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Repeats in the transcribed regions: comprehensive characterization and comparison of

Manosh Kumar BISWAS, Christoph MAYER, Xiuxin DENG

《农业科学与工程前沿（英文）》 2017年 第4卷 第4期   页码 421-432 doi: 10.15302/J-FASE-2017160

摘要： A large number of expressed sequences tags are available for spp., which provides an opportunity to understand genomic organization of the transcribed regions. Here, we report a detailed analysis of repetitive elements including tandem repeats (TRs) and transposable elements (TEs) in the transcribed region of the spp. On average, 22% of the expressed sequence tags (ESTs) contain TRs. The relative density of TR classes is highly taxon-specific. For instance, has a high relative density of mononucleotide repeats, whereas dinucleotide repeats are rare. The proportions of 2–6, 7–30 and 31–50 bp repeats were almost identical in all studied species except for and . We found that<1% of the citrus ESTs have a similarity with transposable elements. Transcriptional activity of transposable element families varied even within the same class of elements. A high proportion of transcriptional activity was observed for -like TEs compare to other TE classes. While TEs are relatively rare, TRs are abundant elements in ESTs of citrus. The high proportion of TRs that have a unit size longer than 6 bp raises the question about a possible functional or evolutionary role of these elements.

关键词： Citrus spp.     tandem repeats     transcribed region     transposable elements    

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Detecting genetic hypermutability of gastrointestinal tumor by using a forensic STR kit

Anqi Chen, Suhua Zhang, Jixi Li, Chaoneng Ji, Jinzhong Chen, Chengtao Li

《医学前沿（英文）》 2020年 第14卷 第1期   页码 101-111 doi: 10.1007/s11684-019-0698-4

摘要： Growing evidence suggests that somatic hypermutational status and programmed cell death-1 overexpression are potential predictive biomarkers indicating treatment benefits from immunotherapy using immune checkpoint inhibitors. However, biomarker-matched trials are still limited, and many of the genomic alterations remain difficult to target. To isolate the potential somatic hypermutational tumor from microsatellite instability low/microsatellite stability (MSI-L/MSS) cases, we employed two commercial kits to determine MSI and forensic short tandem repeat (STR) alternations in 250 gastrointestinal (GI) tumors. Three types of forensic STR alternations, namely, allelic loss, Aadd, and Anew, were identified. 62.4% (156/250) of the patients with GI exhibited STR alternation, including 100% (15/15) and 60% (141/235) of the microsatellite high instability and MSI-L/MSS cases, respectively. 30% (75/250) of the patients exhibited STR instability with more than 26.32% (26.32%–84.21%) STR alternation. The cutoff with 26.32% of the STR alternations covered all 15 MSI cases and suggested that it might be a potential threshold. Given the similar mechanism of the mutations of MSI and forensic STR, the widely used forensic identifier STR kit might provide potential usage for identifying hypermutational status in GI cancers.

关键词： mismatch repair protein deficiency (MMR-D)     microsatellite instability (MSI)     short tandem repeats (STR)     gastrointestinal tumor     hypermutability    

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Alluvial channel hydrodynamics around tandem piers with downward seepage

Rutuja CHAVAN, Wenxin HUAI, Bimlesh KUMAR

《结构与土木工程前沿（英文）》 2020年 第14卷 第6期   页码 1445-1461 doi: 10.1007/s11709-020-0648-x

摘要： In this paper, we report the turbulent flow structures and the scour geometry around two piers with different diameters. An experiment was conducted on a non-uniform sand bed with two types of tandem arrangements, namely, pier (T1) with a 75 mm front and 90 mm rear, and pier (T2) with a 90 mm front and 75 mm rear, with and without-seepage flows, respectively. A strong wake region was observed behind the piers, but the vortex strength diminished with downward seepage. Streamwise velocity was found to be maximum near the bed downstream of the piers and at the edge of the scour hole upstream of the piers. Quadrant analysis was used to recognize the susceptible region for sediment entrainment and deposition. Upstream of the piers near the bed, the moments, turbulent kinetic energy (TKE), and TKE fluxes were found to decrease with downward seepage, in contrast to those in a plane mobile bed without piers. The reduction percentages of scour depth at the rear pier compared with the front one were approximately 40% for T1 and 60% for T2. Downward seepage also resulted in restrained growth of scouring with time.

关键词： scour     seepage     Strouhal number     tandem arrangement     turbulent characteristics    

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Design of tandem genes cluster for isoflavone engineering

Xunli XIA PhD , Guangxiao YANG PhD , Guangyuan HE PhD ,

《医学前沿（英文）》 2009年 第3卷 第3期   页码 292-296 doi: 10.1007/s11684-009-0057-y

摘要： In this paper, a universal effective novel method of constructing tandem genes cluster for isoflavone engineering was reported. A tandem genes cluster () of secondary metabolites of plant isoflavones was constructed by using the chalcone synthase (CHS), chalcone isomerase (CHI), and isoflavone synthase (IFS) (GenBank accession numbers EU526827, EU526829, EU526830) in only one recombination with the pET22b vector. The resulting expression vector pET- was heterogeneously expressed and co-incubated with barrenwort extractions, and the genistein-like component was detected.

关键词： isoflavones engineering     secondary metabolism     tandem genes cluster    

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Available energy analysis of new tandem double-capillary tube refrigeration system for refrigerator-freezers

HE Maogang, ZHANG Ying, SONG Xinzhou, ZHANG Jiantao

《能源前沿（英文）》 2008年 第2卷 第1期   页码 36-42 doi: 10.1007/s11708-008-0013-6

摘要： A new tandem double-capillary tube refrigeration system for refrigerator-freezers is proposed. A capillary tube was added between the two evaporators in the fresh and frozen food storage chests to raise the evaporation temperature of the refrigerating chamber, and reduce the heat exchange temperature difference and the available energy loss. Peng-Robinson (P-R) equation of state was adopted to calculate the thermodynamic properties of the refrigerants, and the available energy analysis of the vapor compression refrigeration cycle was programmed to calculate the thermodynamic performances of the new and the conventional refrigeration cycle of the refrigerator-freezer. The calculation results show that the available energy efficiency of the conventional refrigeration cycle of the refrigerator-freezer is 21.20% and 20.57%, respectively when the refrigerant is R12 and R134a, while that of the double-capillary tube refrigeration cycle of the refrigerator-freezer is 23.97% and 23.44%, respectively. By comparison, the available energy efficiency of the new refrigeration system increases by 13.07% and 13.95%, respectively.
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quantification of several classes of antibiotics in water, sediments, and fish muscles by liquid chromatography–tandem

WEI Yimei,ZHANG Yuan,XU Jian,GUO Changsheng,LI Lei,FAN Wenhong

《环境科学与工程前沿（英文）》 2014年 第8卷 第3期   页码 357-371 doi: 10.1007/s11783-013-0580-6

摘要： Precise and sensitive methods for the simultaneous determination of different classes of antibiotics, including sulphonamides, fluoroquinolones, macrolides, tetracyclines, and trimethoprim in surface water, sediments, and fish muscles were developed. In water samples, drugs were extracted with solid-phase extraction (SPE) by passing 1000 mL of water through hydrophilic lipophilic balanced (HLB) SPE cartridges. Sediment samples were solvent-extracted, followed by tandem SPE (strong anion exchange (SAX) + HLB) clean-ups. Fish muscles were extracted by a mixture of acetonitrile and citric buffer (80:20, v/v) solution, and cleaned by SPE. Liquid chromatography–tandem mass spectrometry (LC-MS/MS) with multiple reaction monitoring (MRM) detection was employed to quantify all compounds. The recoveries for the antibiotics in the spiked water, sediment, and fish samples were 60.2%–95.8%, 48.1%–105.3%, and 59.8%–103.4%, respectively. The methods were applied to samples taken from Dianchi Lake, China. It showed that concentrations of the detected antibiotics ranged from limits of quantification (LOQ) to 713.6 ng·L (ofloxacin) in surface water and from less than LOQ to 344.8 μg·kg (sulphamethoxazole) in sediments. The number of detected antibiotics and the overall antibiotic concentrations were higher in the urban area than the rural area, indicating the probable role of livestock and human activities as important sources of antibiotic contamination. In fish muscles, the concentration of norfloxacin was the highest (up to 38.5 μg·kg ), but tetracyclines and macrolides were relatively low. Results showed that the methods were rapid and sensitive, and capable of determining several classes of antibiotics from each of the water, sediment, and fish matrices in a single run.

关键词： antibiotics     liquid chromatography–tandem mass spectrometry (LC-MS/MS)     water     sediment     fish muscle    

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water using liquid-liquid microextraction coupled with gas chromatography—positive chemical ionization-tandem

Jian LU,Paul S. WILLS,P. CHRIS WILSON

《环境科学与工程前沿（英文）》 2016年 第10卷 第3期   页码 477-481 doi: 10.1007/s11783-015-0820-z

摘要： A rapid, inexpensive and laboratory friendly method was developed for analysis of off-flavor/odor compounds in fresh and salt water using gas chromatography with chemical ionization-tandem mass spectrometry. Off-flavor/odor compounds included geosmin, 2-methylisoborneol (MIB), 2-isobutyl-3-methyoxypyrazine (IBMP), and 2-isopropyl-3-methoxypyrazine (IPMP). Using this method, a single sample can be extracted within minutes using only 1 mL of organic solvent. The ion transitions for IPMP, IBMP, MIB, and geosmin were 153>121, 167>125, 152>95, and 165>109, respectively. The linearity of this method for analyzing MIB ranged from 4 to 200 ng·L , and from 0.8 to 200 ng·L for the other analytes. Method recoveries ranged from 97% to 111% and percent relative standard deviations ranged from 3% to 9%, indicating that the method is accurate, precise, and reliable.

关键词： off-flavor/odor compounds     liquid-liquid microextraction     gas chromatography-tandem mass spectrometry    

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Ultrathin microcrystalline hydrogenated Si/Ge alloyed tandem solar cells towards full solar spectrum

Yu Cao, Xinyun Zhu, Xingyu Tong, Jing Zhou, Jian Ni, Jianjun Zhang, Jinbo Pang

《化学科学与工程前沿（英文）》 2020年 第14卷 第6期   页码 997-1005 doi: 10.1007/s11705-019-1906-0

摘要： Thin film solar cells have been proved the next generation photovoltaic devices due to their low cost, less material consumption and easy mass production. Among them, micro-crystalline Si and Ge based thin film solar cells have advantages of high efficiency and ultrathin absorber layers. Yet individual junction devices are limited in photoelectric conversion efficiency because of the restricted solar spectrum range for its specific absorber. In this work, we designed and simulated a multi-junction solar cell with its four sub-cells selectively absorbing the full solar spectrum including the ultraviolet, green, red as well as near infrared range, respectively. By tuning the Ge content, the record efficiency of 24.80% has been realized with the typical quadruple junction structure of a-Si:H/a-Si Ge :H/µc-Si:H/µc-Si Ge :H. To further reduce the material cost, thickness dependent device performances have been conducted. It can be found that the design of total thickness of 4 m is the optimal device design in balancing the thickness and the . While the design of ultrathin quadruple junction device with total thickness of 2 m is the optimized device design regarding cost and long-term stability with a little bit more reduction in . These results indicated that our solar cells combine the advantages of low cost and high stability. Our work may provide a general guidance rule of utilizing the full solar spectrum for developing high efficiency and ultrathin multi-junction solar cells.

关键词： thin films     solar cells     quadruple junction solar cell     amorphous silicon     silicon germanium alloy     quantum efficiency    

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融合深度置信网络的串联隐马尔科夫模型及其在脱机手写识别中的应用 Article

Partha Pratim ROY, Guoqiang ZHONG, Mohamed CHERIET

《信息与电子工程前沿（英文）》 2017年 第18卷 第7期   页码 978-988 doi: 10.1631/FITEE.1600996

摘要： 在文档分析和模式识别领域，自由书写的脱机手写识别是一个非常具有挑战性的研究课题。近年来，为了充分探索隐藏在文档图像中的监督信息，许多研究工作试图将多层感知机以一种混合或串联的形式嵌入隐马尔科夫模型当中。然而，因为多层感知机学习能力的不足，学习到的特征对于后续的识别任务不一定是最优的。在本文中，我们针对自由书写的脱机手写识别提出一种基于深度结构的串联方法。在提出的模型中，深度置信网络被用于学习序列数据的紧致表示，隐马尔科夫模型被用于（子-）词的识别。我们在两个公开的数据集上验证了所提出的模型，这两个数据集是分别基于拉丁和阿拉伯语的RIMES和IFN/ENIT；我们还在Devanagari数据集上验证了所提出的模型，这个数据集是基于印度语的。大量的实验展示了所提出模型的优势，特别是相对于多层感知机-隐马尔科夫模型的串联方法。

关键词： 手写识别；隐马尔科夫模型；深度学习；深度置信网络；串联方法    

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Detecting

Chengkun WANG, Xiaojian ZHANG, Jun WANG, Chao CHEN

《环境科学与工程前沿（英文）》 2012年 第6卷 第6期   页码 770-777 doi: 10.1007/s11783-012-0412-0

摘要： nitrosodimethylamine (NDMA) and several other nitrosamines have been detected as disinfection by-products in drinking waters in many countries around the world. An ultra-performance liquid chromatography-tandem mass spectrometry method with solid phase extraction sample preparation was developed to study the occurrence of nitrosamines in several water treatment plants and distribution systems in China. Isotope labeled nitrosodi- propylamine-d14 (NDPA-d14) was selected as the internal standard for quantification. The solid phase extraction procedures including pH, enrichment process and MS/MS parameters including capillary voltage, cone gas flow, cone voltage, collision energy were optimized to give average recoveries of 26% to 112% for nine nitrosamine species. The instrument detection limits were estimated to range from 0.5 to 5 μg·L for the nine nitrosamine species. NDMA and several other nitrosamines were found at fairly high concentrations in several water treatment plants and distribution systems. NDMA was found in all locations, and the highest concentrations in cities B, G, T, and W were 3.0, 35.7, 21.3, and 19.7 ng·L , respectively. A wide range of nitrosamines concentrations and species were observed in different locations. Higher concentrations of nitrosamines were detected in distribution systems that were further away from the treatment plants, suggesting that the contact time between the residual disinfectant and natural organic matter may play an important role in the formation of these compounds.

关键词： N-nitrosamines     water treatment plant     distribution system     ultra-performance liquid chromatography-tandem mass spectrometry    

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Characteristics and removal mechanism of the precursors of N-chloro-2,2-dichloroacetamide in a drinking water treatment process at Taihu Lake

《环境科学与工程前沿（英文）》 2021年 第15卷 第5期 doi: 10.1007/s11783-020-1338-6

摘要：

• N-Cl-DCAM, an emerging N-DBP in drinking water was investigated.

关键词： N-chloro-2     2-dichloroacetamide     Liquid chromatography with tandem mass spectrometry     Precursors     Removal efficiency     Ozonation integrated with biological activated carbon    

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Perfluorocarboxylic acids (PFCAs) and perfluoroalkyl sulfonates (PFASs) in surface and tap water around Lake Taihu in China

Yong QIU, He JING, Hanchang SHI,

《环境科学与工程前沿（英文）》 2010年 第4卷 第3期   页码 301-310 doi: 10.1007/s11783-010-0236-8

摘要： Perfluorinated compounds (PFCs) are ubiquitously distributed in the environment mainly as perfluoro-carboxylic acids (PFCAs) and perfluoroalkyl sulfonates (PFASs). In this paper, six PFCAs and two PFASs were quantified in surface and tap water samples from 12 sites around Lake Taihu near Shanghai City in East China. Predominant PFCs were perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS), of which the concentration ranges were 6.8–206 and 1.2–45 ng·L, the geometric means were 35.3 and 9.4 ng·L, and the median (quartile range) values were 31.4 (34.4) and 10.4 (10.7) ng·L, respectively. Other PFCs were also detected but in much lower concentrations than PFOA. The sources of the PFCs were expected to be direct industrial discharges in the Lake Taihu area, and this area was also a possible source of PFCs contaminations in Shanghai district in the downstream. PFCs distributions were found different in the upstream, downstream and north part of Lake Taihu. Occurrences of PFCs in the tap water in Lake Taihu area indicated their exposure to the local people. A brief estimation of the environmental risks by PFCs implied no acute or immediate risks from PFCs to local human health, but chronic risks from PFOA in the tap water should be considered in the downstream regions.

关键词： surface and tap water     perfluorocarboxylic acids (PFCAs)     perfluoroalkyl sulfonates (PFASs)     Lake Taihu area     ultra performance liquid chromatography with tandem mass spectrometry (UPLC-MS)    

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Hygroscopicity of ambient submicron particles in urban Hangzhou, China

Jiachen ZHANG, Lin WANG, Jianmin CHEN, Shengmao FENG, Jiandong SHEN, Li JIAO

《环境科学与工程前沿（英文）》 2011年 第5卷 第3期   页码 342-347 doi: 10.1007/s11783-011-0358-7

摘要： In this study, hygroscopicity of size-segregated ambient submicron particles in urban Hangzhou was studied from 28th December 2009 to 18th January 2010, using a hygroscopicity-tandem differential mobility analyzer (H-TDMA). The submicron particles in Hangzhou showed a minor hygroscopic growth at 73% relative humidity (RH), and then grew significantly between 77% and 82% RH. Monomodal distribution accounted for 90% for 30 nm particles, 17% for 50 nm particles, and less than 7% for particles larger than 50 nm at 82% RH. Deconvolution of the bimodal distribution indicated a less hygroscopic group and a more hygroscopic group, with the fraction of the more hygroscopic group increasing with the initial dry particle size and then remaining almost constant for accumulation mode particles. Our results imply that submicron particles in urban Hangzhou were almost entirely externally mixed, and the hygroscopic properties of ambient particles in urban Hangzhou were mainly a function of their size and chemical composition.

关键词： hygroscopicity     hygroscopic tandem differential mobility analyzer (H-TDMA)     submicron ambient particles     Hangzhou    

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An efficient resin for solid-phase extraction and determination by UPLCMS/MS of 44 pharmaceutical personal care products in environmental waters

Feng Zhu, Zhijian Yao, Wenliang Ji, Deye Liu, Hao Zhang, Aimin Li, Zongli Huo, Qing Zhou

《环境科学与工程前沿（英文）》 2020年 第14卷 第3期 doi: 10.1007/s11783-020-1228-y

摘要： A hydrophilic resin (GCHM) was facile synthesis and characterized. Average absolute recovery of GCHM (75.6%) performs better than Oasis® HLB. Detection limits of method (SPE-UPLC-MS/MS) ranged between 0.03 and 0.6 ng/L. 22 PPCPs were determined in environmental waters ranging from 0.5 to 1590 ng/L. In this study, a hydrophilic resin named GCHM was fabricated based on poly(N-vinyl pyrrolidone-co-divinylbenzene), characterized, and applied as a solid-phase extraction (SPE) material. Up to 44 pharmaceuticals and personal care products (PPCPs) belonging to 10 classes were recovered in environmental water samples. Different variables affecting extraction, such as adsorbent amount, sample pH, and loading speed, were optimized. Under optimal conditions, the average absolute recovery of 44 PPCPs was 75.6% using GCHM, indicating a better performance than the commercial Oasis® HLB. SPE with home-made hydrophilic polymeric sorbent followed by ultra-performance liquid chromatography and tandem mass spectrometry was validated, and the method achieved good linearity (r2>0.991, for all analytes). In addition, the method detection limits of target compounds ranged from 0.03 to 0.6 ng/L. The developed method was applied to determine PPCPs in 10 environmental water samples taken from the Yangtze River, Huaihe River, and Taihu Lake, 1 groundwater sample from Changzhou in Jiangsu Province, 1 wastewater sample from Xiamen and 2 seawater samples from the Jiulong River in Fujian Province, China. In these samples, 22 compounds were determined at levels ranging from 0.5 to 1590 ng/L.

关键词： Hydrophilic resin     Solid phase extraction     Pharmaceuticals and personal care product     Ultra-performance liquid chromatography and tandem mass spectrometry     Environmental water    

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四极杆-线形离子阱串联质谱系统及临床生物标志物分析 Article

方向, 谢洁, 楚士颖, 江游, 安育廷, 李畅, 龚晓云, 翟睿, 黄泽建, 裘春玲, 戴新华

《工程（英文）》 2022年 第16卷 第9期   页码 56-64 doi: 10.1016/j.eng.2020.10.021

摘要：

确高效测量小分子疾病标志物对临床诊断具有重要意义。本研究自主研制了四极杆-线形离子阱（quadrupole-linear ion trap, Q-LIT）串联质谱仪。四极杆筛选目标母离子，线形离子阱同时注入、捕获和碎裂，有效降低空间电荷效应，富集目标子离子，提升灵敏度。采用电喷雾离子源（electrospray ionization, ESI），选择反应监测和正离子扫描模式。质量范围为m/z 195~2022。当m/z 达2000，且扫描速度为1218 amu·s−1时，单位分辨率和准确度均优于m/z 0.28。碰撞诱导解离（collision-induced dissociation, CID）由共振激发，其无量纲马修参数q值为0.40。激发50 ms，CID效率达64%。胍基乙酸（guanidinoacetic acid, GAA）和肌酸（creatine, CRE）作为小分子临床生物标志物的模型化合物。GAA和CRE定量限分别为1.0 nmol·L−1和0.2 nmol·L−1。自主研制ESI-Q-LIT串联质谱仪成功分析了77例实际样本。该方法可以削减基质效应，降低空间电荷效应，避免色谱分离，简化前处理过程。新型Q-LIT串联质谱系统有望成为临床诊疗中生物标志物测定的新选择。

关键词： 线形离子阱     四极杆     空间电荷效应     碰撞诱导解离     生物标志物    

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标题 作者 时间 类型 操作

Repeats in the transcribed regions: comprehensive characterization and comparison of

Manosh Kumar BISWAS, Christoph MAYER, Xiuxin DENG

期刊论文

Detecting genetic hypermutability of gastrointestinal tumor by using a forensic STR kit

Anqi Chen, Suhua Zhang, Jixi Li, Chaoneng Ji, Jinzhong Chen, Chengtao Li

期刊论文

Alluvial channel hydrodynamics around tandem piers with downward seepage

Rutuja CHAVAN, Wenxin HUAI, Bimlesh KUMAR

期刊论文

Design of tandem genes cluster for isoflavone engineering

Xunli XIA PhD , Guangxiao YANG PhD , Guangyuan HE PhD ,

期刊论文

Available energy analysis of new tandem double-capillary tube refrigeration system for refrigerator-freezers

HE Maogang, ZHANG Ying, SONG Xinzhou, ZHANG Jiantao

期刊论文

quantification of several classes of antibiotics in water, sediments, and fish muscles by liquid chromatography–tandem

WEI Yimei,ZHANG Yuan,XU Jian,GUO Changsheng,LI Lei,FAN Wenhong

期刊论文

water using liquid-liquid microextraction coupled with gas chromatography—positive chemical ionization-tandem

Jian LU,Paul S. WILLS,P. CHRIS WILSON

期刊论文

Ultrathin microcrystalline hydrogenated Si/Ge alloyed tandem solar cells towards full solar spectrum

Yu Cao, Xinyun Zhu, Xingyu Tong, Jing Zhou, Jian Ni, Jianjun Zhang, Jinbo Pang

期刊论文

融合深度置信网络的串联隐马尔科夫模型及其在脱机手写识别中的应用

Partha Pratim ROY, Guoqiang ZHONG, Mohamed CHERIET

期刊论文

Detecting

Chengkun WANG, Xiaojian ZHANG, Jun WANG, Chao CHEN

期刊论文

Characteristics and removal mechanism of the precursors of N-chloro-2,2-dichloroacetamide in a drinking water treatment process at Taihu Lake

期刊论文

Perfluorocarboxylic acids (PFCAs) and perfluoroalkyl sulfonates (PFASs) in surface and tap water around Lake Taihu in China

Yong QIU, He JING, Hanchang SHI,

期刊论文

Hygroscopicity of ambient submicron particles in urban Hangzhou, China

Jiachen ZHANG, Lin WANG, Jianmin CHEN, Shengmao FENG, Jiandong SHEN, Li JIAO

期刊论文

An efficient resin for solid-phase extraction and determination by UPLCMS/MS of 44 pharmaceutical personal care products in environmental waters

Feng Zhu, Zhijian Yao, Wenliang Ji, Deye Liu, Hao Zhang, Aimin Li, Zongli Huo, Qing Zhou

期刊论文

四极杆-线形离子阱串联质谱系统及临床生物标志物分析

方向, 谢洁, 楚士颖, 江游, 安育廷, 李畅, 龚晓云, 翟睿, 黄泽建, 裘春玲, 戴新华

期刊论文