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Deciphering codon usage patterns and evolutionary forces in chloroplast genes of Camellia sinensis var. assamica and Camellia sinensis var. sinensis in comparison to Camellia pubicosta

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Journal of Integrative Agriculture 2019年第12期18卷 2771-2785页

作者： Sophiarani Yengkhom Arif Uddin Supriyo Chakraborty Department of Biotechnology Assam UniversitySilchar 788011AssamIndia Department of Zoology Moinul Hoque Choudhury Memorial Science CollegeAlgapurHailakandi 788150AssamIndia

Codon usage bias(CUB) is a unique property of genome which refers to non-random usage of synonymous codons in coding sequences. The present study makes an attempt to find out the pattern of CUB in chloroplast(cp) genes among three tea species, i.e., Camellia sinensis var. assamica(Assam tea), Camellia sinensis var. sinensis(Chinese tea) and Camellia pubicosta(wild tea species) as no work on CUB was reported earlier. To understand the patterns of codon usage among the cp genes of three tea groups, we used bioinformatic tools to investigate the protein coding sequences of cp genes. In our present study, the mean nucleobase T was the highest whereas C was the lowest in all the three tea groups. The overall AT content was more than GC content, i.e., genes were AT rich. The scaled chi-square(SCS) value indicated that the CUB of cp genes was low. The codon CGT(Arg) was over-represented in C. sinensis var. sinensis whereas GGA(Pro) was over-represented in C. pubicosta species. Heatmap study revealed that most of the GC ending codons showed positive correlations between codon usage and GC3 while AT ending codons exhibited negative correlations. From neutrality plot analysis, it was evident that natural selection had played a major role, while mutation pressure exerted a minor effect in the CUB of cp genes in three tea groups. Highly significant(P<0.01) positive correlation was found between SCS and synonymous codon usage order(SCUO) of cp genes which suggested that high expression of cp genes was associated with high degree of CUB.

关键词： Camellia sinensis var.assamica Camellia sinensis var.sinensis Camellia pubicosta chloroplast genes codon usage bias mutation natural selection

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The changing landscape of mangroves in Bangladesh compared to four other countries in tropical regions

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Journal of Forestry Research 2014年第3期25卷 605-611页

作者： S.M.Mijan uddin A.T.M.Rafiqul Hoque Saiful arif Abdullah Institute of Forestry and Environmental Sciences University of Chittagong Institute for Environment and Development (LESTARI) National University of Malaysia (UKM)

Loss of mangroves and consequent habitat fragmentation is a major concern throughout the world’s tropical countries. Conversion of mangrove habitat due to aquaculture, agriculture, urbanization and industrialization, ecotourism, overlapping bureaucracy and conflicting policies is occurring at a striking rate. This paper reviews the trends of mangrove area changes in Bangladesh and compares them with four other countries in tropical regions that have significant mangrove areas. The rate of mangrove loss from the 1980 to 2005 was calculated using the compound interest rate formula for its explicit biological implication. In Bangladesh, the area of mangroves was found to have increased due to its higher accretion rate. In India the rate of mangrove loss had fallen. The rate of mangrove loss in Malaysia in the 1990s （-0.008 ha＆#183;a-1） was higher than the 1980s （-0.004 ha＆#183;a-1）. In Indonesia, the rate decreased, from the 1980s （-0.018 ha＆#183;a-1） to the 1990s （-0.010 ha＆#183;a-1）. Finally in Myanmar the rate of mangrove loss gradually accelerated. Aquaculture was found to be the common cause of mangrove conversion in the regions. Loss of mangroves is now a prominent global issue, associated with the loss of biodiversity, deterioration of habitat integrity, climatic changes, the amount of carbon sequestration, and resulting sea-level rise. Therefore, a systematic evaluation of these environmental impacts is prerequisite to realize sustainable mangrove management.

关键词： Mangrove loss accretion aquaculture mangrove landscape land-use change.

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An Abstractive Summarization Technique with Variable Length Keywords as per Document Diversity

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Computers, Materials & Continua 2021年第3期66卷 2409-2423页

作者： Muhammad Yahya Saeed Muhammad Awais Muhammad Younas Muhammad arif Shah Atif Khan M.Irfan uddin Marwan Mahmoud Department of Software Engineering Government College UniversityFaisalabadFaisalabad38000Pakistan Department of IT and Computer Science Pak-Austria Fachhochschule Institute of Applied Sciences and TechnologyHaripurPakistan Department of Computer Science Islamia College PeshawarPeshawarPakistan Institute of Computing Kohat University of Science and TechnologyKohatPakistan Faculty of Applied Studies King Abdulaziz UniversityJeddahSaudi Arabia

Text Summarization is an essential area in text mining,which has procedures for text extraction.In natural language processing,text summarization maps the documents to a representative set of descriptive words.Therefore,the objective of text extraction is to attain reduced expressive contents from the text documents.Text summarization has two main areas such as abstractive,and extractive summarization.Extractive text summarization has further two approaches,in which the first approach applies the sentence score algorithm,and the second approach follows the word embedding principles.All such text extractions have limitations in providing the basic theme of the underlying documents.In this paper,we have employed text summarization by TF-IDF with PageRank keywords,sentence score algorithm,and Word2Vec word embedding.The study compared these forms of the text summarizations with the actual text,by calculating cosine similarities.Furthermore,TF-IDF based PageRank keywords are extracted from the other two extractive summarizations.An intersection over these three types of TD-IDF keywords to generate the more representative set of keywords for each text document is performed.This technique generates variable-length keywords as per document diversity instead of selecting fixedlength keywords for each document.This form of abstractive summarization improves metadata similarity to the original text compared to all other forms of summarized text.It also solves the issue of deciding the number of representative keywords for a specific text document.To evaluate the technique,the study used a sample of more than eighteen hundred text documents.The abstractive summarization follows the principles of deep learning to create uniform similarity of extracted words with actual text and all other forms of text summarization.The proposed technique provides a stable measure of similarity as compared to existing forms of text summarization.

关键词： Metadata page rank sentence score word2vec cosine similarity This

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Liver-Tumor Detection Using CNN ResUNet

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Computers, Materials & Continua 2021年第5期67卷 1899-1914页

作者： Muhammad Sohaib Aslam Muhammad Younas Muhammad Umar Sarwar Muhammad arif Shah Atif Khan MIrfan uddin Shafiq Ahmad Muhammad Firdausi Mazen Zaindin Department of Computer Science Government College University FaisalabadFaisalabad38000Pakistan Department of IT and Computer Science Pak-Austria Fachhochschule Institute of Applied Sciences and TechnologyHaripur22620Pakistan Department of Computer Science Islamia College PeshawarPeshawarKPPakistan Institute of Computing Kohat University of Science and TechnologyKohatPakistan Department of Industrial Engineering College of EngineeringKing Saud UniversityRiyadh11421Saudi Arabia Department of Statistics and Operations Research College of ScienceKing Saud UniversityRiyadh11421Saudi Arabia

Liver tumor is the fifth most occurring type of tumor in men and the ninth most occurring type of tumor in women according to recent reports of Global cancer statistics 2018.There are several imaging tests like Computed Tomography(CT),Magnetic Resonance Imaging(MRI),and ultrasound that can diagnose the liver tumor after taking the sample from the tissue of the liver.These tests are costly and time-consuming.This paper proposed that image processing through deep learning Convolutional Neural Network(CNNs)ResUNet model that can be helpful for the early diagnose of tumor instead of conventional methods.The existing studies have mainly used the two Cascaded CNNs for liver segmentation and evaluation of Region Of Interest(ROI).This study uses ResUNet,an updated version of U-Net and ResNet Models that utilize the service of Residential blocks.We apply over method on the 3D-IRCADb01 dataset that is based on CT slices of liver tumor affected patients.The results showed the True Value Accuracy around 99%and F1 score performance around 95%.This method will be helpful for early and accurate diagnose of the Liver tumor to save the lives of many patients in the field of Biotechnology.

关键词： Liver tumor diagnose ResUNet CNNs segmentation

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α-GLUCOSIDASE AND CHYMOTRYPSIN INHIBITING LIGNANS FROM COMMIPHORA MUKUL

α-GLUCOSIDASE AND CHYMOTRYPSIN INHIBITING LIGNANS FROM COMM...

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The 1st Session of 2005 Workshop of Pakistan Academy of Sciences

作者： Muhammad Athar Abbasi Viqar uddin Ahmad Muhammad Zubair Shamsun Nahar Khan Muhammad arif Lodhi M.Iqbal Choudhary HEJ Research Institute of Chemistry International Center for Chemical SciencesUniversity of KarachiKarachi 75270Pakistan

Phytochemical investigation of the whole plant of Commiphora mukul Engl.resulted in the isolation of two lignans,epiexcelsin（1） and 5′-demethoxyepiexcelsin（2） which are reported for the first time from this species.The structure elucidation of the isolated compounds was based on 1D and 2DNMR analysis and by the comparison with the published data.The lignans 1 and 2 showed significant inhibitory activity against α-glucosidase with the IC50 of 59.8 ± 3.63455 μM and 75.2 ± 8.1616 μM respectively.They also showed weak inhibitory potential against chymotrypsin with the IC50 of 110 ±0.025 μM and 649 ± 0.013 μM respectively.

关键词： Commiphora mukul ligans α-glucosidase chymotrypsin inhibitors

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Evaluation of Lipid Profile in Obese and Non-Obese Hypertensive Adult Patients Attended in Medicine Department of a Medical College Hospital of Bangladesh

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World Journal of Cardiovascular Diseases 2020年第8期10卷 520-544页

作者： Md Reaz uddin Chowdhury Kazi Shanzida Akter Sahedul Islam Bhuiyan Mainuddin Sohel Mahbub Majumder arif Mohammad Sohan Mahfuzur Rahman Muhammad Anwarul Kabir Zaman Ahmed Abdul Malek Ukil Medical College Noakhali Bangladesh Trauma Center Feni Bangladesh Brahmanbaria Medical College Brahmanbaria Bangladesh Cumilla Medical College Cumilla Bangladesh Ad-Din Akij Medical College Khulna Bangladesh

Background: By the dawn of this modern era of science, the prime challenge of physician is cardiovascular disease (CVD). The most important modifiable risk factors of CVDs are unhealthy diet, physical inactivity and tobacco use. The effects of unhealthy diet and physical inactivity include abnormal blood lipid, obesity and hypertension. We tried to evaluate and correlate the pattern of lipid profile in obese and non-obese hypertensive patients. Objectives: This study was conducted at medicine department of Cumilla Medical College Hospital. The principal aim was to evaluate the lipid profile in obese and non-obese adult hypertensive patients. Methodology: During this cross sectional analytical study, a total of 100 adult hypertensive patients were taken by purposive sampling. Among them 50 (group 1) patients were taken those were obese and 50 (group 2) patients taken those were non-obese according to BMI measurement on operational definition. Diagnosis of hypertension would be established with the help of ambulatory BP measurements two occasions few minutes apart. The staging of hypertension was done according to JNC7 Criteria. Morning blood samples were taken after 8 - 12 hours of fasting and lipid profiles were done on authentic laboratories. The laboratory values were interpreted according to the operational definition of dyslipidaemia. The ethical research and review committee approved the study protocol and signed informed consent was obtained from the participants. The statistics was analyzed using the IBM SPSS software of version 19.0. Statistical significance was set at p Results: Among the two groups, there were 56 (56%) males and 44 (44%) females. The mean age of group 1 (46.10 ± 11.09) was compared to that of group 2 (45.5 ± 10.6). Lipid profile abnormalities were s

关键词： Lipid Profile Dyslipidaemia Obese Non-Obese Hypertension

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