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TSUNAMI:Translational Bioinformatics Tool Suite for Network Analysis and Mining

Genomics, Proteomics & Bioinformatics 2021年第6期19卷 1023-1031页

作者： Zhi Huang Zhi Han Tongxin Wang Wei Shao Shunian Xiang Paul Salama maher Rizkalla Kun Huang Jie Zhang School of Electrical and Computer Engineering Purdue UniversityWest LafayetteIN 47907USA Department of Electrical and Computer Engineering Indiana University-Purdue University IndianapolisIndianapolisIN 46202USA Department of Medicine Indiana University School of MedicineIndianapolisIN 46202USA Department of Computer Science Indiana UniversityBloomingtonIN 47405USA Department of Medical and Molecular Genetics Indiana University School of MedicineIndianapolisIN 46202USA Department of Biostatistics and Health Data Science Indiana University School of MedicineIndianapolisIN 46202USA

Gene co-expression network(GCN)mining identifies gene modules with highly correlated expression profiles across samples/*** enables researchers to discover latent gene/molecule interactions,identify novel gene functions,and extract molecular features from certain disease/condition groups,thus helping to identify disease ***,there lacks an easy-to-use tool package for users to mine GCN modules that are relatively small in size with tightly connected genes that can be convenient for downstream gene set enrichment analysis,as well as modules that may share common *** address this need,we developed an online GCN mining tool package:TSUNAMI(Tools SUite for Network Analysis and MIning).TSUNAMI incorporates our state-of-the-art lmQCM algorithm to mine GCN modules for both public and user-input data(microarray,RNA-seq,or any other numerical omics data),and then performs downstream gene set enrichment analysis for the identified *** has several features and advantages:1)a user-friendly interface and real-time co-expression network mining through a web server;2)direct access and search of NCBI Gene Expression Omnibus(GEO)and The Cancer Genome Atlas(TCGA)databases,as well as user-input gene ex-pression matrices for GCN module mining;3)multiple co-expression analysis tools to choose from,all of which are highly flexible in regards to parameter selection options;4)identified GCN modules are summarized to eigengenes,which are convenient for users to check their correlation with other clinical traits;5)integrated downstream Enrichr enrichment analysis and links to other gene set enrichment tools;and 6)visualization of gene loci by Circos plot in any step of the *** web service is freely accessible through URL:https://***/.Source code is available at https://***/huangzhii/TSUNAMI/.

关键词： Network mining Gene co-expression network Transcriptomic data analysis lmQCM Web server Survival analysis

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Induction of sub-G0 arrest and apoptosis by seed extract of Moringa peregrina（Forssk.） Fiori in cervical and prostate cancer cell lines

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Journal of Integrative Medicine 2019年第6期17卷 410-422页

作者： Maged Mohamed maher Abou-Hashem Dina Mohamed Abo-elmatty Noha Mostafa Mesbah Ahmed Mohamed Abd EL-Mawgoud Faculty of Pharmacy Pharmacognosy DepartmentZagazig UniversityZagazig 44511Egypt Faculty of Pharmacy Biochemistry DepartmentSuez Canal UniversityIsmailia 41522Egypt Egyptian International Pharmaceuticals Industries Company Tenth of Ramadan City 44629Egypt

Objective: This study investigated cytotoxicity and induction of apoptosis in human cervical cancer cells(HELA) and prostate cancer cells(PC-3) using the most active fraction of Moringa peregrina seed ***: Dried and powdered seeds were extracted using 95% ethanol. The total ethanolic extract was further dissolved in distilled water and separated into petroleum ether, chloroform, ethyl acetate and aqueous extracts. Based on the results of in vitro anticancer studies of all extracts, the most highly active extract was selected for evaluation of apoptosis induction and cell cycle analysis on HELA and PC-3 cells at its half maximal inhibitory concentration using flow cytometry;DNA fragmentation by agarose gel electrophoresis and the expression of protein were measured by Western ***: The chloroform fraction from the ethanolic extract of M. peregrina(CFEE) was the most active antitumor fraction. The selectivity index, determined using the normal Vero cell line, indicated that CFEE had a high degree of selectivity against HELA and PC-3 cells. CFEE induced apoptosis, confirmed by cell cycle arrest at sub-G0 phase and DNA fragmentation. CFEE induced an increase in mRNA expression of caspase-3, a decrease in Bcl-2 mRNA expression, and decreased ATP levels. CFEE increased protein expression of caspase-3 and decreased protein expression of poly-ADP-ribose polymerase-1(PARP-1).Flow cytometric analysis showed an appreciable increase in the number of cells in the early apoptotic stage in CFEE-treated HELA and PC-3 cells. CFEE treatment significantly increased lipid peroxidation(malondialdehyde level) in HELA and PC-3 ***: Seed extract of M. peregrina displayed a significant antitumor effect through apoptosis induction in HELA and PC-3 cells.

关键词： Moringa peregrina Fractionation Antiproliferation Apoptosis

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Traditional Chinese Medicine’s Challenge to Clinical Science and Health Policy

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Chinese Medicine and Culture 2018年第2期1卷 97-102页

作者： Justin Thomas maher Department of Foreign Languages International Education CollegeShanghai University of Traditional Chinese MedicineShanghaiChina

Traditional Chinese medicine(TCM)has been improving human health for *** for that,it has gradually gained the attention of the global scientific *** clinical research progresses,but slowly.I see it as being held back ... 详细信息

关键词： Clinical research policy principal-agent problem statistical significance traditional Chinese medicine

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Modeling and Numerical Simulation of Wings Effect on Turbulent Flow between two contra-rotating cylinders

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Journal of Modern Physics 2011年第5期2卷 392-397页

作者： maher Raddaoui 不详

Many industries in the world take part in the pollution of the environment. This pollution often comes from the reactions of combustion. To optimize these reactions and to minimize pollution, turbulence is a funda- mental tool. Several factors are at the origin of turbulence in the complex flows, among these factors, we can quote the effect of wings in the rotating flows. The interest of this work is to model and to simulate numeri- cally the effect of wings on the level of turbulence in the flow between two contra-rotating cylinders. We have fixed on these two cylinders eight wings uniformly distributed and we have varied the height of the wings to have six values from 2 mm to 20 mm by maintaining the same Reynolds number of rotation. The numerical tool is based on a statistical model in a point using the closing of the second order of the transport equations of the Reynolds stresses (Reynolds Stress Model: RSM). We have modelled wings effect on the flow by a source term added to the equation tangential speed. The results of the numerical simulation showed that all the average and fluctuating variables are affected the value of the kinetic energy of turbulence as those of Reynolds stresses increase with the height of the wings.

关键词： Pollution Turbulence Combustion Wing Modeling Numerical Simulation Contra-Rotating Cylinders Reynolds Stress Model Source Term

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Concentration–discharge patterns of weathering products from global rivers

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Acta Geochimica 2017年第3期36卷 405-409页

作者： Daniel E.Ibarra Seulgi Moon Jeremy K.Caves C.Page Chamberlain Kate maher Earth System Science Stanford University StanfordCA 94305-4216 USA Earth Planetary and Space Sciences University of California Los Angeles CA 90095-1567 USA Earth Science ETH Ziirich 8092 Zurich Switzerland Geological Sciences Stanford University StanfordCA 94305-2115 USA

Quantifying the functional relationships relating river discharge and weathering products places key constraints on the negative feedback between the silicate weathering and climate. In this study we analyze the concentration–discharge relationships of weathering products from global rivers using previously compiled time-series datasets for concentrations and discharge from global rivers. To analyze the nature of the covariation between specific discharge and concentrations, we use both a power law equation and a recently developed solute production equation. The solute production equation allows us to quantify weathering efficiency, or the resistance to dilution at high runoff, via the Damkohler coefficient. These results are also compared to those derived using average concentration–discharge *** the power law exponent and the Damkohler coefficient increase and asymptote as catchments exhibit increasingly chemostatic behavior, resulting in an inverse relationship between the two parameters. We also show that using thedistribution of average concentration–discharge pairs from global rivers, rather than fitting concentration–discharge relationships for each individual river, underestimates global median weathering efficiency by up to a factor of ～10. This study demonstrates the utility of long time-series sampling of global rivers to elucidate controlling processes needed to quantify patterns in global silicate weathering rates.

关键词： Concentration–discharge Rivers Silicate weathering Solutes

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In-situ measurement on air-water flux of CH_(4),CO_(2) and their carbon stable isotope in lakes of northeast Tibetan Plateau

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Advances in Climate Change Research 2022年第2期13卷 279-289页

作者： Lei WANG Cun-De XIAO Zhi-Heng DU Damien T.maher Jing-Feng LIU Zhi-Qiang WEI State Key Laboratory of Earth Surface Processes and Resource Ecology Beijing Normal UniversityBeijing 100875China State Key Laboratory of Cryospheric Science Northwest Institute of Eco-Environment and ResourcesChinese Academy of SciencesLanzhou 730000China Southern Cross Geoscience Southern Cross UniversityLismoreNSW 2480Australia College of Geography and Environmental Science Northwest Normal UniversityLanzhou 730070China Zhuhai Branch of State Key Laboratory of Earth Surface Process and Resource Ecology Beijing Normal UniversityZhuhai 519087China

Inland waters are important sources of greenhouse gases(GHGs)to the atmosphere that may partially offset the terrestrial carbon ***,GHG emissions from high altitude saline lakes on the Tibetan Plateau are currently poorly *** this study,we measured methane(CH_(4))and carbon dioxide(CO_(2))concentrations and their carbon stable isotope(δ13C),and calculated diffusive water-to-air fluxes from two saline high-altitude lakes,Qinghai Lake and Hala Lake,located in northeast Tibetan Plateau in October *** two lakes were mostly supersaturated in CH_(4)(89.8%-4623.9%sat)and acted as sources of CH_(4) to the ***,more than 96%investigated area of Qinghai Lake and all investigated area of Hala Lake was a sink of CO_(2).The average diffusive fluxes of CH_(4) and CO_(2) in the surface waters of Qinghai Lake were 34.51μmol m−2 d−1 and−1.29 mmol m−2 d−1,while diffusive fluxes of CH_(4) and CO_(2) in Hala Lake averaged 5.48μmol m−2 d−1 and−5.24 mmol m−2 d−1,***(Sal),fluorescent dissolved organic matter(fDOM),temperature(Temp)and dissolved oxygen(DO)are key factors for diffusive CH_(4) and CO_(2) flux in Qinghai Lake and Hala ***_(4) diffusive fluxes across water-air interface from Qinghai Lake and Hala Lake were found to be significantly lower than other freshwater lakes,likely due to their saline nature.A simple isotope mixing model(Miller-Tans plots)revealed a distinctly different isotopic source values of CO_(2) and CH_(4) in Qinghai Lake and Hala *** CH_(4) production pathway of Qinghai Lake was mainly by the acetate fermentation,while that of Hala Lake was mainly by the CO_(2) *** results show that the continuous measurement can help capture the spatial variability of GHGs fluxes in saline lakes.

关键词： Greenhouse gas Air-water flux Carbon stable isotope Tibetan Plateau Saline lakes

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SOX9 in biliary atresia: New insight for fibrosis progression

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Hepatobiliary & Pancreatic Diseases International 2021年第2期20卷 154-162页

作者： Hanaa Ahmed El-Araby Magdy Anwar Saber Noha Mohamed Radwan Doha maher Taie Nermin Mohamed Adawy Ahmad Mohamed Sira Department of Pediatric Hepatology Gastroenterologyand NutritionNational Liver InstituteMenoufia University32511 Shebin El-koomMenoufiaEgypt Department of Pathology National Liver InstituteMenoufia University32511 Shebin El-koomMenoufiaEgypt

Background:Liver fibrosis is a hallmark determinant of morbidity in biliary atresia(BA)even in successfully operated *** factors for this rapid progression of fibrosis are not completely *** expression of the transcription factor SOX9 and hepatic progenitor cells(HPCs)proliferation have roles in fibrogenesis in cholestatic ***,they were not investigated sufficiently in *** aimed to delineate the relation of SOX9 and HPCs to fibrosis and its progression in ***:Forty-eight patients with BA who underwent an initial diagnostic liver biopsy(LB)and consequent intraoperative LB were recruited and compared to 28 cases with non-BA cholestasis that had an LB in their diagnostic *** fibrosis,tissue SOX9 and HPC expressions were studied in both BA and non-BA-cholestasis *** fibrosis,SOX9,and HPCs’dynamic changes in BA cases were *** of fibrosis and its progression to SOX9 and HPCs in BA was ***:SOX9 and HPCs in ductular reaction(DR)form were expressed in 100%of BA and their grades increased significantly in the second *** rapidly progressive fibrosis in BA,represented by fibrosis grade of the intraoperative LB,correlated significantly to SOX9-DR and HPC-DR at the diagnostic(r=0.420,P=0.003 and r=0.405,P=0.004,respectively)and the intraoperative(r=0.460,P=0.001 and r=0.467,P=0.001,respectively)*** the other hand,fibrosis,SOX9-DR,and HPC-DR were significantly lower in non-BA cases at a comparable age(P<0.001,P=0.006,and P=0.014,respectively).Conclusions:Fibrosis in BA is rapidly progressive within a short time and is significantly correlated to SOX9 and *** of targeting SOX9 and HPCs on fibrosis progression is warranted.

关键词： Biliary atresia Fibrosis Hepatic progenitor cells Immunohistochemistry Neonatal cholestasis SOX9

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Students’Mathematical Reasoning,Communication,and Language Representations:A Video-Narrative Analysis

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ECNU Review of Education 2018年第3期1卷 1-22页

作者： Louise C.Wilkinson Alison L.Bailey Carolyn A.maher Psychology and Communication Sciences at Syracuse University University of California-Los Angeles Rutgers the State University of New Jersey

Purpose-Learning mathematics is a complex process,requiring many conceptual lenses and rich data sources to document and understand students’construction of *** purpose of this article is both to introduce a unique database on students’mathematical learning and to describe analytical techniques used to study students’growth of the knowledge of mathematics and ***/Approach/Methods-Our approach includes the following aspects:First,we describe a unique collection of video-taped recordings of longitudinal and cross-sectional studies of diverse,***,learning mathematics(Video Mosaic Collaborative,VMC).Second,we introduce our analytical methods,which utilize the database for collaborative study of students’*** methods include video-narrative analyses that display fine-grained examinations of interactions among students who are solving engaging problems that require them to reason mathematically and to represent their understandings with language and non-language *** analyses,referenced as VMCAnalytics,demonstrate the accessibility and flexibility of the database to study relationships among students’mathematics and language ***-The findings generated are illustrated by two examples demonstrating the accessibility and flexibility of the database to study relationships between mathematics and language learning(mathematics register).Originality/Value-The contribution of our work is illustrated by describing the rich database;employing a collaborative research approach;and signifying our understanding of relationships among students’mathematical and language learning.

关键词： Mathematics register communication mathematical understanding video-narratives academic language

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基于区块链的双重可验证云存储方案

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通信学报 2021年第12期42卷 192-201页

作者：冯涛孔繁琪柳春岩马蓉 maher Albettar 兰州理工大学计算机与通信学院甘肃兰州730050 兰州理工大学经济与管理学院甘肃兰州730050 康考迪亚大学康考迪亚信息系统工程研究所蒙特利尔H3G 1M8

针对工业物联网(IIoT)中,工业设备将数据存储到云端,导致数据易被篡改且无法追踪恶意用户,引起恶性循环的问题,借助区块链的可溯源性和不可篡改性等特点,提出了一种基于区块链的双重可验证云存储方案。首先,使用同态加密技术加密数据并... 详细信息

针对工业物联网(IIoT)中,工业设备将数据存储到云端,导致数据易被篡改且无法追踪恶意用户,引起恶性循环的问题,借助区块链的可溯源性和不可篡改性等特点,提出了一种基于区块链的双重可验证云存储方案。首先,使用同态加密技术加密数据并上传至云端,确保传输安全性,实现数据的隐私保护;其次,将聚合密文和上传者信息存储在区块链上,有效避免数据被非法用户篡改的风险,并能对恶意用户进行追溯,实现对云端数据完整性的双重验证;最后,进行安全性分析,证明所提方案比同类方案更加安全可靠。

关键词：区块链可验证计算隐私保护云存储

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Non-integer Order Control Scheme for Pressurized Water Reactor Core Power

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Computers, Materials & Continua 2022年第7期72卷 651-662页

作者： Ibrahim M.Mehedi maher H.AL-Sereihy Asmaa Ubaid Al-Saggaf Ubaid M.Al-Saggaf Department of Electrical and Computer Engineering(ECE) King Abdulaziz UniversityJeddah21589Saudi Arabia Center of Excellence in Intelligent Engineering Systems(CEIES) King Abdulaziz UniversityJeddah21589Saudi Arabia

Tracking load changes in a pressurized water reactor(PWR)with the help of an efficient core power control scheme in a nuclear power station is very *** reason is that it is challenging to maintain a stable core power according to the reference value within an acceptable tolerance for the safety of *** overcome the uncertainties,a non-integer-based fractional order control method is demonstrated to control the core power of *** available dynamic model of the reactor core is used in this *** power is controlled using a modified state feedback approach with a non-integer integral scheme through two different approximations,CRONE(Commande Robuste d’Ordre Non Entier,meaning Non-integer orderRobust Control)and FOMCON(non-integer order modeling and control).Simulation results are produced using MATLAB■*** non-integer results are compared with an integer order PI(Proportional Integral)algorithm to justify the effectiveness of the proposed ***-spacemodel Core power control Non-integer control Pressurized water reactor PI controller CRONE FOMCON.

关键词： Sate-space model core power control non-integer control pressurized water reactor PI controller CRONE FOMCON

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