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Gene regulatory network inference based on causal discovery integrating with graph neural network

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Quantitative Biology 2023年第4期11卷 434-450页

作者： Ke Feng Hongyang Jiang Chaoyi Yin Huiyan Sun School of Artificial Intelligence Jilin UniversityChangchunChina international center of Future Science Jilin UniversityChangchunChina Engineering research center of Knowledge-Driven human-Machine Intelligence Ministry of EducationChangchunChina

Gene regulatory network (GRN) inference from gene expression data is asignificant approach to understanding aspects of the biological *** with generalized correlation-based methods, causality-inspiredones seem more rational to infer regulatory relationships. We proposeGRINCD, a novel GRN inference framework empowered by graph representationlearning and causal asymmetric learning, considering both linearand non-linear regulatory relationships. First, high-quality representation ofeach gene is generated using graph neural network. Then, we apply theadditive noise model to predict the causal regulation of each regulator-targetpair. Additionally, we design two channels and finally assemble them forrobust prediction. Through comprehensive comparisons of our frameworkwith state-of-the-art methods based on different principles on numerousdatasets of diverse types and scales, the experimental results show that ourframework achieves superior or comparable performance under variousevaluation metrics. Our work provides a new clue for constructing GRNs,and our proposed framework GRINCD also shows potential in identifyingkey factors affecting cancerdevelopment.

关键词： causal discovery ensemble learning gene regulatory network inference gene regulatory networks graph neural network key regulators of disease development

Real-time measurements of PM_(2.5),PM_(10-2.5),and BC in an urban street canyon

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Particuology 2015年第3期13卷 134-140页

作者： Yan Cheng Shun Cheng Lee Yuan Gao Long Cui Wenjing Deng Junji Cao Zhenxing Shen Jian Sun Department of Environmental Science and Technology School of Human Settlements and Civil EngineeringXi'an Jiaotong University SKLLQG Institute of Earth and EnvironmentCAS Department of Civil and Environmental Engineering Research Center for Environmental Technology and ManagementThe Hong Kong Polytechnic University Department of Science and Environmental Studies and Centre for education for Environmental Sustainability The Hong Kong Institute of Education

A continuous dichotomous beta gauge monitor was used to characterize the hourly content of PM2.5, PM10-2.5, and Black Carbon （BC） over a 12-month period in an urban street canyon of Hong Kong. Hourly vehicle counts for nine vehicle classes and meteorological data were also recorded. The average weekly cycles of PM2.5, PM10-2.5, and BC suggested that all species are related to traffic, with high concentrations on workdays and low concentrations over the weekends. PM2.s exhibited two comparable concentrations at 10：00-11：00 （63.4 μg/m3） and 17：00-18：00 （65.0 p.g/m3 ） local time （LT） during workdays, correspond- ing to the hours when the numbers of diesel-fueled and gasoline-fueled vehicles were at their maximum levels： 3179 and 2907 h-1, respectively. BC is emitted mainly by diesel-fueled vehicles and this showed the highest concentration （31.2μg/m3） during the midday period （10：00-11：00 LT） on workdays. A poor correlation was found between PM2.s concentration and wind speed （R= 0.51, P-value 〉 0.001 ）. In contrast, the concentration of PM10-2.s was found to depend upon wind speed and it increased with obvious statistical significance as wind speed increased （R = 0,98, P-value 〈 0.0001 ）.

关键词： PM2.5 PMl0 2.5BCHong KongUrban street canyon

The challenge of emerging SARS-CoV-2 mutants to vaccine development

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Journal of Genetics and Genomics 2021年第2期48卷 102-106页

作者： Rong Li Jun Liu Hui Zhang Institute of human Virology Key Laboratory of Tropical Disease Control of Ministry of EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhouGuangdong 570080China

Since the outbreak of the pandemic,waves of epidemics caused by severe acute respiratory syndrome coronavirus 2(SARS-Co V-2)variants that harbor novel mutations have never ***,it undergoes rapid mutations that involve single-nucleotide polymorphism(SNP)dominantly,whereas ORF1ab and spike genes contain the most of more than 20,000 mutation sites reported within a year(Fang et al.,2021).Mutations inside spike protein are highly concerned for their potential impact on viral transmissibility and immune evasion,as spike protein is responsible for the interaction with the viral receptor angiotensin-converting enzyme 2(ACE2)to mediate viral entry to the target cells.D614G identified in early 2020 is a globally dominant mutation(Korber et al.,2020).In late 2020,several variants were reported,which had caused continental and eventually worldwide *** notable variants include B.1.1.7 lineage(501Y.V1,Variant of Concern[VOC]202012/01),501Y.V2 variant(known as B.1.351 lineage),and P.1 lineage(also named 501Y.V3).In comparison with the D614G and D614 lineages identified in early 2020,they contain a large number of mutations within spike protein(Fig.1).

关键词： respiratory acute eventually

Interferon-λ polymorphisms and response to pegylated interferon in Iranian hepatitis C patients

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World Journal of Gastroenterology 2015年第29期21卷 8935-8942页

作者： Arghavan Haj-sheykholeslami Maryam Keshvari Heidar Sharafi Ali Pouryasin Khalil Hemmati Fatemeh Mohammadzadehparjikolaei The Liver Pancreatic and Biliary Diseases Research Center Digestive Diseases Research Institute Tehran University of Medical Sciences Blood Transfusion research center High Institute for Research and Education in Transfusion Medicine Middle East Liver Disease center Armin Pathobiology Laboratory

AIM: To evaluate the efficacy of pegylated interferon in Iranian chronic hepatitis C patients in relation to interferon-λ(IFNL) polymorphisms. METHODS: This study enrolled patients with chronic hepatitis C referred to the Tehran Blood Transfusion Hepatitis Clinic in 2011. Patients were included in the study if they had no concomitant hepatic illness, were negative for human immunodeficiency virus antibodies, and had no prior history of treatment with any type ofpegylated interferon. Patients were treated with 180 μg pegylated interferon alpha-2a(Pegaferon®) weekly and 800-1200 mg ribavirin daily for 24 or 48 wk depending on weight and hepatitis C virus(HCV) genotype. Blood samples were collected from patients to obtain DNA for determination of IFNL rs12979860 and rs8099917 polymorphisms. The virologic response in patients was then evaluated and compared between the different IFNL ***: A total of 152 patients with a mean age of 41.9 ± 10.0 years were included in the study, of which 141/152 were men(92.8%). The most frequent HCV genotype was type-1, infecting 93/152(61.2%) patients. Sustained virologic response(SVR) was achieved in 81.9% of patients with HCV genotype-1 and 91.1% of patients with HCV genotype-3. Treatment success was achieved in 91.2%(52/57) of patients with the IFNL rs12979860 CC genotype and 82.1%(78/95) in those with other genotypes. Similar treatment response rates were also observed in patients with rs8099917 TT(39/45; 86.7%) and non-TT(61/68; 89.7%) genotypes. Univariate analyses identified the following factors which influenced treatment response for inclusion in a multivariate analysis: age, HCV RNA level, stage of liver fibrosis, rs12979860 CC genotype, and aspartate transaminase level. A logistic regression analysis revealed that only the rs12979860 CC genotype was significantly associated with achievement of SVR(OR = 6.2; 95%CI: 1.2-31.9; P = 0.03).CONCLUSION: The rs12979860 CC genotype was associated with SVR in patients

关键词： Chronic hepatitis C Pegylated interferon rs12979860 rs8099917 Sustained virologic response

Adipose-derived stromal cell in regenerative medicine:A review

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World Journal of Stem Cells 2017年第8期9卷 107-117页

作者： Reza Tabatabaei Qomi Mohsen Sheykhhasan Department of Stem Cell the Academic Center for EducationCulture and ResearchPO Box QOM-***QomIran

The application of appropriate cell origin for utilizing inregenerative medicine is the major issue. Various kinds of stem cells have been used for the tissue engineering and regenerative medicine. Such as, several stromal cells have been employed as treat option for regenerative medicine. For example, human bone marrow-derived stromal cells and adipose-derived stromal cells(ADSCs) are used in cell-based therapy. Data relating to the stem cell therapy and processes associated with ADSC has developed remarkably in the past 10 years. As medical options, both the stromal vascular and ADSC suggests good opportunity as marvelous cell-based therapeutics. The some biological features are the main factors that impact the regenerative activity of ADSCs, including the modulation of the cellular immune system properties and secretion of bioactive proteins such as cytokines, chemokines and growth factors, as well as their intrinsic anti-ulcer and anti-inflammatory potential. A variety of diseases have been treated by ADSCs, and it is not surprising that there has been great interest in the possibility that ADSCs might be used as therapeutic strategy to improve a wider range of diseases. This is especially important when it is remembered that routine therapeutic methods are not completely effective in treat of diseases. Here, it was discuss about applications of ADSC to colitis, liver failure, diabetes mellitus, multiple sclerosis, orthopaedic disorders, hair loss, fertility problems, and salivary gland damage.

关键词： Adipose-derived stromal cell Colitis disease Liver failure Diabetes mellitus Multiple sclerosis Orthopedic disorders Hair loss Fertility problems Salivary gland damage

Acetylated HOXB9 at lysine 27 is of differential diagnostic value in patients with pancreatic ductal adenocarcinoma

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Frontiers of Medicine 2020年第1期14卷 91-100页

作者： Xiaoran Sun Jiagui Song Jing Zhang Jun Zhan Weigang Fang Hongquan Zhang Department of human Anatomy Histology and EmbryologyKey Laboratory of Carcinogenesis and Translational ResearchMinistry of Educationand State Key Laboratory of Natural and Biomimetic DrugsPeking University Health Science CenterBeijing 100191China Department of Pathology Peking University Health Science CenterBeijing 100191China

Pancreatic ductal adenocarcinoma(PDAC)is the ninth most common human malignancy and the sixth leading cause of cancer-related death in ***27-HOXB9 is a newly identified HOXB9 post-transcriptional modification that can predict the outcome in lung adenocarcinoma and colon cancer ***,the role of AcK27-HOXB9 in PDAC is *** present study aims to investigate the differential diagnostic role of patients with AcK27-HOXB9 *** microarrays consisting of 162 pancreatic tumor tissue samples from patients with PDAC and paired normal subjects were used to examine HOXB9 and AcK27-HOXB9 levels and localizations by immunohistochemical analysis and Western blot assay,***9 was upregulated(P<0.0001),and AcK27-HOXB9(P=0.0023)was downregulated in patients with ***9 promoted(P=0.0115),while AcK27-HOXB9(P=0.0279)inhibited PDAC ***27-HOXB9 predicted favorable outcome in patients with PDAC(P=0.0412).AcK27-HOXB9 also suppressed PDAC cell migration in a cell migration *** results of this study showed that HOXB9 promoted and AcK27-HOXB9 suppressed PDAC *** determination of ratio between HOXB9 and AcK27-HOXB9 exhibited potential diagnostic value in patients with PDAC.

关键词： HOXB9 AcK27-HOXB9 PDAC

The Formation Mechanism of the Outlook on human rights Development in Contemporary China

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The Journal of human rights 2022年第2期21卷 248-268页

作者：齐延平 SU Yilong the center for Science Technology and Human Rights of Beijing University of Technology 不详

The Western fundamentalist view of human rights,in contrast to Chinese society and culture,is external,and thus provides"conceptual form," "thinking method" and "theoretical technique"but not concrete *** the traditional Chinese ideology,the time-honored group standard cannot be replaced by the individual *** New China,priority is given to the freedom and independence of "everyone" and the realization of rights and interests for"all".Contemporary China combines the human rights conception in Marxism with China’s concrete ***,it integrates the socialist idea of equality with the traditional culture of the Chinese nation,creating a dual-guarantee system for universal values and individual *** gives a clear-cut expression to contemporary China’s rich traits of the cultural tradition of emphasizing progress for all and the equality for all,the priority of realizing the survival and development of the people,and the reference to the achievements of human rights civilizations of other *** rights development in contemporary China must further consolidate the political conditions and institutional base for realizing the "public " goal of human rights and build a solid institutional guarantee for the "private" value orientation of human rights,by means of the construction of the whole-process people’s democracy.

关键词： human rights in China progress for all equality for all logic of practice formation mechanism

Design and investigation of novel ultra-high-voltage junction field-effect transistor embedded with NPN

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Chinese Physics B 2021年第7期30卷 619-623页

作者： Xi-Kun Feng Xiao-Feng Gu Qin-Ling Ma Yan-Ni Yang Hai-Lian Liang Engineering research center of Internet of Things Technology Applications(Ministry of education) Department of Electronic EngineeringJiangnan UniversityWuxi 214122China

Ultra-high-voltage(UHV)junction field-effect transistors(JFETs)embedded separately with the lateral NPN(JFETLNPN),and the lateral and vertical NPN(JFET-LVNPN),are demonstrated experimentally for improving the electrostatic discharge(ESD)*** ESD characteristics show that both JFET-LNPN and JFET-LVNPN can pass the 5.5-k V human body model(HBM)*** JFETs embedded with different NPNs have 3.75 times stronger in ESD robustness than the conventional *** failure analysis of the devices is performed with scanning electron microscopy,and the obtained delayer images illustrate that the JFETs embedded with NPN transistors have good voltage endurance ***,the internal physical mechanism of the JFETs embedded with different NPNs is investigated with emission microscopy and Sentaurus simulation,and the results confirm that the JFET-LVNPN has stronger ESD robustness than the JFET-LNPN,because the vertical NPN has a better electron collecting *** JFET-LVNPN is helpful in providing a strong ESD protection and functions for a power device.

关键词： junction field-effect transistors NPN electrostatic discharge(ESD)robustness ESD protection

human rights Protection and Defusing Public Disputes

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The Journal of human rights 2014年第5期13卷 19-23页

作者： CHANG JIAN the human rights research center at Nankai University the Zhou Enlai School of Government Management at Nankai University

The concept of human rights has already become the shared value of the majority of countries in the international community. However, realization of human rights is decided not only by lofty ideals but also pragmatic values. That is, can human rights be used for solving major issues of society？ With regard to the pragmatic value of human rights, the relationship between human rights and defusing public disputes is one of the questions debated by academic researchers and practitioners. Their focus is whether human rights protection helps in defusing public disputes.

关键词： human rights Protection and Defusing Public Disputes