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Identification of Proteins and Genes Associated with Hedgehog Signaling Pathway Involved in Neoplasm Formation Using Text-Mining Approach

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Big Data Mining and Analytics 2024年第1期7卷 107-130页

作者： Nadezhda Yu.Biziukova Sergey M.Ivanov Oga A.Tarasova Department of bioinformatics Institute of Biomedical ChemistryMoscow 119121Russia Department of bioinformatics Pirogov Russian National Research Medical UniversityMoscow 117997Russia

Analysis of molecular mechanisms that lead to the development of various types of tumors is essential for biology and medicine,because it may help to find new therapeutic opportunities for cancer treatment and cure including personalized treatment *** of the pathways known to be important for the development of neoplastic diseases and pathological processes is the Hedgehog signaling pathway that normally controls human embryonic *** accumulation of various types of biological data,including interactions between proteins,regulation of genes transcription,proteomics,and metabolomics experiments results,allows the application of computational analysis of these big data for identification of key molecular mechanisms of certain diseases and pathologies and promising therapeutic *** aim of this study is to develop a computational approach for revealing associations between human proteins and genes interacting with the Hedgehog pathway components,as well as for identifying their roles in the development of various types of *** automatically collect sets of abstract texts from the NCBI PubMed bibliographic *** recognition of the Hedgehog pathway proteins and genes and neoplastic diseases we use a dictionary-based named entity recognition approach,while for all other proteins and genes machine learning method is *** association extraction,we develop a set of semantic *** complete the results of the text analysis with the gene set enrichment *** identified key pathways that may influence the Hedgehog pathway and their roles in tumor development are then verified using the information in the literature.

关键词： text-mining data mining Hedgehog pathway neoplastic processes enrichment analysis pathology molecularmechanisms

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Nonlinear system dynamics of calcium and nitric oxide due to cell memory and superdiffusion in neurons

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Communications in Theoretical Physics 2024年第5期76卷 16-32页

作者： Anand Pawar Kamal Raj Pardasani Department of Mathematics Bioinformatics and Computer ApplicationsMaulana Azad National Institute of TechnologyBhopal-462003Madhya PradeshIndia

The integer-order interdependent calcium([Ca^(2+)])and nitric oxide(NO)systems are unable to shed light on the influences of the superdiffusion and memory in triggering Brownian motion(BM)in ***,a mathematical model is constructed for the fractional-order nonlinear spatiotemporal systems of[Ca^(2+)]and NO incorporating reaction-diffusion equations in *** two-way feedback process between[Ca^(2+)]and NO systems through calcium feedback on NO production and NO feedback on calcium through cyclic guanosine monophosphate(cGMP)with plasmalemmal[Ca^(2+)]-ATPase(PMCA)was incorporated in the *** Crank–Nicholson scheme(CNS)with Grunwald approximation along spatial derivatives and L1 scheme along temporal derivatives with Gauss–Seidel(GS)iterations were *** numerical outcomes were analyzed to get insights into superdiffusion,buffer,and memory exhibiting BM of[Ca^(2+)]and NO *** conditions,events and mechanisms leading to dysfunctions in calcium and NO systems and causing different diseases like Parkinson’s were explored in neurons.

关键词： [Ca^(2+)]and nitric oxide signaling reaction-diffusion equations fractional-order systems Grunwald approximation Gauss-Seidel iterations

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Deciphering gastric inflammation-induced tumorigenesis through multi-omics data and AI methods

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Cancer Biology & Medicine 2024年第4期21卷 312-330页

作者： Qian Zhang Mingran Yang Peng Zhang Bowen Wu Xiaosen Wei Shao Li Institute for TCM-X MOE Key Laboratory of BioinformaticsBioinformatics DivisionBNRISTDepartment of AutomationTsinghua UniversityBeijing 100084China

Gastric cancer(GC), the fifth most common cancer globally, remains the leading cause of cancer deaths worldwide. Inflammation-induced tumorigenesis is the predominant process in GC development;therefore, systematic research in this area should improve understanding of the biological mechanisms that initiate GC development and promote cancer hallmarks. Here, we summarize biological knowledge regarding gastric inflammation-induced tumorigenesis, and characterize the multi-omics data and systems biology methods for investigating GC development. Of note, we highlight pioneering studies in multi-omics data and state-of-the-art network-based algorithms used for dissecting the features of gastric inflammation-induced tumorigenesis, and we propose translational applications in early GC warning biomarkers and precise treatment strategies. This review offers integrative insights for GC research, with the goal of paving the way to novel paradigms for GC precision oncology and prevention.

关键词： Gastric cancer inflammation-induced tumorigenesis multi-omics artificial intelligence network-based methods

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Interplant communication:an emerging battlefield in plant-aphid-virus interactions

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Science China(Life Sciences) 2024年第5期67卷 1069-1071页

作者： Yunjing Wang Qian Gong Yule Liu MOE Key Laboratory of bioinformatics and center for Plant Biology School of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking center for Life Sciences Beijing 100084China

Plants constantly face threats from various organisms,including pathogens and *** the pathogens,plant viruses are obligate intracellular parasites that infect plants and cause serious crop yield losses.

关键词： plant Plants communication

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scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data

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Journal of Genetics and Genomics 2024年第4期51卷 462-465页

作者： Zijing Gao Xiaoyang Chen Zhen Li Xuejian Cui Qun Jiang Keyi Li Shengquan Chen Rui Jiang Ministry of Education Key Laboratory of bioinformatics Bioinformatics Division at the Beijing National Research Center for Information Science and TechnologyCenter for Synthetic and Systems BiologyDepartment of AutomationTsinghua UniversityBeijing 100084China School of Mathematical Sciences and LPMC Nankai UniversityTianjin 300071China

Recent advances in single-cell sequencing technologies provide significant implications for understanding cellular heterogeneity,developmental biology,and disease *** fully exploit the potential of these data,numerous tools have been proposed for upstream and downstream *** the the single-cell RNA sequencing(scRNA-seq)community,scRNA-tools(Zappia et al.,2018)was proposed to help researchers navigate the plethora of tools by *** its inception,scRNA-tools has been widely used and its updated version further reveals trends in the field with over 1000 collected tools(Zappia and Theis,2021),providing a valuable guidance in selecting tools for analyses.

关键词： analytic selecting Tools

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Development and validation of a novel non-invasive test for diagnosing nonalcoholic fatty liver disease in Chinese children

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World Journal of Pediatrics 2024年第4期20卷 413-421页

作者： Zhe-Wen Qin Qian-Nan Ren Hong-Xi Zhang Ya-Ru Liu Ke Huang Wei Wu Guan-Ping Dong Yan Ni Jun-Fen Fu Division of Endocrinology National Clinical Research Center for Child HealthNational Children’s Regional Medical CenterThe Children’s HospitalDepartment of EndocrinologyNational Clinical Research Center for Child HealthNational Children’s Regional Medical CenterThe Children’s HospitalZhejiang University School of MedicineHangzhou310052China

With the exploding prevalence of obesity,many children are at risk of developing nonalcoholic fatty liver *** anthropometric and laboratory parameters,our study aimed to develop a model to quantitatively evaluate liver fat content(LFC)in children with *** A well-characterized cohort of 181 children between 5 and 16 years of age were recruited to the study in the Endocrinology Department as the derivation *** external validation cohort comprised 77 *** assessment of liver fat content was performed using proton magnetic resonance *** and laboratory metrics were measured in all subjects.B-ultrasound examination was carried out in the external validation *** Kruskal-Wallis test,Spearman bivariate correlation analyses,univariable linear regressions and multivariable linear regression were used to build the optimal predictive *** The model was based on indicators including alanine aminotransferase,homeostasis model assessment of insulin resistance,triglycerides,waist circumference and Tanner *** adjusted R^(2)of the model was 0.589,which presented high sensitivity and specificity both in internal[sensitivity of 0.824,specificity of 0.900,area under curve(AUC)of 0.900 with a 95%confidence interval:0.783–1.000]and external validation(sensitivity of 0.918 and specificity of 0.821,AUC of 0.901 with a 95%confidence interval:0.818–0.984).Conclusions Our model based on five clinical indicators was simple,non-invasive,and inexpensive;it had high sensitivity and specificity in predicting LFC in ***,it may be useful for identifying children with obesity who are at risk for developing nonalcoholic fatty liver disease.

关键词： Biochemical markers Children Magnetic resonance spectroscopy Nonalcoholic fatty liver disease Pediatric obesity

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Ferromagnetism and insulating behavior with a logarithmic temperature dependence of resistivity in Pb_(10-x)Cux(PO_(4))_(6)O

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Science China(Physics,Mechanics & Astronomy) 2024年第1期67卷 106-111页

作者： Yuhang Zhang Cong Liu Xiyu Zhu Hai-Hu Wen center for Superconducting Physics and Materials National Laboratory of Solid State Microstructures and Department of PhysicsNational Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China

Recent claim of discovering above-room-temperature superconductivity(Tc≈400 K)at ambient pressure in copper doped apatite Pb10(PO_(4))_(6)O has stimulated world-wide enthusiasm and impulse of motion.A lot of follow-up works have been carried out with controversial *** check whether superconductivity is really present or absent in the material,we need samples which should have a rather pure phase of Pb_(10-x)Cux(PO_(4))_(6)*** we report the characterization results from the Pb_(10-x)Cux(PO_(4))_(6)O with a fraction of about 97 wt.%inferred from the fitting to the X-ray diffraction pattern,if assuming Cu2S as the only *** resistivity measurements show that it is a semiconductor characterized roughly by a ln(1/T)temperature dependence in wide temperature region without trace of *** measurements show that it has a general ferromagnetic signal with a weak superparamagnetic *** grains of the sample show clear interactions with a Nb Fe B *** detected Cu concentration is much lower than the expected nominal *** results show the absence of metallicity and superconductivity in Pb_(10-x)Cux(PO_(4))_(6)O at ambient pressure,and suggest the presence of strong correlation effect.

关键词： superconductivity Pb10(PO4)6O ferromagnetic correlation effect

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Incidence and Mortality of Cancers in Female Genital Organs—China,2022

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China CDC weekly 2024年第10期6卷 195-202,I0003,I0004页

作者： Kexin Sun Bingfeng Han Hongmei Zeng Shaoming Wang Li Li Ru Chen Rongshou Zheng Wenqiang Wei national Central Cancer Registry National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina

Introduction:This study presented the incidence and mortality rates of cancers affecting the female genital organs in China,along with their trends spanning from 2010 to ***:700 population-based cancer registries provided relevant cancer incidence and mortality data for the year *** these,106 registries had continuous monitoring data suitable for trend analysis from 2010 to *** focused specifically on cancers affecting female genital organs(ICD10=C51-C54,C56)and projected their incidences and mortalities in China for 2022 based on data from 2018 and the trends observed from 2010 to ***-standardized incidence rate(ASIR)and mortality rate(ASMR)were calculated using Segi’s world standard ***:In 2022,there were an estimated 296,300 new cases and 104,900 deaths from female cancers in *** for vulva(C51),vagina(C52),cervix uteri(C53),corpus uteri(C54),and ovary(C56)were 0.32,0.23,13.83,6.84,and 5.68 per 100,000 *** for corpus uteri and ovary cancers were higher in urban *** for vulva,vagina,cervix,corpus uteri,and ovary cancers were 0.14,0.08,4.54,1.05,and 2.64 per 100,000 population,*** for ovarian cancer was higher in urban *** and ASMRs for most female genital organ cancers increased from 2010 to 2018,although the rate of increase for vulvar and cervical cancers in rural areas has slowed ***:Tailored cancer prevention and control programs specific to each region are necessary to address the growing disease burden.

关键词： ICD10 mortality organs

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Review on Security Defense Technology Research in Edge Computing Environment

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Chinese Journal of Electronics 2024年第1期33卷 1-18页

作者： Ke SHANG Weizhen HE Shuai ZHANG national Digital Switching System Engineering and Technological R&D center

Edge computing, which achieves quick data processing by sinking data computing and storage to the network edge, has grown rapidly along with the Internet of things. The new network architecture of edge computing brings new security challenges. Based on this, this paper investigates the edge computing security literature published in recent years and summarizes and analyzes research work on edge computing security from different attack surfaces. We start with the definition and architecture of edge computing. From the attack surface between device and edge server, as well as on edge servers, the research describes the security threats and defense methods of edge computing. In addition, the cause of the attack and the pros and cons of defense methods is introduced. The challenges and future research directions of edge computing are given.

关键词： Cloud computing Systems architecture Computer architecture Network architecture Data processing Security Servers

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Recent progress in functional modification and crosslinking of bioprosthetic heart valves

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Regenerative Biomaterials 2024年第1期3卷 1-16页

作者： Cheng Zheng Li Yang Yunbing Wang national Engineering Research center for Biomaterials Sichuan UniversityChengdu 610064China

Valvular heart disease(VHD),clinically manifested as stenosis and regurgitation of native heart valve,is one of the most prevalent cardiovascular diseases with high *** valve replacement surgery has been recognized as golden standard for the treatment of *** to the clinical application of transcatheter heart valve replacement technic and the excellent hemodynamic performance of bioprosthetic heart valves(BHVs),implantation of BHVs has been increasing over recent years and gradually became the preferred choice for the treatment of ***,BHVs might fail within 10-15 years due to structural valvular degeneration(SVD),which was greatly associated with drawbacks of glutaraldehyde crosslinked BHVs,including cytotoxicity,calcification,component degradation,mechanical failure,thrombosis and immune *** prolong the service life of BHVs,much effort has been devoted to overcoming the drawbacks of BHVs and reducing the risk of *** this review,we summarized and analyzed the research and progress on:(i)modification strategies based on glutaraldehyde crosslinked BHVs and(ii)nonglutaraldehyde crosslinking strategies for BHVs.

关键词： bioprosthetic heart valves modification crosslinking anticalcification antithrombosis

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