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Staged-probability strategy of processing shotgun proteomic data to discover more functionally important proteins

Protein & Cell 2012年第2期3卷 140-147页

作者： Hong Xu guijun Ma Qingqiao Tan Qiang Zhou Wen Su Rongxiu li State Key Laboratory of Microbial Metabolism(Shanghai Jiao Tong University)and School of life Sciences&Biotechnology Shanghai Jiao Tong UniversityShanghai 200240China Department of Bioinformatics and Biostatistics College of Life Sciences&BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Software Engineering Institute East China Normal UniversityShanghai 200062China

Biologically important proteins related to membrane receptors,signal transduction,regulation,transcription,and translation are usually low in abundance and identified with low probability in mass spectroscopy(MS)-based *** valuable proteomics information on them were hitherto discarded due to the application of excessively strict data filtering for accurate *** this study,we present a stagedprobability strategy for assessing proteomic data for potential functionally important protein ***-based protein identifications from the second(L2)and third(L3)layers of the cascade affinity fractionation using the Trans-Proteomic Pipeline software were classified into three probability stages as 1.00–0.95,0.95–0.50,and 0.50–0.20 according to their distinctive identification correctness rates(i.e.100%–95%,95%–50%,and 50%–20%,respectively).We found large data volumes and more functionally important proteins located at the previously unacceptable lower probability stages of 0.95–0.50 and 0.50–0.20 with acceptable correctness *** importantly,low probability proteins in L2 were verified to exist in *** with some MS spectrogram examples,comparisons of protein identifications of L2 and L3 demonstrated that the stagedprobability strategy could more adequately present both quantity and quality of proteomic information,especially for researches involving biomarker discovery and novel therapeutic target screening.

关键词： lower minimum probability threshold probability grade TPP low-abundant protein

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SMART/ASTC dynamic soft reduction technology and its application on the bloom continuous caster at Pangang

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Journal of University of Science and Technology Beijing 2006年第2期13卷 121-124页

作者： guijun li Kaijian Zhang Chuanfi Han Yong Chen Guoyan Zhao Kaike Cai Metallurgical and Ecological Engineering School University of Science and Technology Beijing Beijing 100083 China Panzhihua Iron ＆ Steel Co. Panzhihua Sichuan 617000 China

The SMART/ASTC dynamic soft reduction technology of VAI and its application on the 6-strand bloom continuous caster at Pangang, China are presented. The operation results show that soft reduction technology is effective to improve the inner quality of continuously cast blooms. At Pangang, both the central porosity and the central segregation ratings are no more than 1.0, the central shrinkage cavity rating is no more than 0.5, and the central segregation index of carbon is no more than 1.05. Rails made from the blooms have excellent quality and are used for high-speed tracks.

关键词： bloom continuous casting dynamic soft reduction heavy rail steel

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A numerical estimation of the impact of Stokes drift on upper ocean temperature

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Acta Oceanologica Sinica 2014年第7期33卷 48-55页

作者： ZHANG Xiaoshuang WANG Zhifeng WANG Bin WU Kejian HAN guijun li Wei Key Laboratory of Marine Environmental Information Technology National Marine Data and Information ServiceState Oceanic Administration Ocean University of China National Ocean Technology Center State Oceanic Administration

The impact of Stokes drift on the mixed layer temperature variation was estimated by taking into account an advective heat transport term induced by the Stokes drift in the equation of mixed layer temperature and using the oceanic and wave parameters from a global ocean circulation model （HYCOM） and a wave model （Wave Watch III）. The dimensional analysis and quantitative estimation method were conducted to assess the importance of the effect induced by the Stokes drift and to analyze its spatial distribution and seasonal variation characteristics. Results show that the contribution of the Stokes drift to the mixed layer temperature variation at mid-to-high latitudes is comparable with that of the mean current, and a substantial part of mixed layer temperature change is induced by taking the Stokes drift effect into account. Although the advection heat transport induced by the Stokes drift is not the leading term for the mixed layer temperature equation, it cannot be neglected and even becomes critical in some regions for the simulation of the upperocean temperature.

关键词： sea surface waves Stokes drift mixed layer temperature

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Diatom-inspired multiscale mineralization of patterned protein–polysaccharide complex structures

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National Science Review 2021年第8期8卷 186-197页

作者： Ke li Yingfeng li Xinyu Wang Mengkui Cui Bolin An Jiahua Pu Jintao liu Boyang Zhang guijun Ma Chao Zhong School of Physical Science and Technology Shanghai Tech University Center for Materials Synthetic Biology Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences

Marine diatoms construct their hierarchically ordered, three-dimensional(3D) external structures called frustules through precise biomineralization processes. Recapitulating the remarkable architectures and functions of diatom frustules in artificial materials is a major challenge that has important technological implications for hierarchically ordered composites. Here, we report the construction of highly ordered,mineralized composites based on fabrication of complex self-supporting porous structures—made of genetically engineered amyloid fusion proteins and the natural polysaccharide chitin—and performing in situ multiscale protein-mediated mineralization with diverse inorganic materials, including SiO2, TiO2and Ga2O3. Subsequently, using sugar cubes as templates, we demonstrate that 3D fabricated porous structures can become colonized by engineered bacteria and can be functionalized with highly photoreactive minerals,thereby enabling co-localization of the photocatalytic units with a bacteria-based hydrogenase reaction for a successful semi-solid artificial photosynthesis system for hydrogen evolution. Our study thus highlights the power of coupling genetically engineered proteins and polysaccharides with biofabrication techniques to generate hierarchically organized mineralized porous structures inspired by nature.

关键词： biomimetic mineralization patterned porous structure genetic engineering amyloid protein artificial photosynthesis

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直觉折线模糊数空间的完备可分性和逼近性

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浙江大学学报（理学版） 2022年第5期49卷 532-539页

作者：李丹王贵君三亚学院理工学院海南三亚572000 天津师范大学数学科学学院天津300387

折线模糊数可借助一组实数的有序表示确定模糊信息,不仅可以实现一般模糊数之间的近似线性运算,而且克服了基于Zadeh扩展原理的模糊数四则运算复杂问题。基于直觉模糊数和折线模糊数,提出了直觉折线模糊数的概念。通过引入距离公式,证... 详细信息

折线模糊数可借助一组实数的有序表示确定模糊信息,不仅可以实现一般模糊数之间的近似线性运算,而且克服了基于Zadeh扩展原理的模糊数四则运算复杂问题。基于直觉模糊数和折线模糊数,提出了直觉折线模糊数的概念。通过引入距离公式,证明了直觉折线模糊数可构建完备可分的度量空间,给出了直觉折线模糊数的逼近定理。进一步用实例验证了直觉折线模糊数对直觉模糊数具有逼近性。

关键词：直觉模糊数折线模糊数直觉折线模糊数逼近性

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Persistent inflammation and neuronal loss in the mouse brain induced by a modified form of attenuated herpes simplex virus type I

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Virologica Sinica 2023年第1期38卷 108-118页

作者： Erlin Wang Xinwei Huang Yunshuang Ye Shiqing Zou guijun Chen liping Yang Nigel W.Fraser Fukai Bao Jumin Zhou Xia Cao Key Laboratory of Second Affiliated Hospital of Kunming Medical University Kunming650000China Key Laboratory of Animal Models and Human Disease Mechanism of the Chinese Academy of Science/Key Laboratory of Healthy Aging Research of Yunnan Province Kunming Institute of ZoologyThe Chinese Academy of SciencesKunming650223China Kunming College of life Science University of Chinese Academy of SciencesKunming650204China Department of Microbiology Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA Department of Biology and Immunology Kunming Medical UniversityKunming650101China KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases Kunming650223China

Herpes simplex virus-1(HSV-1)is a widespread neurotropic virus that can reach the brain and cause a rare but acute herpes simplex encephalitis(HSE)with a high mortality *** patients present with changes in neurological and behavioral status,and survivors suffer long-term neurological *** date,the pathogenesis leading to brain damage is still not well ***-1 induced encephalitis in the central nervous system(CNS)in animals are usually very diffuse and progressing rapidly,and mostly fatal,making the analysis ***,we established a mouse model of HSE via intracerebral inoculation of modified version of neuralattenuated strains of HSV-1(deletion of ICP34.5 and inserting a strong promoter into the latency-associated transcript region),in which the LMR-αΔpA strain initiated moderate productive infection,leading to strong host immune and inflammatory response characterized by persistent microglia *** viral replication activity and prolonged inflammatory response activated signaling pathways in neuronal damage,amyloidosis,Alzheimer's disease,and neurodegeneration,eventually leading to neuronal loss and behavioral changes characterized by *** study reveals detailed pathogenic processes and persistent inflammatory responses in the CNS and provides a controlled,mild and non-lethal HSE model for studying long-term neuronal injury and increased risk of neurodegenerative diseases due to HSV-1 infection.

关键词： Herpes simplex virus-1(HSV-1) Herpes simplex encephalitis(HSE) ICP34.5 Neuroinflammation Neuronal loss

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毕达哥拉斯模糊环境下海明距离测度的证明及推广

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浙江大学学报（理学版） 2023年第4期50卷 402-408页

作者：李丹王贵君三亚学院理工学院海南三亚572000 天津师范大学数学科学学院天津300387

距离测度是毕达哥拉斯(Pythagorean)模糊决策的一个基本概念,其在用权重向量进行有序集成运算、有序加权距离和相似度构造时具有重要作用。然而,早期发表于International Journal of Intelligent Systems中的文章Extension of TOPSIS to... 详细信息

距离测度是毕达哥拉斯(Pythagorean)模糊决策的一个基本概念,其在用权重向量进行有序集成运算、有序加权距离和相似度构造时具有重要作用。然而,早期发表于International Journal of Intelligent Systems中的文章Extension of TOPSIS to multiple criteria decision making with Pythagorean fuzzy sets,在首次引入海明距离测度时,对距离公理化条件的证明存在不妥。为此,通过反例和分析指出了其在证明公理化条件的有界性和三点不等式时存在的错误,并统筹考虑犹豫度的绝对值项和其他绝对值项,通过分情况讨论给出了海明距离测度的严格证明,进一步,证明了其推广形式(欧几里得距离测度)的公理化条件。

关键词：毕达哥拉斯模糊数海明距离测度欧几里得距离测度公理化条件

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Turbulent mixing above the Atlantic Water around the Chukchi Borderland in 2014

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Acta Oceanologica Sinica 2018年第3期37卷 31-41页

作者： ZHONG Wenli GUO guijun ZHAO Jinping li Tao WANG Xiaoyu MU Longjiang Key Laboratory of Physical Oceanography Ocean University of China Center for Ocean and Climate Research The First Institute of Oceanography Key Laboratory of Research on Marine Hazards Forecasting National Marine Environmental Forecasting CenterState Oceanic Administration

This study presents an analysis of the CTD data and the turbulent microstructure data collected in 2014, the turbulent mixing environment above the Atlantic Water（AW） around the Chukchi Borderland region is *** wind becomes more efficient in driving the upper ocean movement along with the rapid decline of sea ice,thus results in a more restless interior of the Arctic Ocean. The turbulent dissipation rate is in the range of4.60×10–10（–3.31×10–9 W/kg with a mean value of 1.33×10–9 W/kg, while the diapycnal diffusivity is in the range of1.45×10–6–1.46×10–5m2/s with a mean value of 4.84×10–6 m2/s in 200–300 m（above the AW）. After investigating on the traditional factors（i.e., wind, topography and tides） that may contribute to the turbulent dissipation rate, the results show that the tidal kinetic energy plays a dominating role in the vertical mixing above the AW. Besides, the swing of the Beaufort Gyre（BG） has an impact on the vertical shear of the geostrophic current and may contribute to the regional difference of turbulent mixing. The parameterized method for the double-diffusive convection flux above the AW is validated by the direct turbulent microstructure results.

关键词： Atlantic Water Chukchi Borderland turbulent dissipation rate diapycnal diffusive surface stress

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An atypical pituitary adenoma with a high degree of malignancy: a case report

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Chinese Neurosurgical Journal 2018年第2期4卷 100-103页

作者： Songquan Wang Deling li guijun Jia Ming Ni Department of Neurosurgery Beijing Tiantan Hospital Capital Medical University Beijing China China National Clinical Research Center for Neurological Diseases (NCRC-ND) 6 Tiantan Xili Street Dongcheng District Beijing China

Background: Pituitary carcinoma is very rare and hard to diagnose. However, some atypical pituitary adenomas present with a high rate of proliferation and extensive invasion, suggesting a tumor with a high degree of malignancy. Case presentation: Here, we present a case study of this type of tumor. A 46 years old women was admitted for headaches and impaired vision, and MRI and CT revealed a sellar lesion. She underwent a transsphenoidal surgery followed by radiotherapy, but the tumor recurred only one month later. She decided to undergo a second and third operation. The final pathology showed a non-functioning adenoma that was approximately 80% ki-67-positive and extensively p53-positive. No metastasis was found. The tumor progressed extremely quickly, and the patient died 7 months after the initial diagnosis. Conclusions: A pituitary adenoma like this should be treated like a carcinoma, and early treatment may increase the likelihood of survival. A traditional diagnosis standard is unfit for this type of tumor.

关键词： Atypical pituitary adenoma Pituitary carcinoma Pathology Invasiveness

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Improvement of short-term forecasting in the northwest Pacific through assimilating Argo data into initial fields

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Acta Oceanologica Sinica 2013年第7期32卷 57-65页

作者： FU Hongli CHU Peter C HAN guijun HE Zhongjie li Wei ZHANG Xuefeng Key Laboratory of State Oceanic Adminstration for Marine Environmental Information Technology National Marine Data and Information ServiceState Oceanic Administration Naval Ocean Analysis and Prediction Laboratory Naval Postgraduate School

The impact of assimilating Argo data into an initial field on the short-term forecasting accuracy of temper- ature and salinity is quantitatively estimated by using a forecasting system of the western North Pacific, on the base of the Princeton ocean model with a generalized coordinate system （POMgcs）. This system uses a sequential multigrid three-dimensional variational （3DVAR） analysis scheme to assimilate observation da- ta. Two numerical experiments were conducted with and without Argo temperature and salinity profile data besides conventional temperature and salinity profile data and sea surface height anomaly （SSHa） and sea surface temperature （SST） in the process of assimilating data into the initial fields. The forecast errors are estimated by using independent temperature and salinity profiles during the forecasting period, including the vertical distributions of the horizontally averaged root mean square errors （H-RMSEs） and the horizontal distributions of the vertically averaged mean errors （MEs） and the temporal variation of spatially averaged root mean square errors （S-RMSEs）. Comparison between the two experiments shows that the assimila- tion of Argo data significantly improves the forecast accuracy, with 24% reduction of H-RMSE maximum for the temperature, and the salinity forecasts are improved more obviously, averagely dropping of 50% for H-RMSEs in depth shallower than 300 m. Such improvement is caused by relatively uniform sampling of both temperature and salinity from the Argo drifters in time and space.

关键词： data assimilation Argo data western North Pacific ocean prediction

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