017年 第11卷 第2期   页码 178-190 doi: 10.1007/s11684-017-0507-x

摘要：

Zebrafish is an emerging animal model for studies on auditory system. This model presents high comparability with humans, good accessibility to the hearing organ, and high throughput capacity. To better utilize this animal model, methodologies need to be used to quantify the hearing function of the zebrafish. Zebrafish displays a series of innate and robust behavior related to its auditory function. Here, we reviewed the advantage of using zebrafish in auditory research and then introduced three behavioral tests, as follows: the startle response, the vestibular-ocular reflex, and rheotaxis. These tests are discussed in terms of their physiological characteristics, up-to-date technical development, and apparatus description. Test limitation and areas to improve are also introduced. Finally, we revealed the feasibility of these applications in zebrafish behavioral assessment and their potential in the high-throughput screening on hearing-related genes and drugs.

关键词： zebrafish (Danio rerio)     behavior     auditory     startle response     vestibular-ocular reflex     rheotaxis    

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Characterization and comparison of organic functional groups effects on electrolyte performance for vanadium

《化学科学与工程前沿（英文）》 2023年 第17卷 第9期   页码 1221-1230 doi: 10.1007/s11705-023-2298-8

摘要： The vanadium redox flow battery with a safe and capacity-controllable large-scale energy storage system offers a new method for the sustainability. In this case, acetic acid, methane sulfonic acid, sulfonic acid, amino methane sulfonic acid, and taurine are used to overcome the low electrolyte energy density and stability limitations, as well as to investigate the effects of various organic functional groups on the vanadium redox flow battery. When compared to the pristine electrolyte (0.22 Ah, 5.0 Wh·L–1, 85.0%), the results show that taurine has the advantage of maintaining vanadium ion concentrations, discharge capacity (1.43 Ah), energy density (33.9 Wh·L–1), and energy efficiency (90.5%) even after several cycles. The acetic acid electrolyte is more conducive to the low-temperature stability of the V(II) electrolyte (177 h at −25 °C) than pristine (82 h at −2 °C). The –SO3H group, specifically the coaction of the –NH2 and –SO3H groups, improves electrolyte stability. The –NH2 and –COOH additive groups improved conductivity and electrochemical activity.

关键词： vanadium redox flow battery     functional groups     organic additives     energy density     stability    

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A density functional theory study on the mechanism of Dimethyl ether carbonylation over heteropolyacids

Kai Cai, Ying Li, Hongbao Shen, Zaizhe Cheng, Shouying Huang, Yue Wang, Xinbin Ma

《化学科学与工程前沿（英文）》 2021年 第15卷 第2期   页码 319-329 doi: 10.1007/s11705-020-1957-2

摘要： Dimethyl ether (DME) carbonylation is considered as a key step for a promising route to produce ethanol from syngas. Heteropolyacids (HPAs) are proved to be efficient catalysts for DME carbonylation. In this work, the reaction mechanism of DME carbonylation was studied theoretically by using density functional theory calculations on two typical HPA models (HPW, HSiW). The whole process consists of three stages: DME dissociative adsorption, insertion of CO into methoxyl group and formation of product methyl acetate. The activation barriers of all possible elementary steps, especially two possible paths for CO insertion were calculated to obtain the most favorable reaction mechanism and rate-limiting step. Furthermore, the effect of the acid strength of Brønsted acid sites on reactivity was studied by comparing the activation barriers over HPW and HSiW with different acid strength, which was determined by calculating the deprotonation energy, Mulliken population analyses and adsorption energies of pyridine.

关键词： dimethyl ether     carbonylation     mechanism     heteropolyacids     density functional theory    

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地图线状要素注记自动配置的算法与实现

殷勇,李成名,丁圣陶

《中国工程科学》 2013年 第15卷 第5期   页码 30-36

摘要：

本文探讨了线状要素自动注记的几个关键问题，提出利用注记参考线计算线状要素的注记定位线，同时提出反Douglas算法进行注记参考线的动态分段，利用动态分段的结果集获取线状要素的平滑位置作为候选注记位，在此基础上获取注记中每个字的备选位置以及评分，最后采用禁忌算法解决注记之间的冲突，从而较好地解决了线状要素注记不可见或表达模糊的问题，实现了自动注记输出的完整性和美观性的统一。

关键词： 线状要素     注记自动配置     参考线     反Douglas算法    

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EEG-controlled functional electrical stimulation rehabilitation for chronic stroke: system design and

《医学前沿（英文）》 2021年 第15卷 第5期   页码 740-749 doi: 10.1007/s11684-020-0794-5

摘要： Stroke is one of the most serious diseases that threaten human life and health. It is a major cause of death and disability in the clinic. New strategies for motor rehabilitation after stroke are undergoing exploration. We aimed to develop a novel artificial neural rehabilitation system, which integrates brain--computer interface (BCI) and functional electrical stimulation (FES) technologies, for limb motor function recovery after stroke. We conducted clinical trials (including controlled trials) in 32 patients with chronic stroke. Patients were randomly divided into the BCI-FES group and the neuromuscular electrical stimulation (NMES) group. The changes in outcome measures during intervention were compared between groups, and the trends of ERD values based on EEG were analyzed for BCI-FES group. Results showed that the increase in Fugl Meyer Assessment of the Upper Extremity (FMA-UE) and Kendall Manual Muscle Testing (Kendall MMT) scores of the BCI-FES group was significantly higher than that in the sham group, which indicated the practicality and superiority of the BCI-FES system in clinical practice. The change in the laterality coefficient (LC) values based on μ-ERD (ΔLCm-ERD) had high significant positive correlation with the change in FMA-UE(r= 0.6093, P=0.012), which provides theoretical basis for exploring novel objective evaluation methods.

关键词： brain–computer interface     functional electrical stimulation     electroencephalogram     laterality coefficient     chronic stroke    

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标题 作者 时间 类型 操作

A post-GWAS replication study confirming the association of

Shaohua YANG,Chao QI,Yan XIE,Xiaogang CUI,Yahui GAO,Jianping JIANG,Li JIANG,Shengli ZHANG,Qin ZHANG,Dongxiao SUN

期刊论文

Profiling and annotation combined method formultimedia application specificMPSoCperformance estimation

Kai HUANG,Xiao-xu ZHANG,Si-wen XIU,Dan-dan ZHENG,Min YU,De MA,Kai HUANG,Gang CHEN,Xiao-lang YAN

期刊论文

Annotation and validation of genes involved in photosynthesis and starch synthesis from a

Yang ZHANG,Xin CHEN,Haiyan WANG,Zhiqiang XIA,Peng LING,Wenquan WANG

期刊论文

Comprehensive functional annotation of susceptibility variants identifies genetic heterogeneity between

Na Qin, Yuancheng Li, Cheng Wang, Meng Zhu, Juncheng Dai, Tongtong Hong, Demetrius Albanes, Stephen Lam, Adonina Tardon, Chu Chen, Gary Goodman, Stig E. Bojesen, Maria Teresa Landi, Mattias Johansson, Angela Risch, H-Erich Wichmann, Heike Bickeboller, Gadi Rennert, Susanne Arnold, Paul Brennan, John K. Field, Sanjay Shete, Loic Le Marchand, Olle Melander, Hans Brunnstrom, Geoffrey Liu, Rayjean J. Hung, Angeline Andrew, Lambertus A. Kiemeney, Shan Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil Caporaso, Penella Woll, Philip Lazarus, Matthew B. Schabath, Melinda C. Aldrich, Victoria L. Stevens, Guangfu Jin, David C. Christiani, Zhibin Hu, Christopher I. Amos, Hongxia Ma, Hongbing Shen

期刊论文

Development and applications of functional gene microarrays in the analysis of the functional diversity

Zhili HE, Joy D. VAN NOSTRAND, Ye DENG, Jizhong ZHOU

期刊论文

Fluorescent probes and functional materials for biomedical applications

期刊论文

Temporal dimension and water quality control in an emission trading scheme based on water environmental functional

Zhaoxing HAN, Zhenyao SHEN, Yongwei GONG, Qian HONG

期刊论文

A Study of the Functional Mechanism of Petrochemical Engineering Construction Project Management

Ji-ming Wang

期刊论文

Effects of functional groups for CO

Chenkai Gu, Yang Liu, Weizhou Wang, Jing Liu, Jianbo Hu

期刊论文

Microbial community and functional genes in the rhizosphere of alfalfa in crude oil-contaminated soil

Yi ZHONG, Jian WANG, Yizhi SONG, Yuting LIANG, Guanghe LI

期刊论文

Behavioral methods for the functional assessment of hair cells in zebrafish

null

期刊论文

Characterization and comparison of organic functional groups effects on electrolyte performance for vanadium

期刊论文

A density functional theory study on the mechanism of Dimethyl ether carbonylation over heteropolyacids

Kai Cai, Ying Li, Hongbao Shen, Zaizhe Cheng, Shouying Huang, Yue Wang, Xinbin Ma

期刊论文

地图线状要素注记自动配置的算法与实现

殷勇,李成名,丁圣陶

期刊论文

EEG-controlled functional electrical stimulation rehabilitation for chronic stroke: system design and

期刊论文