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乳腺癌相关新关键基因和生物学通路的生物信息学识别

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乳腺癌相关新关键基因和生物学通路的生物信息学识别

作者： md.shahin alam 苏州大学

学位级别：硕士

癌症对世界各地的人类健康有多种影响,它是仅次于心血管疾病的全球第二大死亡原因。全世界范围内不同地区的癌症发病率和死亡率不同,尤其是在不同国家之间,因为人口、生态、文化、环境和遗传变量等因素的差异会导致癌症发病率的异质性... 详细信息

癌症对世界各地的人类健康有多种影响,它是仅次于心血管疾病的全球第二大死亡原因。全世界范围内不同地区的癌症发病率和死亡率不同,尤其是在不同国家之间,因为人口、生态、文化、环境和遗传变量等因素的差异会导致癌症发病率的异质性。根据最新的全球癌症数据,2018年癌症新增1810万例新病例,960万例死亡病例。其中前列腺癌、胃癌和肝癌在男性中最为常见,而乳腺癌、宫颈癌和甲状腺癌在女性中最为常见,肺癌和结直肠癌在两者中都具有较高的患病率。癌症的发病率最高的前三位是肺癌、乳腺癌和结直肠癌,它们的死亡率排名分别为第一、第五和第二。全球乳腺癌发病率自20世纪70年代末一直呈上升趋势,是全世界女性癌症死亡的第二大主要原因,99%发生在女性,男性仅占1%,约占女性所有癌症的26%。早期乳腺癌往往不具备典型的症状和体征,不易引起重视,常通过体检或乳腺癌筛查发现。与乳腺癌相关的危险因素有肥胖、酗酒、更年期激素替代疗法、电离辐射、月经初潮、晚育或不生育、年龄大、患乳腺癌的既往史、家庭乳腺癌史、缺乏体育锻炼等。乳腺癌是一种恶性肿瘤,是由某种基因突变导致的异常细胞的无节制增殖所致,这种基因异常通常发生在乳腺导管（连接乳腺与乳头的导管）或乳腺小叶（分泌乳汁的部分）中。随着科技时代日新月异的发展以及人们对乳腺癌认识的不断深入,乳腺癌的治疗进入了综合治疗时代,形成了局部治疗与全身治疗并重的治疗模式。医生会根据肿瘤的分期和患者的身体状况,酌情采用手术、放疗、化疗、生物靶向治疗等多种手段。外科手术在乳腺癌治疗中发挥着重要作用。但较其缺点来说——把病人体内肿瘤切除,并不能直接“消灭”肿瘤,也不是战胜癌症的良方。控癌是场持久战,不能单独地“一刀切”来解决问题。放疗是利用放射线破坏癌细胞的生长、繁殖,达到控制和消灭癌细胞的作用,但放射性在破坏和杀死肿瘤细胞的同时,对周围正常组织细胞也有破坏作用。手术、放疗均属于局部治疗。化学治疗是一种应用抗癌药物抑制癌细胞分裂,破坏癌细胞的治疗方法,简称化疗。化疗也可能会导致患者出现消化道反应,引起恶心、呕吐、头晕以及食欲不振等。分子靶向治疗是近年来最为活跃的研究领域之一,与化疗药物相比,是具有多环节作用机制的新型抗肿瘤治疗药。因此,更好地应用已发布的生物标志物、发现新的生物标志物以及潜在的治疗靶标对改善乳腺癌的预后和治疗至关重要。人表皮生长因子受体2（HER2）和雌激素受体α（ERα）常常被用于预后和激素治疗反应预测中,是目前最有效的乳腺癌生物标志物。但是,由于某些乳腺癌亚型并不表达ER α或HER2,因此需要应用其他生物标志物。然而,目前并没有发现其他生物标志物与靶向治疗的之间是否存在精准的关联。因此,迫切需要评估潜在的新生物标志物,以用于乳腺癌的诊断和治疗改善。癌症的发生率随着年龄的增长而增加,因此癌症的预防和治疗以及慢性病的管理已成为影响社会经济发展的关键因素。生物医学和信息技术的快速发展,以及主动健康、精准医疗和大数据范式的出现,为癌症的预防和治疗带来了新的机遇。本课题的研究方向包括癌症的异质性和外部综合征、癌症深度表型的挖掘、用于癌症治疗的联合用药算法、癌症的预防和治疗信息模型和慢性病的管理以及系统和平台构建。基于此,本研究的目的是通过生物信息学的方法来评估潜在的新基因作为乳腺癌诊断的生物标志物和药物靶标,并了解其分子机制,改进乳腺癌的治疗策略。首先,通过比较8个乳腺癌组织和相应对照组织的基因表达谱,我们检测到236个具有统计学意义的差异表达基因（包括167个上调基因和69个下调基因）。以***＜0.01和logFC＞1作为上调基因的阈值,***＜0.01和logFC＜-1作为下调基因的阈值,绘制火山图。根据| logFC |的值绘制热图。前20个上调的差异表达基因包括C2、IFITM1、AKR1C1、PCDH7、TIMP3、TDO2、AKR1C1、PMEPA1、IRF9、AQPI、KNDC1、OAS3、DDX60、FAM105A、DDX60、AQP3、IFI27、IFI44L和FN1;下调的差异表达基因包括EVL、CLDN1、CREB5、FBX015、CASP4、NOC2L、ATF6B、RELB、CCDC74B、MATN3、POLR3E、OSR2、CITED4、CASP4、LINC01016、C14orf37、TCTN1、CDADC1、CFAP206 和 C5orf45。为了了解筛选出的差异表达基因的生物学功能和意义,本研究使用了可用于注释、可视化和集成发现的DAVID数据库。使用在线工具“DAVID”对候选差异表达基因进行GO功能富集分析（基因本体论（Gene Ontology,GO）是一种广泛用于整合生物学的方法,它为大规模的基因注释编写结构化、定义化和规范化的词汇）和KEGG途径分析（京都基因与基

关键词：生物信息学微阵列乳腺癌差异表达基因新关键基因

The link between intracellular calcium signaling and exosomal PD-L1 in cancer progression and immunotherapy

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Genes & Diseases 2024年第1期11卷 321-334页

作者： md Rakibul alam md Mizanur Rahman Zhiguo Li Department of Toxicology and Cancer Biology College of MedicineUniversity of KentuckyLexingtonKY 40506USA Department of Medicine(Nephrology) Faculty of Medicine and DentistryUniversity of AlbertaEdmontonAlberta T6E2H7Canada

Exosomes are small membrane vesicles containing microRNA,RNA,DNA fragments,and proteins that are transferred from donor cells to recipient *** cells release exo-somes to reprogram the factors associated with the tumor microenvironment(TME)causing tu-mor metastasis and immune *** evidence revealed that cancer cell-derived exosomes carry immune inhibitory molecule program death ligand 1(PD-L1)that binds with re-ceptor program death protein 1(PD-1)and promote tumor progression by escaping immune ***,some FDA-approved monoclonal antibodies are clinicallyused for cancer treatment by blocking PD-1/PD-L1 *** notable treatment outcomes,some pa-tients show poor drug *** PD-L1 plays a vital role in lowering the treatment response,showing resistance to PD-1/PD-L1 blockage therapy through recapitulating the ef-fect of cell surface *** enhance therapeutic response,inhibition of exosomal PD-L1 is *** signaling is the central regulator of tumorigenesis and can regulate exosome biogenesis and secretion by modulating Rab GTPase family and membrane fusion ***-mune checkpoints are also connected with calcium signaling and calcium channel blockers like amlodipine,nifedipine,lercanidipine,diltiazem,and verapamil were also reported to suppress cellular PD-L1 ***,to enhance the PD-1/PD-L1 blockage therapy response,the reduction of exosomal PD-L1 secretion from cancer cells is in our therapeutic *** this review,we proposed a therapeutic strategy by targeting calcium signaling to inhibit the expression of PD-L1-containing exosome levels that could reduce the anti-PD-1/PD-L1 therapy resistance and increase the patient's drug response rate.

关键词： Calcium signaling CD8^(+)T cells Exosomal PD-L1 Exosomes biogenesis Immunosuppression Immunotherapy

The Influence of Rice Husk Ash on Mechanical Properties of the Mortar and Concrete: A Critical Review

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Open Journal of Civil Engineering 2024年第1期14卷 65-81页

作者： md Jahangir alam Mithun Biswas Mohammad Biplab Mia shahin alam md Mosabber Hossain College of Civil and Transportation Engineering Hohai University Nanjing China School of Civil Engineering Chang’an University Xi’an China

Increasing the population and infrastructure in both emerging and developed countries requires a considerable amount of cement, which significantly affects the environment. The primary materials of concrete (‘cement’) production emit a large quantity of CO2 into the environment. Also, the cost of conventional building materials like cement gives motivation to find geopolymer waste materials for concrete. To reduce harmful effects on the environment and cost of traditional concrete substance, alternative waste materials like rice husk ash (RHA), ground granulated blast-furnace (GGBS), fly ash (FA), and metakaolin (MK) can be used due to their pozzolanic behavior. RHA waste material with a high silica concentration obtained from burning rice husks can possibly be used as a supplementary cementitious material (SCM) in the manufacturing of concrete, and its strong pozzolanic properties can contribute to the strength and impermeability of concrete. This review paper highlights a summary of the positive effect of using RHA as a partial substitute for cement in building construction, as well as its optimal inclusion of enhanced mechanical properties like compressive strength, flexural strength, and split tensile strength of mortar and concrete.

关键词： Cement Rice Husk Ash RHA Properties Mechanical Properties Carbon Di-oxide Emission and Greenhouse Gas

Turning Trash into Treasure: Developing an Intelligent Bin for Plastic Bottle Recycling

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Journal of Social Computing 2024年第1期5卷 1-14页

作者： Sirajam Munira Niloy Paul md Ashraful alam md.Mahmudur Rahman M.Shamim Kaiser Institute of Information Technology Jahangirnagar UniversityDhaka 1342Bangladesh

Plastic pollution has emerged as a major global concern due to its enduring nature and limited recycling *** response to this critical challenge,this paper presents a novel approach utilizing a Detection-Based Reward System(DBRS)alongside an innovative business model to promote effective plastic waste management,reduce plastic waste accumulation in the nature,and uphold environmental *** the YOLOv5 algorithm for its exceptional accuracy,speed,and open-source availability,plastic bottle detection becomes a pivotal aspect of this *** seamlessly enroll in the system,triggering an automated detection process that computes reward points corresponding to their deposited plastic *** reward points are meticulously stored within a centralized *** its operational facets,this comprehensive system encompasses a robust business model,strategically poised to capture widespread engagement with waste disposal practices,thereby contributing to the realization of Sustainable Development Goals(SDGs)geared towards fostering a healthier ***,the DBRS attains cutting-edge performance in plastic bottle detection,boasting an impressive mean Average Precision(mAP)of 0.973,underscoring its efficacy in tackling plastic pollution.

关键词： smart environment reward system YOLOv5 deep learning business model

Energy Harvesting in the Wake of An Inverted C-Shaped Bluff Body

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China Ocean Engineering 2024年第1期38卷 68-80页

作者： WANG Jun-lei LI Shen-fang md.Mahbub alam ZHU Hong-jun HU Guo-biao School of Mechanical and Power Engineering Zhengzhou UniversityZhengzhou 450000China Center for Turbulence Control Harbin Institute of Technology(Shenzhen)Shenzhen 518055China State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation Southwest Petroleum UniversityChengdu 610500China Internet of Things Thrust The Hong Kong University of Science and Technology(Guangzhou)Guangzhou 511400China

This paper proposes a novel wake-induced vibration(WIV)-based energy harvesting system consisting of two bluff *** inverted C-shaped bluff body is stationary installed at the upstream position to generate an interference wake street,and a cylinder bluff body equipped with a transducer is elastically suspended at the downstream position to harness WIV *** hydrodynamics and energy harvesting(EH)performance of the proposed system are investigated via experimental *** reduced velocity(U*)ranging from 2 to 14(the corresponding Reynolds number ranging from 15100 to 106200)is considered in the present *** is found that the wake generated by the inverted C-shaped bluff body significantly affects the EH *** the opening angle(α)of the C-shaped bluff body increases the vibration amplitude of the downstream cylinder,thereby increasing the harvested *** the spacing(L)between two bluff bodies is two times the cylinder diameter(D),the wake-induced vibration(WIV)mode is observed,while the combined WIV and wake galloping(WG)mode occurs whenαis 150°,and L equals 3D or *** average drag coefficient becomes negative when L is 2D,3D,or *** carefully configuring a C-shaped bluff body,the wake generated by it can bring an augmenting effect on the vibration of the downstream EH *** example,the RMS power output of the proposed EH system reaches a maximum of 0.31 W at U*=8 and L=4D,which is 300%greater than that of its traditional ***,after a number of case stud-ies,it is identified that the proposed EH system can achieve the best performance whenαis 150°and L=2D.

关键词： wake-induced vibration vortex-induced vibration galloping energy harvesting bluff body

Repercussion of salinity on hematological parameters and tissue morphology of gill and kidney at early life of tilapia

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Aquaculture and Fisheries 2024年第2期9卷 256-264页

作者： Azhar Ali md Golam Azom Bhakta Supratim Sarker Hasu Rani md Samsul alam m.sadiqul islam*department of fisheries biology and genetics bangladesh agricultural universitymymensingh2202bangladesh

This study was attempted to reveal the changes in three hematological parameters such as blood hemoglobin,number of white blood cells(WBCs)and number of red blood cells(RBCs)and one biochemical(e.g.,glucose)parameter along with the changes in histomorphological structures of gills and kidney of Nile tilapia fry reared in saline *** experimental set up were used for two different age groups-5 days-after-hatch(5DAH)and 15 days-after-hatch(15DAH)-to test a novel hypothesis:if a little difference in the age during the first exposure to saline water could produce any variation in the *** were placed into 6 plastic drums having six different salinity levels:0,5,10,15,20 and *** 60 days,at least 5 individuals were taken out from each drum to observe the above-hematological and histomorphological parameters.A two-way-ANOVA revealed that,except for hemoglobin,all the observed parameters have been affected the effect of age×salinity interaction(P<0.05).Between the two age groups,only the overall average glucose value and RBC count were significantly *** various salinity levels,only RBC and WBC counts differed ***,the mean glucose value,RBC counts and WBC count at different salinities differed significantly from the base mean value of each *** regard to the histomorphological structure of the gills and kidney,various malformations were *** hypertrophy,epithelial uplifting and epithelial necrosis were present as gill degenerations,hyperplasia was prevalent across almost all salinity *** the other hand,glomerular necrosis,pyknotic nucleus,hyaline droplets degeneration,shrinking of the glomeruli,*** observed in kidney *** assisting to understand the effects of salinity stress,all these data on tilapia fry will help to determine the prospects and scope of culturing the species in high-salinity water.

关键词： Nile tilapia Salinity Blood parameters Histomorphology Age groups

Assessing the pomfret stock for setting catch limits in the northern Bay of Bengal,Bangladesh

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Aquaculture and Fisheries 2024年第2期9卷 324-335页

作者： Mohammed Shahidul alam Qun Liu md Mostafa Monwar md Enamul Hoque Suman Barua md Leion Hassan Abdullah Munzer College of Fisheries Ocean University of ChinaQingdao266003China Department of Fisheries University of ChittagongChattogram4331Bangladesh Institute of Marine Sciences University of ChittagongChattogram4331Bangladesh Department of Oceanography University of ChittagongChattogram4331Bangladesh Department of Fisheries Ministry of Fisheries and LivestockDhaka1215Bangladesh

Pampus argenteus and Pampus chinensis form the high-value demersal Pomfret fishery of ***,due to a monotonic decline in catches over the last five years,it is essential to explore the current stock status concerning the removal rate to ensure the sustainability of this ***,given the reliability and minimal data requirements,this study employed an extended Bayesian State-Space Surplus Production Model,JABBA(Just Another Bayesian Biomass Assessment),to assess the stock *** results revealed that the stock biomass of the Pomfret fishery in the final year of the time series is significantly lower than BMSY,the biomass required to produce ***,this study recommends a yearly catch limit(TAC)of 10,000 metric tons to prevent further depletion of the stock ***,to avoid growth overfishing by allowing all immature fishes to reproduce at least once before being caught,this study also calculated the optimum length(Lopt)for catch for both species at which biologically maximum yield and revenue can be *** estimated Lopt is 25 cm for *** and 30 cm for ***,and not to capture fishes with lengths lower than these limits,this study further calculated the minimum mesh size limits for gill and set bag nets is 7.5 *** the mesh size regulation was estimated using length-based reference points derived from an empirical equation,this regulation can be used as an associate reference point when TAC is applied to assure the sustainability of this fishery.

关键词： Pomfret fishery Stock assessment JABBA TAC Lower length limits for catches Mesh size regulation

Coleus forskohlii shows anti-psoriatic activity in imiquimod-induced psoriasis rats

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Asian Pacific Journal of Tropical Biomedicine 2024年第9期14卷 382-390,I0002-I0007页

作者： Sagarika Majhi Iti Chauhan Deepak Kumar md.Niyaz alam md.Sarfaraj Hussain Muzaffar Iqbal Faculty of Pharmacy I.T.S College of PharmacyMuradnagarGhaziabadU.P.India Lord Buddha Koshi Pharmacy College of Pharmacy BaijanathpurNH 107Saharsa(Bihar)852201India Department of Pharmaceutical Chemistry College of PharmacyKing Saud UniversityP.O.Box 2457Riyadh 11451Saudi Arabia

Objective:To evaluate anti-psoriatic activity of Coleus forskohlii in rats with imiquimod-induced ***:Imiquimod was used to induce psoriasis in *** weight,skin thickness,erythema,scaling,spleen weight,and histological alternations were measured to assess the effect of Coleus ***,an emulgel formulation containing Coleus forskohlii 10%was prepared and characterized along with its ex vivo permeation ***:The emulgel formulation containing Coleus forskohlii 10%had a pH of 5.40±0.36,with optimum spreadability of(31.67±2.08)g/(cm·s)and viscosity of(15966.67±1274.10)cps,and enhanced both the rate and the extent of drug permeation through psoriatic *** an ex vivo study,the quantity of drug permeated(19.18%),deposited(52.38%),and drug remaining in the donor compartments(28.31%)was *** forskohlii significantly alleviated imiquimod-induced psoriasis by increasing glutathione and superoxide dismutase activity,decreasing malondialdehyde and nitric oxide levels,and alleviating histological alternations in rat ***:Coleus forskohlii can alleviate imiquimod-induced psoriasis,which may be used as a therapeutic candidate for the treatment of psoriasis.

关键词： Psoriasis Coleus forskohlii Emulgel Ex vivo Imiquimod Carbopol

An Enhanced Hybrid Model Based on CNN and BiLSTM for Identifying Individuals via Handwriting Analysis

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Computer Modeling in Engineering & Sciences 2024年第8期140卷 1689-1710页

作者： md.Abdur Rahim Fahmid Al Farid Abu Saleh Musa Miah Arpa Kar Puza md.Nur alam md.Najmul Hossain Sarina Mansor Hezerul Abdul Karim Department of Computer Science and Engineering Pabna University of Science and TechnologyPabna6600Bangladesh Faculty of Engineering Multimedia UniversityCyberjaya63100Malaysia Department of Computer Science and Engineering Bangladesh Army University of Science and TechnologySaidpur5311Bangladesh Department of Mathematics Pabna University of Science and TechnologyPabna6600Bangladesh Department of Electrical Electronic and Communication EngineeringPabnaUniversity of Science and TechnologyPabna6600Bangladesh Department of Electrical and Communication Engineering Pabna University of Science and TechnologyPabna6600Bangladesh

Handwriting is a unique and significant human feature that distinguishes them from one *** are many researchers have endeavored to develop writing recognition systems utilizing specific signatures or symbols for person identification through ***,such systems are susceptible to forgery,posing security *** response to these challenges,we propose an innovative hybrid technique for individual identification based on independent handwriting,eliminating the reliance on specific signatures or *** response to these challenges,we propose an innovative hybrid technique for individual identification based on independent handwriting,eliminating the reliance on specific signatures or *** innovative method is intricately designed,encompassing five distinct phases:data collection,preprocessing,feature extraction,significant feature selection,and *** key advancement lies in the creation of a novel dataset specifically tailored for Bengali handwriting(BHW),setting the foundation for our comprehensive ***-preprocessing,we embarked on an exhaustive feature extraction process,encompassing integration with kinematic,statistical,spatial,and composite *** meticulous amalgamation resulted in a robust set of 91 *** enhance the efficiency of our system,we employed an analysis of variance(ANOVA)F test and mutual information scores approach,meticulously selecting the most pertinent *** the identification phase,we harnessed the power of cutting-edge deep learning models,notably the Convolutional Neural Network(CNN)and Bidirectional Long Short-Term Memory(BiLSTM).These models underwent rigorous training and testing to accurately discern individuals based on their handwriting ***,our methodology introduces a groundbreaking hybrid model that synergizes CNN and BiLSTM,capitalizing on fine motor features for enhanced individual ***,our experimental results unde

关键词： Bengali handwriting(BHW) person identification convolutional neural network(CNN) BiLSTM