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Computational Methods for Single-cell DNA Methylome Analysis

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 48-66页

作者： waleed Iqbal Wanding Zhou Center for Computational and Genomic Medicine Children’s Hospital of PhiladelphiaPhiladelphiaPA 19104USA Department of Pathology and Laboratory Medicine University of PennsylvaniaPhiladelphiaPA 19104USA

Dissecting intercellular epigenetic differences is key to understanding tissue *** advances in single-cell DNA methylome profiling have presented opportunities to resolve this heterogeneity at the maximum *** these advances enable us to explore frontiers of chromatin biology and better understand cell lineage relationships,they pose new challenges in data processing and *** review surveys the current state of computational tools developed for single-cell DNA methylome data *** discuss critical components of single-cell DNA methylome data analysis,including data preprocessing,quality control,imputation,dimensionality reduction,cell clustering,supervised cell annotation,cell lineage reconstruction,gene activity scoring,and integration with transcriptome *** also highlight unique aspects of single-cell DNA methylome data analysis and discuss how techniques common to other single-cell omics data analyses can be adapted to analyze DNA ***,we discuss existing challenges and opportunities for future development.

关键词： Single-cell genomics Bioinformatics DNA methylation Computational tool Epigenetics

Global research trends in the microbiome related to irritable bowel syndrome: A bibliometric and visualized study

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World Journal of Gastroenterology 2021年第13期27卷 1341-1353页

作者： Sa'ed H Zyoud Simon Smale W Stephen Waring waleed Sweileh Samah W al-Jabi Poison Control and Drug Information Center(PCDIC) College of Medicine and Health SciencesAn-Najah National UniversityNablus 44839West BankPalestine Department of Clinical and Community Pharmacy College of Medicine and Health SciencesAn-Najah National UniversityNablus 44839West BankPalestine Department of Clinical Research Centre An-Najah National University HospitalNablus 44839West BankPalestine Department of Gastroenterology York HospitalYork Teaching Hospital NHS Foundation TrustYork YO318HEUnited Kingdom Acute Medical Unit York Teaching Hospitals NHS Foundation TrustYork YO318HEUnited Kingdom Department of Pharmacology and Toxicology College of Medicine and Health SciencesAn-Najah National UniversityNablus 44839West BankPalestine

BACKGROUND Irritable bowel syndrome(IBS) is a common functional gastrointestinal disorder. Dysregulation of the gut–brain axis plays a central role in the pathophysiology of IBS. It is increasingly clear that the microbiome plays a key role in the development and normal functioning of the gut–brain *** To facilitate the identification of specific areas of focus that may be of relevance to future research. This study represents a bibliometric analysis of the literature pertaining to the microbiome in IBS to understand the development of this *** The data used in our bibliometric analysis were retrieved from the Scopus database. The terms related to IBS and microbiome were searched in titles or abstracts within the period of 2000–2019. VOSviewer software was used for data *** A total of 13055 documents related to IBS were retrieved at the global level. There were 1872 scientific publications focused on the microbiome in IBS. There was a strong positive correlation between publication productivity related to IBS in all fields and productivity related to the microbiome in IBS(r = 0.951, P aly(n = 151, 8.1%). The h-index for all retrieved publications related to the microbiome in IBS was 138. The hot topics were stratified into four clusters:(1) The gut–brain axis related to IBS;(2) Clinical trials related to IBS and the microbiome;(3) Drugmediated manipulation of the gut microbiome;and(4) The role of the altered composition of intestinal microbiota in IBS *** This is the first study to evaluate and quantify global research productivity pertaining to the microbiome in IBS. The number of publications regarding the gut microbiota in IBS has continuously grown since 2013. This finding suggests that the future outlook for interventions targeting the gut microbiota in

关键词： Irritable bowel syndrome Bibliometric Microbiota Microbiome Scopus Brain gut axis

Laboratory study on efficiency of three calcium carbonate scale inhibitors in the presence of EOR chemicals

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Petroleum 2018年第4期4卷 375-384页

作者： Qiwei Wang Feng Liang waleed al-Nasser Faez al-Dawood Tawfiq al-Shafai Hameed al-Badairy Shouwen Shen Hassan al-Ajwad Saudi Aramco Research&Development CenterP.O.Box 62Dhahran 31311Saudi Arabia Aramco Services Company Aramco Research Center e Houston16300 Park RowHoustonTX 77084USA

Chemical flooding has been widely used in the oil industry since the 1980s for enhanced oil recovery(EOR)*** studies have shown that the effectiveness of calcium carbonate scale inhibitors is affected by many factors,such as water composition,system pressure,temperature,production rates,pH *** breakthrough of the EOR chemicals in the production well could also affect scale formation process and interfere with the scale treatment program as ***,the studies on the impacts of injected EOR chemicals to scale inhibitor performances are very *** paper presents the comprehensive laboratory study on the impacts of the EOR chemicals on CaCO3 scale formation and prevention using static bottle and dynamic tube blocking *** EOR chemicals used in this study are a combination of surfactants and *** different types of inhibitors were evaluated:triphosphonate,penta-phosphonate,and polyacrylate based ***(%)from the bottle test and minimum effective dose(MED)based on the tube blocking method were determined for each inhibitor at 160*** precipitates from the bottle tests were also characterized for morphology and polymorphs using environmental scanning electron(ESEM)and X-ray diffraction(XRD)*** suggest that the performance of scale inhibitors could be substantially affected by the EOR *** dynamic tube blocking tests,the MED values of inhibitors were increased roughly 10 times with the EOR *** static bottle tests showed considerable changes under the test *** impact of EOR chemicals were also demonstrated by the remarkable ranges of crystal morphologies,changing from simple aragonite columns to nanorod,distorted spheroid,and flower-like superstructure in the presence of EOR chemicals and inhibitors.

关键词： Calcium carbonate Scaling Inhibitor Chemical flooding Enhanced oil recovery

Fabrication of stable organometallic halide perovskite NWs based optoelectronic devices

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Science Bulletin 2017年第9期62卷 645-647页

作者： Aashir waleed Zhiyong Fan Department of Electronic and Computer Engineering The Hong Kong University of Science and Technology Hong Kong China

Organometallic halide perovskite materials have triggered global attention in recent years due to their exciting and optimistic high performance energy conversion properties(high luminescence efficiency and tremendous optical absorption ability[1,2]).These interesting photovoltaic properties together make them a promising candidate for high performance optoelectronic

关键词： Fabrication of stable organometallic halide perovskite NWs based optoelectronic devices NH Pb

Daftardar-Jafari Method for Fractional Heat-Like and Wave-Like Equations with Variable Coefficients

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Applied Mathematics 2017年第2期8卷 215-228页

作者： waleed al-Hayani Department of Mathematics College of Computer Science and Mathematics University of Mosul Iraq

In this paper, Daftardar-Gejji and Jafari method is applied to solve fractional heat-like and wave-like models with variable coefficients. The method is proved for a variety of problems in one, two and three dimensional spaces where analytical approximate solutions are obtained. The examples are presented to show the efficiency and simplicity of this method.

关键词： Daftardar-Jafari Method Heat-Like Equations Wave-Like Equations Fractional Calculus

Adomian Decomposition Method with Green’s Function for Solving Tenth-Order Boundary Value Problems

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Applied Mathematics 2014年第10期5卷 1437-1447页

作者： waleed al-Hayani Department of Mathematics College of Computer Science and Mathematics University of Mosul Mosul Iraq

In this paper, the Adomian decomposition method with Green’s function (Standard Adomian and Modified Technique) is applied to solve linear and nonlinear tenth-order boundary value problems with boundary conditions defined at any order derivatives. The numerical results obtained with a small amount of computation are compared with the exact solutions to show the efficiency of the method. The results show that the decomposition method is of high accuracy, more convenient and efficient for solving high-order boundary value problems.

关键词： Adomian Decomposition Method Adomian’s Polynomials Tenth-Order Boundary Value Problems Green’s Function

Visual rehabilitation in low-moderate keratoconus:intracorneal ring segment implantation followed by same-day topography-guided photorefractive keratectomy and collagen cross linking

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International Journal of Ophthalmology(English edition) 2014年第5期7卷 800-806页

作者： Ferial M.Zeraid Asma A Jawkhab waleed S al-Tuwairqi Uchechukwu L.Osuagwu Department of Optometry&Vision Sciences College of Applied Medical SciencesKing Saud University Senior Ophthalmology Consultant Elite Medical&Surgical CenterUlaya School of Optometry&Vision Science and Institute of Health&Biomedical Innovation Chronic Disease and Aging DomainQueensland University of Technology

AIMTo present the results of same-day topography-guided photorefractive keratectomy (TG-PRK) and corneal collagen crosslinking (CXL) after previous intrastromal corneal ring segment (ISCR) implantation for keratoconus.

关键词： keratoconus astigmatism photorefractive keratectomy corneal collagen crosslinking intrastromal corneal rings

Can we suppress excessive post-surgical scar formation:A case report

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World Journal of Orthopedics 2023年第3期14卷 166-170页

作者： Mir Sadat-ali Sulaiman A al-Mousa Khalid waleed al-Tabash Mohamed M Abotaleb Fawaz M al-Anii Department of Orthopaedic Surgery Imam Abdulrahman Bin Faisal UniversityDammam 31142Saudi Arabia

BACKGROUND Hypertrophic scars(HSs)formation is a complication that occurs after wounds heal with secondary intention and sometimes after clean surgical *** treatments are in vogue now with varying *** the mechanism or mechanisms that cause a HS to form are not clearly understood,one thing that is clear is that once scar tissue matures,any intervention will not be *** this paper,we report on a case where a patient who was known to develop HS was treated with a new combination of ingredients(Phyto-chemicals+Silicone JUMI)to suppress HS *** SUMMARY A 68-year-old female of African descent presented a severe HS post total knee replacement(TKR),which the patient describes as itchy and *** to complications caused by the scar,she was apprehensive about undergoing TKR on her other ***,after the TKR of the contralateral side post-removal of skin clips,JUMI anti-scar cream(JASC)was used to suppress excessive scar *** JASC appears potent and efficacious at suppressing excessive scar *** believe that this warrants further studies on larger patient groups and on different surgical sites.

Global output of research on epidermal parasitic skin diseases from 1967 to 2017

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Infectious Diseases of Poverty 2018年第1期7卷 730-739页

作者： waleed M.Sweileh Department of Physiology Pharmacology/ToxicologyDivision of Biomedical SciencesCollege of Medicine and Health SciencesAn-Najah National UniversityNablusPalestine

Background:Epidermal parasitic skin diseases(EPSD)occur in most countries and cause a considerable health and economic burden,particularly in the tropics and *** aim of this study was to assess and analyse peerreviewed literature on EPSD in *** results of this study serve as an indicator of the extent the scientific community,health authorities,and international health agencies interact with EPSD as a health problem that is commonly associated with poverty and poor ***:A bibliometric analysis methodology was *** Scopus database was used to retrieve documents about EPSD for the study period(1967-2017).The study focused on scabies,tungiasis,pediculosis,hookwormrelated cutaneous larva migrans(HrCLM),myiasis,and cutaneous *** that specifically and explicitly discuss EPSD in animals,aquatic organisms,and birds were ***:In total,4186 documents were retrieved.A fluctuated growth of publications on EPSD in the past five decades was *** retrieved documents received 43301 citations,an average of 10.3 citations per article and an h-index of *** keywords“scabies”and was the most commonly encountered keyword followed by the keywords“head lice”and“pediculosis”.The most active journal involved in publishing articles on EPSD was the International Journal of Dermatology(164;3.9%).Researchers from 93 different countries published the retrieved *** USA led with 735(17.6%)documents,followed by the UK(274;6.5%),and Germany(259;6.2%).In terms of institutions,the Charite-Universitätsmedizin Berlin in Germany was the most active in this field with 78(1.9%)publications,followed by the Universidade Federal do Cearáin Brazil with 52(1.2%)***:Research on scabies and pediculosis dominated the field of EPSD research to the expense of tungiasis,HrCLM,myiasis,and cutaneous *** was an underrepresentation of literature from the tropics and subtropics despite EPSD being com

关键词： Epidermal parasitic skin diseases Bibliometric analysis Keyword mapping Scopus