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| 1 | PLMD:An updated data resource of protein lysine modifications显示文摘Post-translational modifications(PTMs) occurring at protein lysine residues,or protein lysine modifications(PLMs),play critical roles in regulating biological processes.Due to the explosive expansion of the amount of PLM substrates and the discovery of novel PLM types,here we greatly updated our previous studies,and presented a much more integrative resource of protein lysine modification database(PLMD).In PLMD,we totally collected and integrated 284,780 modification events in 53,501 proteins across 176 eukaryotes and prokaryotes for up to 20 types of PLMs,including ubiquitination,acetylation,sumoylation,methylation,succinylation,malonylation,glutarylation,giycation,formylation,hydroxylation,butyrylation,propionylation,crotonylation,pupylation,neddylation,2-hydroxyisobutyrylation,phosphoglycerylation,carboxylation,lipoylation and biotinylation.Using the data set,a motif-based analysis was performed for each PLM type,and the results demonstrated that different PLM types preferentially recognize distinct sequence motifs for the modifications.Moreover,various PLMs synergistically orchestrate specific cellular biological processes by mutual crosstalks with each other,and we totally found 65,297 PLM events involved in 90 types of PLM co-occurrences on the same lysine residues.Finally,various options were provided for accessing the data,while original references and other annotations were also present for each PLM substrate.Taken together,we anticipated the PLMD database can serve as a useful resource for further researches of PLMs.PLMD 3.0 was implemented in PHP + MySQL and freely available at http://gffzz60b5e5c25d7e4f27hk5q9n66bcn666q0f.ffgz.tsg.suse.edu.cn. | Haodong Xu Jiaqi Zhou Shaofeng Lin Wankun Deng Ying Zhang Yu Xue | 2017 | Journal of Genetics and Genomics2017，44，5： | 6 |
| 2 | Syn-tectonic sedimentation and its linkage to fold-thrusting in the region of Zhangjiakou, North Hebei, China显示文摘The timing of the 'Yanshanian Movement' and the tectonic setting that controlled the Yanshan fold-and-thrust belt during Jurassic time in China are still matters of controversy. Sediments that filled the intramontane basins in the Yanshan belt perfectly record the history of 'Yanshanian Movement' and the tectonic background of these basins. Recognizing syn-tectonic sedimentation, clarifying its relationship with structures, and accurately defining strata ages to build up a correct chronostratigraphic framework are the key points to further reveal the timing and kinematics of tectonic deformation in the Yanshan belt from the Jurassic to the Early Cretaceous. This paper applies both tectonic and sedimentary methods on the fold-and-thrust belt and intramontane basins in the Zhangjiakou area, which is located at the intersection between the western Yanshan and northern Taihangshan. Our work suggests that the pre-defined 'Jurassic strata' should be re-dated and sub-divided into three strata units: a Late Triassic to Early Jurassic unit, a Middle Jurassic unit, and a Late Jurassic to early Early Cretaceous unit. Under the control of growth fold-and-thrust structures, five types of growth strata developed in different growth structures: fold-belt foredeep type,thrust-belt foredeep type, fault-propagation fold-thrust structure type, fault-bend fold-thrust structure type, and fault-bend foldthrust plus fault-propagation fold composite type. The reconstructed 'source-to-sink' systems of Late Triassic to Early Jurassic,Middle Jurassic and Late Jurassic to early Early Cretaceous times, which are composed of a fold-and-thrust belt and flexure basins, imply that the 'Yanshanian Movement' in our study area started in the Middle Jurassic. During Middle Jurassic to early Early Cretaceous times, there have been at least three stages of fold-thrust events that developed 'Laramide-type' basementinvolved fold-thrust structures and small-scale intramontane broken 'axial basins'. The westward migration of a 'pair' of basement-involved fold-thrust belt and flexure basins might have been controlled by flat subduction of the western Paleo-Pacific slab from the Jurassic to the Early Cretaceous. | Shaofeng LIU Chengfa LIN Xiaobo LIU Qitian ZHUANG | 2018 | Science China Earth Sciences2018，61，6： | 6 |
| 3 | Increased Expression of Intercellular Adhesion Molecule-1,Vascular Cellular Adhesion Molecule-1 and Leukocyte Common Antigen in Diabetic Rat Retina显示文摘Purpose: To understand the expression and distribution of intercellular adhesion molecule- 1(ICAM- 1),vascular cellular adhesion molecule- 1 (VCAM- 1)and CD45 (Leukocyte Common Antigen) in the control nondiabetic and various courses of diabetic rats retina. To explore the role of adhesion molecules (Ams) and the adhesion of leukocytes to vascular endothelial cells via Ams in diabetic retinopathy(DR).Methods: Sixty healthy adult male Wistar rats were randomly divided into diabetic groups(induced by Streptozotocin, STZ) and normal control groups. Rats in these two groups were further randomly divided into 3, 7, 14, 30, 90 and 180 days-group,including 5 rats respectively. The immunohistochemical studies of ICAM-1, VCAM-1 and CD45 were carried out in the retinal digest preparations or retinal paraffin sections, and the results were analyzed qualitatively, semi-quantitatively.Results: No positive reaction of VCAM-1 was found, and weak reactions of ICAM-1,CD45 were found in nondiabetic rats retina. The difference of 6 control groups had no statistical significance(P > 0.05). The increased ICAM-1 and CD45 staining pattern were detectable 3 days after diabetes induction, and a few VCAM-1 positive cells were observed in the retinal blood capillaries. The difference of diabetes and control is significant( P < 0.05).Following the course, the expressions of ICAM-1, VCAM-1 and CD45 were increasingly enhanced, reaching a peak at the 14th day.Conclusion: Increased expression of ICAM-1, VCAM-1 and leukocytes adhering and stacking in retinal capillaries are the very early events in DR. Coherence of expression and distribution of the three further accounts for it is the key point for the onset of DR that Ams mediates leukocytes adhesion and endothelial cell injury. | Ningyan Bai, Shibo Tang~#, Jing Ma, Yan Luo, Shaofeng Lin Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China | 2003 | Eye Science2003，19，3： | 4 |
| 4 | Growth structures and growth strata of the Qianjiadian Basin in the western Yanshan fold and thrust belt, North China显示文摘The northwestward subduction of the Izanagi Plate beneath the eastern Eurasian Plate during the Late Mesozoic caused a series of compressional deformation events in the Yanshan fold and thrust belt(YFTB), but the tectonic deformation timing, tectonic properties and relationship between tectonic uplift and sediment accumulation in the intermontane basins continue to be debated. For this reason, the sedimentology, sediment provenance, and basin structure of the Qianjiadian Basin(QJB) in the northern Beijing region during the Late Jurassic and Early Cretaceous were studied in detail. The results suggest that a fault-propagation fold-type(FPFT) growth structure and growth strata developed on the western edge of the QJB and that the top part of Member 2 and Member 3 of the Tuchengzi Formation are growth strata controlled by the limb rotation mechanism. In two small thrust faults in the QJB, the Mesoproterozoic Xiamaling Formation is thrust over the Tuchengzi Formation, and these faults may have controlled the development of the fault-bend fold-type growth strata. An analysis of the 'source-to-sink' process suggests that the hanging wall succession of the Shangyi-Pingquan fault(SPF) was the main source area of the Late Jurassic to early Early Cretaceous strata in the QJB. A zircon206 Pb/238 U age of 140.8±2.4 Ma for the volcanic rocks at the bottom of the FPFT growth strata represents the timing of the initiation of FPFT growth structure development. The discovery of the FPFT growth structure and growth strata in the QJB indicate that the QJB was an intermontane flexural basin controlled by fold and thrust structures during the early Early Cretaceous. Near the E-W-trending SPF, the NE-SW-trending Qianjiadian thrust fault(QJTF) and two small intrabasinal thrust faults may constitute a unified right-lateral strike-slip system that formed in response to the northwestward flat subduction of the Izanagi Plate beneath the East Asian continent during the Jurassic-Early Cretaceous. | Xiaofei SHI Shaofeng LIU Chengfa LIN | 2019 | Science China Earth Sciences2019，62，7： | 4 |
| 5 | Investigation and Analysis of Understory Vegetation in Casuarina equisetifolia Forests in Northern Hainan Province显示文摘Understory vegetation in the Casuarina equisetifolia forests at different ages was sampled and analyzed fi rstly, and then the structural features, biomass, and distribution characteristics of carbon stock of the understory vegetation, as well as the quantity and thickness of the understory litter were studied. The results show that the understory vegetation in the C. equisetifolia forests is mainly composed of herbaceous plants, and there are nearly no shrubs in the study area. Moreover, the quantity of herbaceous plants rises obviously with the increase of forest age. There is a big difference between the woodlands at different ages in total biomass of herbaceous plants, and the maximum of total biomass can be found in 15-year-old woodland, reaching 1.68 t/hm^2; the biomass of overground parts of herbaceous plants is higher than that of underground parts. There is a big difference between the woodlands at different ages in thickness of the understory litter, and the thickness of understory litter in 10-yearold woodland is the highest, reaching 6.67 cm. The maximum quantity of the understory litter has reached 14.69 t/hm^2, and the thickness of the half decomposed litter is larger than that of the undercomposed litter in most woodlands. | XUE Yang YANG Zhongyang WANG Xiaoyan SU Shaofeng LIN Zhipan XU Lina | 2016 | Journal of Landscape Research2016，8，3： | 2 |
| 6 | THESEUS1 positively modulates plant defense responses against Botrytis cinerea through GUANINE EXCHANGE FACTOR4 signaling显示文摘The plant cell wall is an important interface for sensing pathogen attack and activating signaling pathways that promote plant immune responses.THESEUS1(THE1) acts as a sensor of cell wall integrity that controls cell elongation during plant growth.However, no specific role for THE1 in plant defense responses has been reported. Here, we found that THE1 interacts with GUANINE EXCHANGE FACTOR4(GEF4)and that both proteins play regulatory roles in plant resistance to the necrotrophic fungus Botrytis cinerea.Genetic analysis showed that THE1 and GEF4 function in the same genetic pathway to mediate plant defense responses. In addition, using transcriptome analysis, we identified various genes(such as defense-related,secondary metabolite-related, and transcription factor genes) that are likely downstream targets in the THE1-GEF4 signaling pathway. Our results suggest that THE1 functions as an upstream regulator of GEF4 signaling to positively regulate defense responses against B. cinerea in Arabidopsis. | shaofeng qu xi zhang yutong song jinxing lin xiaoyi shan | 2017 | Journal of Integrative Plant Biology2017，59，11： | 2 |
| 7 | PTMD: A Database of Human Disease-associated Post-translational Modifications显示文摘Various posttranslational modifications(PTMs) participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM–disease associations(PDAs)would be a great help for both academic research and clinical use. In this work, we reported PTMD,a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of diseaseassociated PTM events. By reconstructing a disease–gene network, we observed that breast cancershave the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http://gffzz7d3e84778ac14081hk5q9n66bcn666q0f.ffgz.tsg.suse.edu.cn. | Haodong Xu Yongbo Wang Shaofeng Lin Wankun Deng Di Peng Qinghua Cui Yu Xue | 2018 | Genomics, Proteomics & Bioinformatics2018，16，4： | 2 |
| 8 | Perparation and properties of halogen-free flame-retarded pol- yamide 6/organoclay nanocomposite 显示文摘 | Song Lei Hu Yuan Lin Zhihua Xuan Shanyong Wang Shaofeng Chen Zuyao | 2004 | Polymer Degradation and Stability2004，86，： | 1 |
| 9 | Separation of structurally related estrogens using isocratic elution pressurized capillary electrochromatography显示文摘 | Shaofeng Liu Zenghong Xie Xiaoping Wu Xucong Lin Liangqia Guo Guonan Chen | 2005 | Journal of Chromatography A2005，，2： | 1 |
| 10 | Diffusion mechanism of dezincification in double phase brass exposed to seawater显示文摘Zinc diffusion kinetics of double phase brass as they were corroded in seawater was investigated by means of metallography microscope and mathematics regression analysis. The results showed that, the dezincification corrosion of β phase continuous HMn58 2 brass is characterized by β phase volume diffusion, while that of α phase continuous HSn62 1 brass is controlled by α phase grain boundary diffusion. Apparent diffusion coefficients of zinc in both types alloys were calculated out by founding diffusion equation and boundary conditions. It was found that the value of theoretical calculation is close to that of experimentally measured, and it confirmed that Sn element inhibits dezincification of brass. The relativity between the dezincification depth and corrosion rate of different double phase brasses immersed in seawater was revealed. : Zinc diffusion kinetics of double phase brass as they were corroded in seawater was investigated by means of metallography microscope and mathematics regression analysis. The results showed that, the dezincification corrosion of β phase continuous HMn58 2 brass is characterized by β phase volume diffusion, while that of α phase continuous HSn62 1 brass is controlled by α phase grain boundary diffusion. Apparent diffusion coefficients of zinc in both types alloys were calculated out by founding diffusion equation and boundary conditions. It was found that the value of theoretical calculation is close to that of experimentally measured, and it confirmed that Sn element inhibits dezincification of brass. The relativity between the dezincification depth and corrosion rate of different double phase brasses immersed in seawater was revealed. | Liu Zengcai(刘增才) Lin Leyun(林乐耘) Liu Shaofeng(刘少峰) Zhao Yuehong(赵月红) | 1999 | 中国有色金属学会会刊:英文版1999，9，3： | 1 |
| 11 | Potential Antiviral Target for SARS-CoV-2:A Key Early Responsive Kinase during Viral Entry显示文摘Currently,there is no effective antiviral medication for coronavirus disease 2019(COVID-19)and the knowledge on the potential therapeutic target is in great need.Guided by a time-course transmission electron microscope(TEM)imaging,we analyzed early phosphorylation dynamics within the first 15 min during severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)viral entry.Based on alterations in the phosphorylation events,we found that kinase activities such as protein kinase C(PKC),interleukin-1 receptor-associated kinase 4(IRAK4),MAP/microtubule affinity-regulating kinase 3(MARK3),and TANK-binding kinase 1(TBK1)were affected within 15 min of infection.Application of the corresponding kinase inhibitors of PKC,IRAK4,and p38 showed significant inhibition of SARS-CoV-2 replication.Additionally,proinflammatory cytokine production was reduced by applying PKC and p38 inhibitors.By an acquisition of a combined image data using positiveand negative-sense RNA probes,as well as pseudovirus entry assay,we demonstrated that PKC contributed to viral entry into the host cell,and therefore,could be a potential COVID-19 therapeutic target. | Siwen Liu Lin Zhu Guangshan Xie Bobo Wing-Yee Mok Zhu Yang Shaofeng Deng Siu-Ying Lau Pin Chen Pui Wang Honglin Chen Zongwei Cai | 2022 | CCS Chemistry2022，4，1： | 1 |
| 12 | WocEA:The visualization of functional enrichment results in word clouds显示文摘The integration,analysis and visualization of the big omics data are critical for addressing a broad spectrum of biological questions.One of the most frequently conducted procedures is enrichment analysis,which statistically tests whether individual functional annotations of Gene Ontology (GO)or Kyoto Encyclopedia of | Wanshan Ning Shaofeng Lin Jiaqi Zhou Yaping Guo Ying Zhang Di Peng Wankun Deng Yu Xue | 2018 | Journal of Genetics and Genomics2018，45，7： | 1 |
| 13 | Value Assessment of Ecosystem Service Function of Ecological Public Welfare Forests in Wenchang City显示文摘Based on the measurement parameters and index in the Specifications for Assessment of Forest Ecosystem Services in China(LY/T 1721-2008),the value of ecological service functions of ecological public welfare forest in Wenchang City was evaluated and analyzed.The results show that the total value of ecosystem service function of ecological public welfare forests in Wenchang City is about 4.020 billion yuan,of which storage capacity,water purification,soil fixation,fertilizer(N,P and K fertilizer) conservation,carbon sequestration,oxygen release,forest nutrient accumulation,providing anion,absorbing SO_2,absorbing fluoride,absorbing NxO,absorbing soil heavy metals,dust retention,noise reduction,sterilization,forest protection,forest biodiversity protection,and forest recreation(ecological tourism) are about 1.510 billion,582.256 million,3.769 million,268.220 million,116.360 million,2.747 million,22.682 million,42.817 million,1.722 million,74,600,131,900,187.918 million,77.409 million,28.721 million,43.090 million,180.696 million,571.036 million,and 108.677 million yuan | XUE Yang WANG Xiaoyan SU Shaofeng LIN Zhipan LIN Mei | 2016 | Journal of Landscape Research2016，8，4： | 1 |
| 14 | A fundamental principle and systematic procedures for process intensification in reactive distillation columns显示文摘 | Kejin Huang Quanquan Lin Huan Shao Chao Wang Shaofeng Wang | 2010 | Chemical Engineering & Processing: Process Intensification2010，，3： | 1 |
| 15 | Preparation and combustion properties of flame retardand Nylon 6/montmorillonite nanocomposite 显示文摘 | Yuan Hu Shaofeng Wang Zhihua Lin | 2003 | Macromolecular Materials and Engineering2003，288，3： | 1 |
| 16 | Impact of Terminal Bud Quality on the Growth of Different Growth Forms of Seedlings in Tropical Secondary Forest显示文摘Health condition and replacement time of terminal bud were selected as quality indexes of regenerated seedlings in 3 different growth forms to analyze their impact on seedling height and ground diameter. The results showed that quality of terminal bud was related to the seedling growth, the regenerated seedlings with healthy terminal buds but no replacement experienced the largest growth amount and slight damage of terminal bud or one replacement stimulated growth of ground diameter. Multiple replacements of terminal bud would reduce seedling quality and influence its growth. Exploration of the quality characters of seedlings helped to know the dynamic features of early seedling growth, and provided theoretical support for the tending operation to improve quality of natural tropical forest. | CHEN Yiqing ZHENG Tingting XUE Yang LIN Zhipan SU Shaofeng WANG Xiaoyan | 2016 | Journal of Landscape Research2016，8，5： | 0 |
| 17 | High-performance piezoresistive sensors based on transfer-free large-area PdSe2 films for human motion and health care monitoring显示文摘Two-dimensional transition metal dichalcogenides(TMDs)are needed in highperformance piezoresistive sensors due to their strong strain-induced bandgap modification and thereby large gauge factors.However,integrating a conventional high-temperature chemical vapor deposition(CVD)-grown TMD with a flexible substrate necessitates a transfer process that inevitably degrades the sensing properties of the TMDs and increases the overall fabrication complexity.We present a high-performance piezoresistive strain sensor that employs largearea PdSe2 films grown directly on polyimide(PI)substrates via plasma-assisted selenization of a sputtered Pd film.The reliable strain transfer from the substrate to the PdSe2 film ensures an outstanding strain-sensing capability of the sensor.Specifically,the sensors have a gauge factor of up to315±2.1,a response time under 25 ms,a detection limit of 8×10^(-6),and an exceptional stability of over 104 loading–unloading cycles.By attaching the sensors to the skin surface,we demonstrate their application for measuring physiological parameters in health care monitoring,including motion,voice,and arterial pulse vibration.Furthermore,using the PdSe2 film sensor combined with deep learning technology,we achieved intelligent recognition of artery temperature from arterial pulse signals with only a 2%difference between predicted and actual temperatures.The excellent sensing performance,together with the advantages of low-temperature fabrication and simple device structure,make the PdSe2 film sensor promising for wearable electronics and health care sensing systems. | Rui Zhang Jie Lin Tao He Jiafang Wu Zhuojun Yang Liwen Liu Shaofeng Wen Yimin Gong Haifeng Lv Jing Zhang Yi Yin Fangjia Li Changyong Lan Chun Li | 2024 | InfoMat2024，6，1： | 0 |
| 18 | An All‑In‑One Multifunctional Touch Sensor with Carbon‑Based Gradient Resistance Elements显示文摘Human–machine interactions using deep-learning methods are important in the research of virtual reality,augmented reality,and metaverse.Such research remains challenging as current interactive sensing interfaces for single-point or multipoint touch input are trapped by massive crossover electrodes,signal crosstalk,propagation delay,and demanding configuration requirements.Here,an all-inone multipoint touch sensor(AIOM touch sensor)with only two electrodes is reported.The AIOM touch sensor is efficiently constructed by gradient resistance elements,which can highly adapt to diverse application-dependent configurations.Combined with deep learning method,the AIOM touch sensor can be utilized to recognize,learn,and memorize human–machine interactions.A biometric verification system is built based on the AIOM touch sensor,which achieves a high identification accuracy of over 98%and offers a promising hybrid cyber security against password leaking.Diversiform human–machine interactions,including freely playing piano music and programmatically controlling a drone,demonstrate the high stability,rapid response time,and excellent spatiotemporally dynamic resolution of the AIOM touch sensor,which will promote significant development of interactive sensing interfaces between fingertips and virtual objects. | Chao Wei Wansheng Lin Shaofeng Liang Mengjiao Chen Yuanjin Zheng Xinqin Liao Zhong Chen | 2022 | Nano-Micro Letters2022，14，8： | 0 |
| 19 | Enhanced removal of high-As(Ⅲ)from Cl(-Ⅰ)-diluted SO_(4)(-Ⅱ)-rich wastewater at pH 2.3 via mixed tooeleite and(Cl(-Ⅰ)-free)ferric arsenite hydroxychloride formation显示文摘An advanced cost-saving method of removal of high-As(Ⅲ)from SO_(4)(-Ⅱ)-rich metallurgical wastewater has been developed by diluting the SO_(4)(-Ⅱ)content with As(Ⅲ)-Cl(-Ⅰ)-rich metallurgical wastewater and then by the direct precipitation of As(Ⅲ)with Fe(Ⅲ)at pH 2.3.As(Ⅲ)removal at various SO_(4)(-Ⅱ)/Cl(-Ⅰ)molar ratios and temperatures was investigated.The results showed that 65.2–98.2%of As(Ⅲ)immobilization into solids occurred at the SO_(4)(-Ⅱ)/Cl(-I)molar ratios of 1:1–32 and 15–60℃in 3 days,which were far higher than those in aqueous sole SO4(-Ⅱ)or Cl(-Ⅰ)media at the equimolar SO_(4)(-Ⅱ)or Cl(-Ⅰ)and the same temperature.SO_(4)(-Ⅱ)/Cl(-Ⅰ)molar ratio of 1:4 and 25℃were optimal conditions to reach the As removal maximum.Mixed aqueous SO4(-Ⅱ)and Cl(-Ⅰ)played a synergetic role in the main tooeleite formation together with(Cl(-Ⅰ)-free)ferric arsenite hydroxychloride(FAHC)involving the substitution of AsO_(3)^(3−)for Cl(-Ⅰ)for enhanced As fixation.The competitive complexation among FeH_(2)AsO_(3)^(2+),FeSO_(4)^(+)and FeCl^(2+)complexes was the main mechanism for the maximum As(Ⅲ)precipitation at the SO4(-Ⅱ)/Cl(-I)molar ratio of 1:4.Low As(Ⅲ)immobilization at high temperature with increased Fe(Ⅲ)hydrolysis was due to the formation of As(Ⅲ)-bearing ferrihydrite with the relatively high Fe/As molar ratio at acidic pH. | Zidan Yuan Guoqing Zhang Xing Wu Xu Ma Jinru Lin Shaofeng Wang Yongfeng Jia | 2023 | Journal of Environmental Sciences2023，，2： | 0 |
| 20 | Recommendations for Construction and Management of Ecological Public Welfare Forest in Hainan Province显示文摘This paper firstly evaluated ecological service functions of ecological public welfare forest in Hainan Province. Then,it introduced value structure and existing problems of ecological service functions. Focusing on optimization and adjustment of scale and distribution of ecological public welfare forest,it came up with recommendations for construction and management of ecological public welfare forest in Hainan Province. | Yang XUE Renhui HONG Dunxi LI Zhipan LIN Xiaoyan WANG Shaofeng SU | 2016 | Asian Agricultural Research2016，8，2： | 0 |
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