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Overlap maximum matching ratio (OMMR): a new measure to evaluate overlaps of essential modules

Xiao-xia ZHANG,Qiang-hua XIAO,Bin LI,Sai HU,Hui-jun XIONG,Bi-hai ZHAO

《信息与电子工程前沿（英文）》 2015年 第16卷 第4期   页码 293-300 doi: 10.1631/FITEE.1400282

摘要： Protein complexes are the basic units of macro-molecular organizations and help us to understand the cell’s mechanism. The development of the yeast two-hybrid, tandem affinity purification, and mass spectrometry high-throughput proteomic techniques supplies a large amount of protein-protein interaction data, which make it possible to predict overlapping complexes through computational methods. Research shows that overlapping complexes can contribute to identifying essential proteins, which are necessary for the organism to survive and reproduce, and for life’s activities. Scholars pay more attention to the evaluation of protein complexes. However, few of them focus on predicted overlaps. In this paper, an evaluation criterion called overlap maximum matching ratio (OMMR) is proposed to analyze the similarity between the identified overlaps and the benchmark overlap modules. Comparison of essential proteins and gene ontology (GO) analysis are also used to assess the quality of overlaps. We perform a comprehensive comparison of serveral overlapping complexes prediction approaches, using three yeast protein-protein interaction (PPI) networks. We focus on the analysis of overlaps identified by these algorithms. Experimental results indicate the important of overlaps and reveal the relationship between overlaps and identification of essential proteins.

关键词： Protein-protein interaction network     Essential protein modules     Overlap     Overlap maximum matching ratio    

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expression are associated with clinical phenotype and clinico-hematological response to hydroxyurea in essential

《医学前沿（英文）》 2022年 第16卷 第3期   页码 403-415 doi: 10.1007/s11684-021-0858-1

摘要： The morbidity and mortality of myeloproliferative neoplasms (MPNs) are primarily caused by arterial and venous complications, progression to myelofibrosis, and transformation to acute leukemia. However, identifying molecular-based biomarkers for risk stratification of patients with MPNs remains a challenge. We have previously shown that interferon regulatory factor-8 (IRF8) and IRF4 serve as tumor suppressors in myeloid cells. In this study, we evaluated the expression of IRF4 and IRF8 and the JAK2V617F mutant allele burden in patients with MPNs. Patients with decreased IRF4 expression were correlated with a more developed MPN phenotype in myelofibrosis (MF) and secondary AML (sAML) transformed from MPNs versus essential thrombocythemia (ET). Negative correlations between the JAK2V617F allele burden and the expression of IRF8 (P <0.05) and IRF4 (P<0.001) and between white blood cell (WBC) count and IRF4 expression (P <0.05) were found in ET patients. IRF8 expression was negatively correlated with the JAK2V617F allele burden (P <0.05) in polycythemia vera patients. Complete response (CR), partial response (PR), and no response (NR) were observed in 67.5%, 10%, and 22.5% of ET patients treated with hydroxyurea (HU), respectively, in 12 months. At 3 months, patients in the CR group showed high IRF4 and IRF8 expression compared with patients in the PR and NR groups. In the 12-month therapy period, low IRF4 and IRF8 expression were independently associated with the unfavorable response to HU and high WBC count. Our data indicate that the expression of IRF4 and IRF8 was associated with the MPN phenotype, which may serve as biomarkers for the response to HU in ET.

关键词： myeloproliferative neoplasms     IRF4     IRF8     hydroxyurea     essential thrombocythemia    

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Transcriptional modules related to hepatocellular carcinoma survival: coexpression network analysis

null

《医学前沿（英文）》 2016年 第10卷 第2期   页码 183-190 doi: 10.1007/s11684-016-0440-4

摘要：

We performed weighted gene coexpression network analysis (WGCNA) to gain insights into the molecular aspects of hepatocellular carcinoma (HCC). Raw microarray datasets (including 488 samples) were downloaded from the Gene Expression Omnibus (GEO) website. Data were normalized using the RMA algorithm. We utilized the WGCNA to identify the coexpressed genes (modules) after non-specific filtering. Correlation and survival analyses were conducted using the modules, and gene ontology (GO) enrichment was applied to explore the possible mechanisms. Eight distinct modules were identified by the WGCNA. Pink and red modules were associated with liver function, whereas turquoise and black modules were inversely correlated with tumor staging. Poor outcomes were found in the low expression group in the turquoise module and in the high expression group in the red module. In addition, GO enrichment analysis suggested that inflammation, immune, virus-related, and interferon-mediated pathways were enriched in the turquoise module. Several potential biomarkers, such as cyclin-dependent kinase 1 (CDK1), topoisomerase 2α (TOP2A), and serpin peptidase inhibitor clade C (antithrombin) member 1 (SERPINC1), were also identified. In conclusion, gene signatures identified from the genome-based assays could contribute to HCC stratification. WGCNA was able to identify significant groups of genes associated with cancer prognosis.

关键词： hepatocellular carcinoma     coexpression     module     microarray     prognosis    

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Isomorphism analysis on generalized modules oriented to the distributed parameterized intelligent product

Shasha ZENG, Weiping PENG, Tiaoyu LEI

《机械工程前沿（英文）》 2020年 第15卷 第1期   页码 12-23 doi: 10.1007/s11465-019-0555-9

摘要： The distributed parameterized intelligent product platform (DPIPP) contains many agents of a product minimum approximate autonomous subsystem (generalized module). These distributed agents communicate, coordinate, and cooperate using their knowledge and skills and eventually accomplish the design for mass customization in a loosely coupled environment. In this study, a new method of isomorphism analysis on generalized modules oriented to DPIPP is proposed. First, on the basis of the bill of material partition and generalized module mining, the parameters of the main characteristics are extracted to construct the main characteristic parameter matrix. Second, similarity calculation of generalized modules is realized by improving the clustering using representatives algorithm, and isomorphism model sets are obtained. Generalized modules with a similar structure are combined to complete the isomorphism analysis. The effectiveness of the proposed method is verified by taking high- and medium-pressure valve data as an example.

关键词： distributed parameterized intelligent product platform     generalized module     isomorphism analysis     product family    

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Efficacy and safety of JAK inhibitor INC424 in patients with primary and post-polycythemia vera or post-essential

null

《医学前沿（英文）》 2016年 第10卷 第4期   页码 437-443 doi: 10.1007/s11684-016-0472-9

摘要：

A phase II study (A2202) was performed to evaluate the efficacy and safety of JAK inhibitor ruxolitinib in 63 Chinese MF patients. Ruxolitinib was given twice a day (bid) at a starting dose of 15 mg (n=25) or 20 mg (n=38) based on a baseline platelet count. About 94.7% of the patients achieved a reduction in spleen size, 27.0% of which exhibited significant reduction (≥35%) at week 24. Significant improvement in debilitating constitutional symptoms, as assessed by MFSAF v2.0, was observed in patients treated with ruxolitinib. Ruxolitinib treatment was generally well tolerated by Chinese patients. Although the treatment was associated with an increase in certain adverse events (AEs) that were established as identified risks (anemia and thrombocytopenia), these AEs were considered manageable in this clinical setting. Ruxolitinib provided substantial reductions in splenomegaly and improvements in symptoms, and was well-tolerated by Chinese patients with MF.

关键词： JAK     ruxolitinib     Chinese patients     myelofibrosis    

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Observation of a higher JAK2 V617F homozygous mutated clone in polycythemia vera compared to essential

LIU Hongxing, TONG Chunrong, CAI Peng, GU Jiangying, LIN Yuehui, TENG Wen, WANG He, ZHANG Ying, ZHU Ping

《医学前沿（英文）》 2008年 第2卷 第3期   页码 309-313 doi: 10.1007/s11684-008-0059-1

摘要： Single-tube bi-directional allele specific amplification (SB-ASA) and real-time quantitative polymerase chain reaction (RQ-PCR) assays were developed and performed for JAK2V617F detection on 40 polycythemia vera (PV) samples, 31 essential thrombocythemia (ET) samples, 40 acute leukemia samples, and 40 healthy control samples. Differences between detect limitations of the two assays and their influence on the mutation detection rate were analyzed. The results showed that in some samples, the JAK2V617F burden was as low as nearly 1%, and thus more JAK2V617F-positive samples were detected by RQ-PCR than by SB-ASA assay due to the former higher detect limitation. Mutation allele ratios in PV and ET samples and their relevance to biological characteristics were also analyzed. The results showed that the mutation allele ratio was 0.436 ± 0.261 in PV, higher than the 0.216 ± 0.207 in ET; percentage of certainly homozygous mutation carriers in PV was 40.54%, higher than the 10% in ET. However, statistical analysis showed no relevance between mutation allele burden and sex or age. Our result shows that the pathogenesis of PV and ET may be related to the mutation allele burden of JAK2V617F.

关键词： specific amplification     essential thrombocythemia     Single-tube bi-directional     JAK2V617F-positive     JAK2V617F detection    

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森林火灾预报的新视角

赵宪文

《中国工程科学》 2000年 第2卷 第5期   页码 66-71

摘要：

从森林火灾成灾的三个基本因子（火源、环境和可燃物）入手，在宏观上对西南地区森林火灾预报方法进行了探讨。在预测林火发生方面，考虑到人为火是发生森林火灾的主要原因，有很大随机性，因而采用了马尔科夫随机过程理论。在分析成灾环境时，采用了与天、地、生相关分析的方法。特别在可燃物的贮量估测方面，用航天遥感数据，提出一套新的框算方法，为在区域的尺度上估测森林火灾给出了有效的、定量的方法，从而提高了可信度。

关键词： 森林火灾预报     航天遥感     火灾基本因子     新视角    

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Association study on GNB3 gene polymorphism with essential hypertension in Xinjiang Uygur group

JING Jianying, WANG Dan, WANG Xiaofeng, JIN Jianzhong, JIN Li, JIAO Yi, WEN Hao, LIN Renyong

《医学前沿（英文）》 2007年 第1卷 第2期   页码 230-233 doi: 10.1007/s11684-007-0045-z

摘要： The relationship between the tenth exon C825T of G-protein β3 subunit (GNB) genetic polymorphism and hypertension in the Uygur population of China was investigated. A nested case-control study ( = 738) was carried out. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was used to genotype GNB C825T polymorphism in 354 hypertensive (HT) and 384 normotensive (NT) Uygur subjects. The distributions of GNB C825T genotypes were CC (27.2%), TT (42.9%), and CT (29.9%) in the hypertensive subjects and CC (27.7%), TT (42.4%), CT (29.9%) in the normotensive subjects. There were no significant differences in the genotype distributions between the two groups ( = 0.0262 P = 0.99). The T allele was 51.4% in hypertensive subjects and 51.2% in normotensive subjects, which, between the two groups, was not a significant difference ( = 0.0016 P = 0.97). Further analysis shows that there is no association between C825T genotypes and age, body mass index (BMI), Glucose (GLU), Triglyceride (TG), Cholesterol (CHO), systolic blood pressure (SBP) and diastolic blood pressure (DBP). No evidence was found to suggest an association between GNB C825T polymorphism and hypertension in the Uygur population of China.

关键词： case-control     significant difference     reaction-restriction fragment     C825T polymorphism     evidence    

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Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction

Hong LI,Ziding ZHANG

《农业科学与工程前沿（英文）》 2016年 第3卷 第2期   页码 102-112 doi: 10.15302/J-FASE-2016100

摘要： Plants are frequently affected by pathogen infections. To effectively defend against such infections, two major modes of innate immunity have evolved in plants; pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity. Although the molecular components as well as the corresponding pathways involved in these two processes have been identified, many aspects of the molecular mechanisms of the plant immune system remain elusive. Recently, the rapid development of omics techniques (e.g., genomics, proteomics and transcriptomics) has provided a great opportunity to explore plant–pathogen interactions from a systems perspective and studies on protein–protein interactions (PPIs) between plants and pathogens have been carried out and characterized at the network level. In this review, we introduce experimental and computational identification methods of PPIs, popular PPI network analysis approaches, and existing bioinformatics resources/tools related to PPIs. Then, we focus on reviewing the progress in genome-wide PPI networks related to plant–pathogen interactions, including pathogen-centric PPI networks, plant-centric PPI networks and interspecies PPI networks between plants and pathogens. We anticipate genome-wide PPI network analysis will provide a clearer understanding of plant–pathogen interactions and will offer some new opportunities for crop protection and improvement.

关键词： plant–pathogen interactions     systems biology     omics     plant immunity     protein–protein interaction     network    

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Reactive oxygen species generation is essential for cisplatin-induced accelerated senescence in hepatocellular

null

《医学前沿（英文）》 2014年 第8卷 第2期   页码 227-235 doi: 10.1007/s11684-014-0327-1

摘要：

Accelerated senescence is important because this process is involved in tumor suppression and has been induced by many chemotherapeutic agents. The platinum-based chemotherapeutic agent cisplatin displays a wide range of antitumor activities. However, the molecular mechanism of cisplatin-induced accelerated senescence in hepatocellular carcinoma (HCC) remains unclear. In the present study, the growth inhibitory effect of cisplatin on HepG2 and SMMC-7721 cells was detected by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Cellular senescence was then assessed by β-galactosidase assay. Senescence-related factors, including p53, p21, and p16, were evaluated by quantitative reverse transcription-polymerase chain reaction. Reactive oxygen species (ROS) was analyzed by flow cytometry. Our results revealed that cisplatin reduced the proliferation of HepG2 and SMMC-7721 cells in a dose- and time-dependent manner. Senescent phenotype observed in cisplatin-treated hepatoma cells was dependent on p53 and p21 activation but not on p16 activation. Furthermore, cisplatin-induced accelerated senescence depended on intracellular ROS generation. The ROS scavenger N-acetyl-L-cysteine also significantly suppressed the cisplatin-induced senescence of HepG2 and SMMC-7721 cells. In conclusion, our results revealed a functional link between intracellular ROS generation and cisplatin-induced accelerated senescence, and this link may be used as a potential target of HCC.

关键词： reactive oxygen species     senescence     cisplatin     hepatocellular carcinoma    

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The role of protein kinase C epsilon in neural signal transduction and neurogenic diseases

null

《医学前沿（英文）》 2011年 第5卷 第1期   页码 70-76 doi: 10.1007/s11684-011-0119-9

摘要：

Protein kinase C epsilon (PKC ?) is one of major isoforms in novel PKC family. Although it has been extensively characterized in the past decade, the role of PKC ? in neuron is still not well understood. Advances in molecular biology have now removed significant barriers to the direct investigation of PKC ? functions in vivo, and PKC ? has been increasingly implicated in the neural biological functions and associated neurogenic diseases. Recent studies have provided important insights into the influence of PKC ? on cortical processing at both the single cell level and network level. These studies provide compelling evidence that PKC ? could regulate distinct aspects of neural signal transduction and suggest that the coordinated actions of a number of molecular signals contribute to the specification and differentiation of PKC ? signal pathway in the developing brain.

关键词： protein kinase C ?     signal transduction     neurogenic disease    

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网络安全研究——成功的数字化未来的关键

Jackie Craig

《工程（英文）》 2018年 第4卷 第1期   页码 9-10 doi: 10.1016/j.eng.2018.02.006

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Wheat gluten protein and its impacts on wheat processing quality

Wujun MA, Zitong YU, Maoyun SHE, Yun ZHAO, Shahidul ISLAM

《农业科学与工程前沿（英文）》 2019年 第6卷 第3期   页码 279-287 doi: 10.15302/J-FASE-2019267

摘要：

Before the advent of the wheat genomic era, a wide range of studies were conducted to understand the chemistry and functions of the wheat storage proteins, which are the major determinants of wheat flour the suitability of wheat flour for various end products, such as bread, noodles and cakes. Wheat grain protein is divided into gluten and non-gluten fractions and the wheat processing quality mainly depends on the gluten fractions. Gluten provides the unique extensibility and elasticity of dough that are essential for various wheat end products. Disulfide bonds are formed between cysteine residues, which is the chemical bases for the physical properties of dough. Based on the SDS-extractability, grain protein is divided into SDS-unextractable polymeric protein (UPP) and SDS-extractable polymeric protein. The percentage of UPP is positively related to the formation of disulfide bonds in the dough matrix. In the wheat genomic era, new glutenins with long repetitive central domains that contain a high number of consensus hexapeptide and nonapeptide motifs as well as high content of cysteine and glutamine residues should be targeted.

关键词： wheat gluten     consensus motifs     disulfide bonds     SDS-unextractable polymeric protein     glutenins     gliadins     processing quality     storage protein    

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Construction of sustainable, colored and multifunctional protein silk fabric using biomass riboflavin

《化学科学与工程前沿（英文）》 2023年 第17卷 第8期   页码 1131-1139 doi: 10.1007/s11705-023-2321-0

摘要： Riboflavin sodium phosphate has been confirmed as a promising biomass product derived from natural plants. In this paper, a novel method of dyeing and multifunctional modification of silk fabric by impregnation with riboflavin sodium phosphate was proposed, such that protein silk fabric can be endowed with bright yellow color and multi-functionality. The results of this paper confirmed that the pH and concentration of riboflavin sodium phosphate solution are critical factors for dyeing and multifunctional modification. Attractively, the photochromic performance was one of the most distinctive features of the modified silk fabric, and the dyed silk fabric turned into fluorescent green from original yellow under 365 nm ultraviolet lamp. Furthermore, the modified silk fabric exhibited good antibacterial properties with a high inhibition rate of 92% for Escherichia coli. Besides, the flame retardancy of silk fabric was significantly improved after modification. The damaged length of modified silk fabric with 40% owf riboflavin sodium phosphate was lower than 10.4 cm and passed the B1 classification. As revealed by the result of this paper, riboflavin sodium phosphate is sufficiently effective in serving as an eco-friendly multifunctional agent for strengthening the add-value of silk textiles.

关键词： biomass     riboflavin sodium phosphate     silk protein     multifunctional modification     flame retardant    

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Antithrombin deficiency and decreased protein C activity in a young man with venous thromboembolism:

null

《医学前沿（英文）》 2018年 第12卷 第3期   页码 319-323 doi: 10.1007/s11684-017-0553-4

摘要：

Antithrombin and protein C are two crucial members in the anticoagulant system and play important roles in hemostasis. Mutations in and lead to deficiency or dysfunction of the two proteins, which could result in venous thromboembolism (VTE). Here, we report a Chinese 22-year-old young man who developed recurrent and serious VTE in cerebral veins, visceral veins, and deep veins of the lower extremity. Laboratory tests and direct sequencing of and were conducted for the patient and his family members. Coagulation tests revealed that the patient presented type I antithrombin deficiency combined with decreased protein C activity resulting from a small insertion mutation c.848_849insGATGT in and a short deletion variant c.572_574delAGA in . This combination of the two mutations was absent in 400 healthy subjects each from southern and northern China. Then, we summarized all the mutations of the and gene reported in the Chinese Han population. This study demonstrates that the combination of antithrombin deficiency and decreased protein C activity can result in severe VTE and that the coexistence of different genetic factors may increase the risk of VTE.

关键词： antithrombin deficiency     protein C activity     mutation     variant     venous thromboembolism     anticoagulants    

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标题 作者 时间 类型 操作

Overlap maximum matching ratio (OMMR): a new measure to evaluate overlaps of essential modules

Xiao-xia ZHANG,Qiang-hua XIAO,Bin LI,Sai HU,Hui-jun XIONG,Bi-hai ZHAO

期刊论文

expression are associated with clinical phenotype and clinico-hematological response to hydroxyurea in essential

期刊论文

Transcriptional modules related to hepatocellular carcinoma survival: coexpression network analysis

null

期刊论文

Isomorphism analysis on generalized modules oriented to the distributed parameterized intelligent product

Shasha ZENG, Weiping PENG, Tiaoyu LEI

期刊论文

Efficacy and safety of JAK inhibitor INC424 in patients with primary and post-polycythemia vera or post-essential

null

期刊论文

Observation of a higher JAK2 V617F homozygous mutated clone in polycythemia vera compared to essential

LIU Hongxing, TONG Chunrong, CAI Peng, GU Jiangying, LIN Yuehui, TENG Wen, WANG He, ZHANG Ying, ZHU Ping

期刊论文

森林火灾预报的新视角

赵宪文

期刊论文

Association study on GNB3 gene polymorphism with essential hypertension in Xinjiang Uygur group

JING Jianying, WANG Dan, WANG Xiaofeng, JIN Jianzhong, JIN Li, JIAO Yi, WEN Hao, LIN Renyong

期刊论文

Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction

Hong LI,Ziding ZHANG

期刊论文

Reactive oxygen species generation is essential for cisplatin-induced accelerated senescence in hepatocellular

null

期刊论文

The role of protein kinase C epsilon in neural signal transduction and neurogenic diseases

null

期刊论文

网络安全研究——成功的数字化未来的关键

Jackie Craig

期刊论文

Wheat gluten protein and its impacts on wheat processing quality

Wujun MA, Zitong YU, Maoyun SHE, Yun ZHAO, Shahidul ISLAM

期刊论文

Construction of sustainable, colored and multifunctional protein silk fabric using biomass riboflavin

期刊论文

Antithrombin deficiency and decreased protein C activity in a young man with venous thromboembolism:

null

期刊论文