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From Molecular Pathology of COVID-19 to Nigella Sativum as a Treatment Option:Scientific Based Evidence of Its Myth or Reality

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Chinese Journal of Integrative Medicine 2022年第1期28卷 88-95页

作者： Muhammad Atif Farrah Naz Junaid Akhtar Muhammad Imran Sidrah Saleem Javed Akram Muhammad Imran Muhammad ikram ullah Department of Clinical Laboratory Sciences College of Applied Medical SciencesJouf UniversitySakaka(75471)Saudi Arabia Department of Microbiology Government College UniversityFaisalabad(38000)Pakistan Department of Microbiology University of Health SciencesLahore(54600)Pakistan Department of Allied Health Sciences Sargodha Medical CollegeUniversity of SargodhaSargodha(40100)Pakistan University of Health Sciences Lahore(54600)Pakistan University Institute of Diet and Nutritional Sciences Faculty of Allied Health SciencesThe University of LahoreLahore(54590)Pakistan

COVID-19 virus is a causative agent of viral pandemic in human beings which specifically targets respiratory system of humans and causes viral *** unusual viral pneumonia is rapidly spreading to all parts of the world,currently affecting about 105 million people with 2.3 million *** review described history,genomic characteristics,replication,and pathogenesis of COVID-19 with special emphasis on Nigella sativum(***)as a treatment *** seeds are historically and religiously used over the centuries,both for prevention and treatment of different *** review summarizes the potential role of *** seeds against COVID-19 infection at levels of in silico,cell lines and animal models.

关键词： coronavirus nCoV-19 COVID-19 Nigella sativum review

A novel variant of GALC in a familial case of Krabbe disease:Insights from structural bioinformatics and molecular dynamics simulation

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Genes & Diseases 2023年第6期10卷 2263-2266页

作者： ikram ullah Muhammad Waqas Muhammad Ilyas Sobia Ahsan Halim Akmal Ahmad Natalia Dominik Wahid ullah Muhammad Abbas Muhammad Aamir Henry Houlden Stephanie Efthymiou Ajmal Khan Ahmed Al-Harrasi Centre for Omic Sciences Islamia College University PeshawarPeshawarKhyber Pakhtunkhwa 25120Pakistan Department of Biotechnology and Genetic Engineering Hazara UniversityMansehraDhodial 21120Pakistan Natural and Medical Sciences Research Center University of NizwaNizwa 616Sultanate of Oman Department of Bioengineering University of Engineering and Applied SciencesSwatKhyber Pakhtunkhwa 19060Pakistan Department of Neuromuscular Disorders UCL Queen Square Institute of NeurologyLondon WC1N 3BGUnited Kingdom

Krabbe disease or globoid cell leukodystrophy(GLD;MIM#245200)is a rare and fatal lysosomal storage disease with an autosomal recessive mode of inheritance that results from the deficiency of galactocerebrosidase(GALC;E.C.3.***.1.46),a lysosomal enzyme encoded by the GALC gene.1 GALC breaks down galactosylceramide,a cerebroside located mainly in the myelin *** in GALC cause the accumulation of a cytotoxic metabolite,galactosylsphingosine or psychosine,which can be toxic to oligodendrocytes and Schwann cells.2 The failure to digest galactosylceramide triggers the formation of multi-nucleated globoid cells,causing severe demyelination,axonopathy,and neuronal death.3 The reported frequency of Krabbe disease is 1 in 100,000 live births with symptoms including irritability,loss of motor ability,spasticity,ataxia,visual dysfunction,seizures,andcognitive impairment.

关键词： dynamics birth GAL

Efficient construction of a substitution box based on a Mordell elliptic curve over a finite field

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Frontiers of Information Technology & Electronic Engineering 2019年第10期20卷 1378-1389页

作者： Naveed Ahmed AZAM Umar HAYAT ikram ullah Department of Applied Mathematics and Physics Graduate School of InformaticsKyoto UniversityKyoto 606-8501Japan Department of Mathematics Quaid-i-Azam UniversityIslamabad 44000Pakistan

Elliptic curve cryptography has been used in many security systems due to its small key size and high security compared with other cryptosystems. In many well-known security systems, a substitution box (S-box) is the only non-linear component. Recently, it has been shown that the security of a cryptosystem can be improved using dynamic S-boxes instead of a static S-box. This necessitates the construction of new secure S-boxes. We propose an efficient method to generate S-boxes that are based on a class of Mordell elliptic curves over prime fields and achieved by defining different total orders. The proposed scheme is devel-oped in such a way that for each input it outputs an S-box in linear time and constant space. Due to this property, our method takes less time and space than the existing S-box construction methods over elliptic curves. Computational results show that the pro-posed method is capable of generating cryptographically strong S-boxes with security comparable to some of the existing S-boxes constructed via different mathematical structures.

关键词： Substitution box Finite field Mordell elliptic curve Total order Computational complexity

月季bHLH基因家族的全基因组鉴定及其对灰霉菌（Botrytis cinerea）的响应

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月季bHLH基因家族的全基因组鉴定及其对灰霉菌（Botrytis cinerea...

作者： ikram ullah（韩杰）云南农业大学

学位级别：硕士

月季(Rosa spp.),属蔷薇科薔薇属植物,为世界四大切花之一,在全球占有举足轻重的地位。由于月季种植业的快速和集约化发展,月季病害日益严重,尤其是由灰霉菌(Botrytis cinerea)引起的灰霉病害,造成月季严重的采前和采后损失,尤其时采后... 详细信息

月季(Rosa spp.),属蔷薇科薔薇属植物,为世界四大切花之一,在全球占有举足轻重的地位。由于月季种植业的快速和集约化发展,月季病害日益严重,尤其是由灰霉菌(Botrytis cinerea)引起的灰霉病害,造成月季严重的采前和采后损失,尤其时采后损失,使月季生产遭受严重破坏。bHLH是植物中一个大型转录因子家族,参与许多重要的生理过程,包括参与植物的生长、发育和病菌侵染防御反应等。bHLH基因家族的基序存在于所有真核生物中,但它们与单一蛋白质的关联是植物独有的。bHLH基因是一个包含60个氨基酸的DNA结合域,分别具有两个不同的功能域:第一个为N-末端的10-17个氨基酸结合位点,第二个为C-末端的具有40个氨基酸的HLH区域。基于它们的结构、序列保守性、功能特征和与DNA结合的能力,bHLH分为6个主要类型(从A到F)。本研究从月季(Rosa chinensis)基因组数据库中鉴定了100个bHLH(RcbHLH)基因,并进行了系统发育分析、保守基序分析、染色体作图、GO富集和转录组学分析。此外,根据课题组前期完成的两个抗/感月季品种(A29和XS)灰霉菌侵染前后的转录组数据,筛选出95个RcbHLH基因,并从中筛选获得14个胁迫前后显著差异表达的基因进行实时荧光定量(q RT-PCR)表达谱分析。利用***孢子液接种,检测14个基因分别在两个抗/感月季品种中的表达情况,结果显示14个bHLH家族基因在抗性月季品种和感病月季品种中的表达不同。RcbHLH基因表达分析为月季防控基因功能研究提供了新的认识。研究取得的主要结果如下:1.从月季基因组数据库中鉴定获得100个编码bHLH蛋白的bHLH基因,命名为RcbHLH1-RcbHLH100,这些基因在染色体上分布不均,7号染色体分布最多共20个,3号染色体分布最少共7个。大多数RcbHLHs基因定位于细胞核中,但RcbHLH82和RcbHLH83定位于质膜中。2.利用氨基酸序列基因构建了最大似然系统发育树,深入了解月季和拟南芥bHLH蛋白的进化关系。此外,根据已建立的bHLH分类及其来自拟南芥的同源序列,bHLH蛋白序列家族被分为21个亚家族,并测量了每个亚家族中月季bHLH蛋白的数量。在RcbHLH中,XII亚家族的RcbHLH数量最多(13个基因),而II、IV(d)、VIII(b)和XIV亚家族的数量最少,分别各有1个基因。此外,RcbHLH的个体数量在每个亚家族中都有所不同。3.对月季和拟南芥比较共线性分析的结果表明,月季的RcbHLH与拟南芥的AtbHLH表现出共线性,说明植物的bHLH基因可能是从共同的祖先进化来的。但月季的5号、6号、7号染色体与拟南芥没有任何相同的碱基。4.在RcbHLHs基因的进化中,鉴定到43对串联和片段重复(综合分析)。其中5号染色体上的RcbHLH55和RcbHLH53、1号染色体上的RcbHLH8和RcbHLH12、4号染色体上的T RcbHLH33 on chromosome 3和RcbHLH37显示出自我复制。5.对顺式调节元件进行了评估,发现了生长、激素和应激相关元件。6.对接种灰霉菌后的月季抗性品种(A29)和感病品种(XS)的差异表达基因(DEG)进行了GO和KEGG富集分析。GO富集结果表明,RcbHLH在信号转导、细胞和生长相关的生物过程以及催化和酶活性、DNA结合、膜腔、细胞连接和不同细胞器中发挥作用。鉴定了环境胁迫、植物病原相互作用、激素信号传导和其他与KEGG途径相关的转录因子。***-silico蛋白相互作用结果显示,82个蛋白之间存在互作,而其余18个蛋白没有与任何bHLH蛋白互作。***蛋白的三维(3D)结构预测分析显示,RcbHLH蛋白90-96%的区域显示出高度适合的区域,表明预测的蛋白结构具有较好的稳定性和质量。9.为了分析RcbHLH基因在***胁迫期间的表达,利用FPKM(每百万映射读取的每千碱基转录本片段数)数据生成和绘制RcbHLH成员在成熟阶段表达水平的热图。分别对***胁迫下前后转录组测序分析筛选获得的14个显著差异表达的RcbHLH基因在耐受(A29)和敏感(XS)的两个月季品种中进行了q RT-PCR表达分析与验证。两个品种中,RcbHLH基因在灰霉菌侵染前没有显著的差异,但在***处理12h时,感病品种XS的RcbHLH43、RcbHLH63显示上调,而RcbHLH22、RcbHLH35、RcbHLH41、RcbHLH49和RcbHLH94显示下调;***处理48小时,与抗病品种A29相比,RcbHLHI3、RcbHLH35、RcbHLH41、RcbHLH44和RcbHLH-49基因在感病品种XS中上调,并显著高表

关键词：月季生物胁迫灰霉菌碱性螺旋-环-螺旋(bHLH) 表达

Review of applying X-ray computed tomography for imaging soil-root physical and biological processes

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International Journal of Agricultural and Biological Engineering 2015年第5期8卷 1-14页

作者： Francis Kumi Mao Hanping Hu Jianping ikram ullah Key Laboratory of Modern Agricultural Equipment and Technology Ministry of Education and Jiangsu ProvinceJiangsu UniversityZhenjiang 212013China Department of Agricultural Engineering University of Cape CoastCape CoastGhana

Root growth process in soils has long been a matter of interest to soil and plant *** the opaque nature of the soil has been a barrier to most research attempts aimed at unraveling the full root-soil *** traditional method of separating the roots from the growth media which is common practice tends to be destructive and defeats the purpose of such *** is ineffective in monitoring the interactions within the soil medium and as a result,a fast non-destructive technique is ***,with computing and technological advancements,X-ray computed tomography(CT)has been found to be capable of meeting this need by imaging the processes which are of interest to *** the past three-four decades,the applications of the technology for imaging soil-root studies have attracted the researchers’widespread interests and the future looks more *** purpose of this review is to present an overview of CT applications in imaging root-soil *** main focus is on the use of soil-root interface researches and the way forward for such non-destructive analyses.

关键词： computed tomography soil root imaging non-destructive interactions

Three-dimensional flow of Powell–Eyring nanofluid with heat and mass flux boundary conditions

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Chinese Physics B 2016年第7期25卷 261-268页

作者： Tasawar Hayat ikram ullah Taseer Muhammad Ahmed Alsaedi Sabir Ali Shehzad Department of Mathematics Quaid-I-Azam University Nonlinear Analysis and Applied Mathematics (NAAM) Research Group Department of Mathematics Faculty of ScienceKing Abdulaziz University Department of Mathematics Comsats Institute of Information Technology

This article investigates the three-dimensional flow of Powell–Eyring nanofluid with thermophoresis and Brownian motion effects. The energy equation is considered in the presence of thermal radiation. The heat and mass flux conditions are taken into account. Mathematical formulation is carried out through the boundary layer approach. The governing partial differential equations are transformed into the nonlinear ordinary differential equations through suitable variables. The resulting nonlinear ordinary differential equations have been solved for the series solutions. Effects of emerging physical parameters on the temperature and nanoparticles concentration are plotted and discussed. Numerical values of local Nusselt and Sherwood numbers are computed and examined.

关键词： three-dimensional flow Powell–Eyring fluid nanoparticles thermal radiation

生物入侵过程中的植物-土壤反馈:一种入侵植物的凋落物分解对其本地近缘植物的影响

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Journal of Plant Ecology 2022年第3期15卷 610-624页

作者： Jianfan Sun Susan Rutherford Muhammad Saif ullah ikram ullah Qaiser Javed Ghulam Rasool Muhammad Ajmal Ahmad Azeem Muhammad Junaid Nazir Daolin Du School of Environment and Safety Engineering Institute of Environment and EcologyJiangsuUniversityZhenjiang 212013China School of Agricultural Equipment Engineering Jiangsu UniversityZhenjiang 212013China College of Agricultural Engineering Hohai UniversityNanjing 210024China

植物入侵可通过正或负的植物-土壤反馈效应改变土壤的生物和非生物性质,从而影响入侵栖息地的土壤理化性质。许多入侵物种的凋落物分解可增加土壤养分,降低本地植物多样性,并导致进一步的植物入侵。关于入侵植物凋落物在不同土壤类型及... 详细信息

植物入侵可通过正或负的植物-土壤反馈效应改变土壤的生物和非生物性质,从而影响入侵栖息地的土壤理化性质。许多入侵物种的凋落物分解可增加土壤养分,降低本地植物多样性,并导致进一步的植物入侵。关于入侵植物凋落物在不同土壤类型及深度分解及反馈效应的研究依然很少。本研究旨在明确入侵植物南美蟛蜞菊(Sphagneticola trilobata)凋落物在不同土壤类型和不同土壤深度条件下的分解情况及其对本地近缘植物蟛蜞菊(***)生理生长的影响。将装有南美蟛蜞菊凋落物的尼龙袋加入到不同深度(即0、2、4和6 cm)的砂土、营养土和粘土中,经6个月的分解后,回收凋落物袋并计算分解速率,随后在凋落物分解处理后的土壤中种植本地蟛蜞菊,并在生长期结束时测量其生理生态指标。研究结果表明,所有处理土壤类型中,凋落物在土壤深度为2和4 cm处分解后显著增加了土壤养分,而对本地蟛蜞菊的叶片叶绿素、叶氮含量等生长指标表现为负效应。因此,入侵植物南美蟛蜞菊凋落物分解对土壤养分表现为正的反馈效应,而对本地植物蟛蜞菊的生长表现为负效应。我们的研究结果还表明,入侵植物的凋落物分解对土壤和本地物种的影响还因凋落物分解所在的土壤深度而显著不同。未来的研究应侧重于入侵栖息地中更多本地和入侵物种的植物-土壤反馈效应,以及更多土壤类型和土壤深度的入侵植物凋落物效应。

关键词：植物入侵植物形态学植物生理学土壤深度土壤矿物质

A Novel Framework for Multi-Classification of Guava Disease

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Computers, Materials & Continua 2021年第11期69卷 1915-1926页

作者： Omar Almutiry Muhammad Ayaz Tariq Sadad ikram ullah Lali Awais Mahmood Najam Ul Hassan Habib Dhahri College of Applied Computer Sciences King Saud University(Almuzahmiyah Branch)Riyadh11564KSA Department of Computer Science University of Central PunjabLahore54000Pakistan Department of CS&SE International Islamic UniversityIslamabad44000Pakistan Division of Science and Technology University of EducationLahore54000Pakistan Department of Electrical and Computer Engineering Dhofar UniversitySalalahOman

Guava is one of the most important fruits in Pakistan,and is gradually boosting the economy of *** production can be interrupted due to different diseases,such as anthracnose,algal spot,fruit fly,styler end rot and *** diseases are usually detected and identified by visual observation,thus automatic detection is required to assist *** this research,a new technique was created to detect guava plant diseases using image processing techniques and computer *** automated system is developed to support farmers to identify major diseases in *** collected healthy and unhealthy images of different guava diseases from the *** image labeling was done with the help of an expert to differentiate between healthy and unhealthy *** local binary pattern(LBP)was used for the extraction of features,and principal component analysis(PCA)was used for dimensionality *** classification was carried out using multiple classifiers,including cubic support vector machine,Fine K-nearest neighbor(F-KNN),Bagged Tree and RUSBoosted Tree algorithms and achieved 100%accuracy for the diagnosis of fruit flies disease using Bagged ***,the findings indicated that cubic support vector machines(C-SVM)was the best classifier for all guava disease mentioned in the dataset.

关键词： Classification guava disease image processing machine learning

Potential Inhibitory Effect of Vitamins Against COVID-19

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Computers, Materials & Continua 2021年第1期66卷 707-714页

作者： Kashaf Junaid Sumera Qasim Humaira Yasmeen Hasan Ejaz Abdullah Alsrhani Muhammad ikram ullah Fahad Ahmad Abdul Rehman Department of Clinical Laboratory Sciences College of Applied Medical SciencesJouf UniversitySakakaAl JoufSaudi Arabia College of Pharmacy Jouf UniversitySakakaAl JoufSaudi Arabia Department of Microbiology and Molecular Genetics The Women’s UniversityMultanPakistan Department of Computer Sciences Kinnaird College for WomenLahorePakistan Department of Microbiology and Molecular Genetics University of the PunjabLahorePakistan

Coronavirus disease 2019(COVID-19)is a current pandemic that has affected more than 195 countries *** this severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)pandemic,when treatment strategies are not yet clear and vaccines are not available,vitamins are an excellent choice to protect against this viral *** rationale behind this study was to examine the inhibitory effect of vitamins B,C,and D against the main protease of SARSCoV-2 and angiotensin-converting enzyme 2(ACE2),which have critical rolesin the immune *** docking,performed by using MOE-Dock of the Chemical Computing Group,was used to understand the *** vitamins all docked within the active sites of the Mpro(PDB ID:6LU7)and ACE2 receptor proteins(PDB ID:6VW1).Vitamins B and C delivered maximum energy scores against both targets,while vitamin D displayed a binding energy score of−7.9532 kcal/mol for M^(pro) and−7.9297 for *** efficiency of all three vitamins is higher than the binding energy score of chloroquine(−6.889 kcal/mol),which is now under clinical *** use of vitamins is beneficial,being immune system restorative,and they also act as anti-COVID *** the potential beneficial effects of vitamin B and C are revealed through docking studies,further clinical trials are required for the validation of these results.

关键词： SARS-CoV-2 vitamins docking antivirals chemical computing