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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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An enhanced method for predicting and analysing forest fires using an attention-based CNN model

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Journal of Forestry Research 2024年第4期35卷 115-127页

作者： Shaifali Bhatt Usha Chouhan department of Mathematics Bioinformatics and Computer ApplicationsMANIT BhopalBhopalIndia

Prediction,prevention,and control of forest fires are crucial on at all *** effective fire detection systems can aid in their *** study proposes a novel CNN(convolutional neural network)using an attention blocks module which combines an attention module with numerous input layers to enhance the performance of neural *** suggested model focuses on predicting the damage affected/burned areas due to possible wildfires and evaluating the multilateral interactions between the pertinent *** results show the impacts of CNN using attention blocks for feature extraction and to better understand how ecosystems are affected by meteorological *** selected meteorological data,RMSE 12.08 and MAE 7.45 values provide higher predictive power for selecting relevant and necessary features to provide optimal performance with less operational and computational *** findings show that the suggested strategy is reliable and effective for planning and managing fire-prone regions as well as for predicting forest fire damage.

关键词： CNN Attention module Fire prediction Ecosystem Damage prediction

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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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Optimality of Group Testing with Differential Misclassification

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应用概率统计 2024年第4期40卷 644-662页

作者： LI Yiming ZHANG Hong LIU Aiyi department of Statistics and Finance School of ManagementUniversity of Science and Technology of ChinaHefei230026China biostatistics and bioinformatics Branch National Institute of Child Health and Human DevelopmentUSA

Group testing is a method that can be used to estimate the prevalence of rare infectious diseases,which can effectively save time and reduce costs compared to the method of random ***,previous literature only demonstrated the optimality of group testing strategy while estimating prevalence under some strong *** article weakens the assumption of misclassification rate in the previous literature,considers the misclassification rate of the infected samples as a differentiable function of the pool size,and explores some optimal properties of group testing for estimating prevalence in the presence of differential misclassification conforming to this *** article theoretically demonstrates that the group testing strategy performs better than the sample by sample procedure in estimating disease prevalence when the total number of sample pools is given or the size of the test population is *** simulation experiments were conducted to evaluate the performance of group tests in estimating prevalence in the presence of dilution effect.

关键词： group testing sensitivity specificity dilution effect differential misclassification prevalence

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Multi-omics analysis of adamantinomatous craniopharyngiomas reveals distinct molecular subgroups with prognostic and treatment response significance

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Chinese Medical Journal 2024年第7期137卷 859-870页

作者： Xianlong Wang Chuan Zhao Jincheng Lin Hongxing Liu Qiuhong Zeng Huadong Chen Ye Wang Dapeng Xu Wen Chen Moping Xu En Zhang Da Lin Zhixiong Lin department of bioinformatics School of Medical Technology and EngineeringKey Laboratory of Medical BioinformaticsKey Laboratory of Ministry of Education for Gastrointestinal CancerFujian Medical UniversityFuzhouFujian 350122China department of Neurosurgery Sanbo Brain HospitalCapital Medical UniversityBeijing 100093China

Background:Adamantinomatous craniopharyngioma(ACP)is the commonest pediatric sellar *** effective drug is available and interpatient heterogeneity is *** study aimed to identify distinct molecular subgroups of ACP based on the multi-omics profiles,imaging findings,and histological features,in order to predict the response to anti-inflammatory treatment and ***:Totally 142 Chinese cases diagnosed with craniopharyngiomas were profiled,including 119 ACPs and 23 papillary ***-exome sequencing(151 tumors,including recurrent ones),RNA sequencing(84 tumors),and DNA methylome profiling(95 tumors)were *** clustering and non-negative matrix factorization were used for subgrouping,and Cox regression were utilized for prognostic evaluation,***:Three distinct molecular subgroups were identified:WNT,ImA,and *** WNT subgroup showed higher Wnt/β-catenin pathway activity,with a greater number of epithelial cells and more predominantly solid *** ImA and ImB subgroups had activated inflammatory and interferon response pathways,with enhanced immune cell infiltration and more predominantly cystic ***-activated protein kinases(MEK/MAPK)signaling was activated only in ImA samples,while IL-6 and epithelial-mesenchymal transition biomarkers were highly expressed in the ImB group,mostly consisting of *** degree of astrogliosis was significantly elevated in the ImA group,with severe finger-like protrusions at the invasive front of the *** molecular subgrouping was an independent prognostic factor,with the WNT group having longer event-free survival than ImB(Cox,P=0.04).ImA/ImB cases were more likely to respond to immune checkpoint blockade(ICB)therapy than the WNT group(P<0.01).In the preliminary screening of subtyping markers,CD38 was significantly downregulated in WNT compared with ImA and ImB(P=0.01).Conclusions:ACP comprises three molecular subtypes with distinct

关键词： Craniopharyngioma Central nervous system tumor Precision medicine beta Catenin Proto-Oncogene Proteins B-raf

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Teneligliptin:A potential therapeutic approach for diabetic cardiomyopathy

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World Journal of Diabetes 2024年第8期15卷 1654-1658页

作者： Ashraf Al Madhoun department of Genetics and bioinformatics Dasman Diabetes InstituteDasman 15400Kuwait

In this editorial,we comment on the article by Zhang et *** mellitus is a chronic disorder associated with several complications like cardiomyopathy,neuropathy,and *** prevalence is increasing *** diabetes medications are prescribed based on individual patients’***,the exact mechanisms by which many of these drugs exert their protective effects remain *** et al elucidates molecular mechanisms undelaying cardioprotective effect of the dipeptidyl peptidase-IV inhibitor,***,teneligliptin alleviates the activation of NOD-like receptor protein 3 inflammasome,a multiprotein complex that plays a pivotal role in regulating the innate immune system and inflammatory *** of NOD-like receptor protein 3 inflammasome activity reduces the expression of cytokines,oxygen radicals and *** findings highlight teneligliptin as an anti-diabetic cardioprotective reagent.

关键词： Teneligliptin Diabetes mellitus NOD-like receptor protein 3 inflammasome Inflammation Cardiomyopathy

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Glucokinase regulatory protein rs780094 polymorphism is associated with type 2 diabetes mellitus, dyslipidemia, non-alcoholic fatty liver disease, and nephropathy

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World Journal of Diabetes 2024年第5期15卷 814-817页

作者： Ashraf Al Madhoun department of Genetics and bioinformatics Dasman Diabetes InstituteDasman 15400Kuwait

In this editorial,we comment on the article by Liu et al published in the recent issue of the World Journal of Diabetes(Relationship between GCKR gene rs780094 polymorphism and type 2 diabetes with albuminuria).Type 2 diabetes mellitus(T2DM)is a chronic disorder characterized by dysregulated glucose *** persistent elevated blood glucose level in T2DM significantly increases the risk of developing severe complications,including cardiovascular disease,re-tinopathy,neuropathy,and nephropathy.T2DM arises from a complex interplay between genetic,epigenetic,and environmental *** genomic studies have identified numerous genetic variations associated with an increased risk of ***,variations within the glucokinase regulatory protein(GCKR)gene have been linked to heightened susceptibility to T2DM and its associated *** clinical trial by Liu et al further elucidates the role of the GCKR rs780094 polymorphism in T2DM and nephropathy *** findings demonstrate that individuals carrying the CT or TT genotype at the GCKR rs780094 locus are at a higher risk of developing T2DM with albuminuria compared to those with the CC *** findings highlight the importance of genetic testing and risk assessment in T2DM to develop effective preventive strategies and personalized treatment plans.

关键词： Glucokinase regulatory protein rs780094 Type 2 diabetes mellitus Dyslipidemia Non-alcoholic fatty liver disease Nephropathy

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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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MicroRNA-630:A potential guardian against inflammation in diabetic kidney disease

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World Journal of Diabetes 2024年第9期15卷 1837-1841页

作者： Ashraf Al Madhoun department of Genetics and bioinformatics Dasman Diabetes InstituteDasman 15400Kuwait

In this editorial,we comment on the article by Wu et al published“MicroRNA-630 alleviates inflammatory reactions in rats with diabetic kidney disease by targeting toll-like receptor 4”.Diabetic kidney disease(DKD)stands as a significant complication occurring from diabetes mellitus,which contributes substantially to the morbidity and mortality rates *** tubular epithelial cell damage,often accompanied by inflammatory responses and mesenchymal transdifferentiation,plays a pivotal role in the progression of *** extensive research,the intricate molecular mechanisms underlying these processes remain to be *** et al remarkable work identifies microRNA-630(miR-630)as an emerging potential regulator of cell migration,apoptosis,and autophagy,prompting investigation into its association with DKD *** study endeavors to elucidate the impact of miR-630 on TEC injury and the inflammatory response in DKD *** role of miR-630 in human DKD will be of interest for future studies.

关键词： Diabetic kidney disease MicroRNA MicroRNA-630 Toll-like receptor 4 Inflammation

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Age-specific heterogeneity of genetic susceptibility to cardiovascular disease might have opposite outcomes depending on the presence of prediabetes

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World Journal of Diabetes 2024年第6期15卷 1381-1383页

作者： Chaeyoung Lee department of bioinformatics and Life Science Soongsil UniversitySeoul 06978South Korea

Examining age-specific heterogeneity of susceptibility to cardiovascular disease is also essential in individuals without prediabetes to determine its relative size and direction compared to those with *** particular interest,age-specific heterogeneity in genetic susceptibility may exhibit opposite directions depending on the presence or absence of prediabetes.

关键词： Age-specific difference Cardiovascular disease Genetic heterogeneity by age Genetic susceptibility Prediabetes

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