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The Possibility of Nucleic Acids to Act as Anti-Viral Therapeutic Agents—A Review

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Open Journal of Medical Microbiology 2021年第3期11卷 198-248页

作者： md. selim reza Farzana Mim Mohammad rezaul Quader Mohammad Jahidur Rahman Khan md. Sabir Hossain Kazi Rasel Uddin Salina Akter Sharmin Rahman Sumon Roy md. Abdullah Rumman RT-PCR LAB Bangabandhu Sheikh Mujib Medical College Faridpur Bangladesh Department of Biochemistry and Molecular Biology Jahangirnagar University Dhaka Bangladesh Department of Biochemistry Bangabandhu Sheikh Mujib Medical College Faridpur Bangladesh Department of Microbiology Shaheed Suhrawardy Medical College Dhaka Bangladesh Department of Pharmacology Ibrahim Medical College Dhaka Bangladesh

For just about 30 years, researchers have considered the likelihood to utilize nucleic acids as antiviral therapeutics. In principle, small single-stranded nucleotide sequence (oligonucleotide) could hybridize to a particular gene or messenger RNA and diminish transcription or translation, respectively, in this manner decreasing the amount of protein that is synthesized. Until now, an incredible number of antisense oligonucleotides, double-stranded oligonucleotides, aptamers, ribozymes, deoxyribozymes, interfering RNAs, chimeric RNA-DNA molecules, antibody genes has been created artificially and applied effectively for comprehension and manipulating biological processes and in clinical preliminaries to treat a variety of diseases. Their versatility and potency make them similarly fit candidates for fighting viral infections. However, troubles with their efficiency, off-target effects, toxicity, delivery, and stability halted the development of nucleic acid-based therapeutics that can be utilized in the clinic. The potential for nucleic acid therapeutic agents is significant and is quite recently beginning to be realized. In this review, we have summarized some of the recent advancements made in the area of nucleic acid based therapeutics and focused on the methods of their delivery and associated challenges.

关键词： Antisense Oligonucleotides Aptamers Ribozymes Deoxyribozymes RNA Interference

Renewed Focus on the Threat of Cross-Contamination in Molecular Laboratories: Notes from the COVID-19 Testing Experience in Bangladesh

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Advances in Infectious Diseases 2021年第4期11卷 357-365页

作者： Mohammad Jahidur Rahman Khan Ruksana Raihan S. M. Rashed Ul Islam Nusrat Mannan Mohammad Jamal Uddin Nazia Hasan Khan Tanzila Rawnuck Amirul Huda Bhuiyan Farzana Mim md. selim reza Department of Microbiology Shaheed Suhrawardy Medical College Dhaka Bangladesh Department of Microbiology US-Bangla Medical College Dhaka Bangladesh Department of Virology Bangabandhu Sheikh Mujib Medical University Dhaka Bangladesh Department of Microbiology & Mycology National Institute of Preventive and Social Medicine Dhaka Bangladesh RT-PCR LAB United Hospital Limited Dhaka Bangladesh Department of Pathology & Microbiology Dhaka Dental College Dhaka Bangladesh Department of Virology Dhaka Medical College Dhaka Bangladesh Department of Biochemistry & Molecular Biology Jahangirnagar University Dhaka Bangladesh RT-PCR LAB Bangabandhu Sheikh Mujib Medical College Faridpur Bangladesh

Rapid and accurate laboratory diagnosis of SARS-CoV-2 infection is crucial for the management of COVID-19 patients and control of the spread of the virus. At the start of the COVID-19 pandemic, Bangladesh had only one government molecular laboratory where real-time RT-PCR would be performed to diagnose SARS-CoV-2 infection. With the increasing number of suspected cases requiring confirmation diagnostic testing, there is a requirement to expand capacity for large-scale testing quickly. The government of Bangladesh established over 100 molecular laboratories within one year to test COVID-19. To expand the testing capacity, the government was compelled to recruit laboratory staff with limited experience and technical expertise, especially in molecular assays, to process specimens, interpret results, troubleshoot. As a result, the risk of diagnostic errors, such as cross-contamination, increased, potentially undermining the efficacy of public health policies, public health response, surveillance programs, and restrictive measures aimed toward containing the outbreak. In this piece, we discuss the different sources of cross-contamination in the COVID-19 RT-PCR laboratories and proffer practical preventive measures to avoid them.

关键词： SARS-CoV-2 RT-PCR Cross-Contaminations Quality Control COVID-19 False Positive

Identification of Key Genes as Potential Drug Targets for Gastric Cancer

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清华大学学报:自然科学版(英文版) 2023年第4期28卷 649-664页

作者： md.Tofazzal Hossain md.selim reza Yin Peng Shengzhong Feng Yanjie Wei Center for High Performance Computing Joint Engineering Research Center for Health Big Data Intelligent Analysis TechnologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China School of Computer Science and Technology University of Chinese Academy of SciencesBeijing 100049China Department of Statistics Bangabandhu Sheikh Mujibur Rahman Science and Technology UniversityGopalganj 8100Bangladesh Guangdong Provincial Key Laboratory for Genome Stability and Disease Prevention and Regional Immunity and Diseases Department of PathologyShenzhen UniversityShenzhen 518060China

Gastric cancer(GC)is one of the most common cancers and ranks the third in cancer mortality all over the world.The goal of this study was to identify potential hub-genes,highlighting their functions,signaling pathways,and candidate drugs for the treatment of GC patients.We used publicly available next generation sequencing(NGS)data to identify differentially expressed(DE)genes.The top DE genes were mapped to STRING database to construct the protein-protein interaction(PPI)network and top hub genes were selected for further analysis.We found a total of 1555 DE genes with 870 upregulated and 685 downregulated genes in GC.We selected the top 400(200 upregulated and 200 downregulated)genes to construct a PPI network and extracted the top 15 hub genes.The gene ontology(GO)term and kyoto encyclopedia of genes and genomes(KEGG)pathway enrichment analyses of the 15 hub genes exposed some important functions and signaling pathways that were significantly associated with GC patients.The survival analysis of the hub genes disclosed that the lower expressions of the three hub genes CDH2,COL4A1,and COL5A2 were associated with better survival of GC patients.These three genes might be the candidate biomarkers for the diagnosis and treatment of GC.Then,we considered 3 key proteins(genomic biomarkers)(COL4A1,CDH2,and CO5A2)as the drug target proteins(receptors),performed their docking analysis with the 102 meta-drug agents,and found Everolimus,Docetaxel,Lanreotide,Venetoclax,Temsirolimus,and Nilotinib as the top ranked 6 candidate drugs with respect to our proposed target proteins for the treatment against GC patients.Therefore,the proposed drugs might play vital role for the treatment against GC patients.

关键词： gastric cancer hub genes candidate genes molecular docking candidate drugs

Quantifying River Bank Erosion and Accretion Patterns along the Gorai River in Kushtia, Bangladesh: A Geospatial Analysis Utilizing GIS and Remote Sensing Techniques

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Journal of Geographic Information System 2024年第1期16卷 70-88页

作者： Chisti Muzahid Samsunnahar Popy Rifat Islam md. Shafiqul Ahsan Emon md. selim Reja md. Mustafizur Rahman Jubayer Hoque md. Golam Rabbani Saim Raiyan Department of Environmental Science and Disaster Management Bangabandhu Sheikh Mujibur Rahman Science and Technology University Dhaka Bangladesh

River bank erosion is a natural process that occurs when the water flow of a river exceeds the bank’s ability to withstand it. It is a common phenomenon that causes extensive land damage, displacement of people, loss of crops, and infrastructure damage. The Gorai River, situated on the right bank of the Ganges, is a significant branch of the river that flows into the Bay of Bengal via the Mathumati and Baleswar rivers. The erosion of the banks of the Gorai River in Kushtia district is not a recent occurrence. Local residents have been dealing with this issue for the past hundred years, and according to the elderly members of the community, the erosion has become more severe activities. Therefore, the main objective of this research is to quantify river bank erosion and accretion and bankline shifting from 2003 to 2022 using multi-temporal Landsat images data with GIS and remote sensing technique. Bank-line migration occurs as a result of the interplay and interconnectedness of various factors such as the degree of river-related processes such as erosion, transportation, and deposition, the amount of water in the river during the high season, the geological and soil makeup, and human intervention in the river. The results show that the highest eroded area was 4.6 square kilometers during the period of 2016 to 2019, while the highest accreted area was 7.12 square kilometers during the period of 2013 to 2016. However, the erosion and accretion values fluctuated from year to year.

关键词： Erosion and Accretion Geographic Information System (GIS) Remote Sensing Satellite Image Bankline Shifting

Assessment of Physico-Chemical and Microbial Quality of Sugarcane Juice Sold by Street Vendors in Three Regions of Bangladesh

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Food and Nutrition Sciences 2024年第4期15卷 263-276页

作者： Nargis Akter Khan md. Murtaja reza Linkon Munni Akter md. Alamgir Hossain md. Mahbubur Rahman Tayeba Khan md. Abdul Alim md. Esrafil Department of Food Technology and Nutritional Science Mawlana Bhashani Science and Technology University Tangail Bangladesh Department of Biotechnology and Genetic Engineering Mawlana Bhashani Science and Technology University Tangail Bangladesh

Sugar cane juice is a popular refreshing drink in most part of Bangladesh. It has great taste and health benefits;also it is available most of the public places at reasonable prices which consumed by road side customers including general public, shopping personals, tourists, students. In our country, street vendors crushing sugarcane between roller crusher and sold without any heat treatment or preservative, also served with or without added ice and lemon juice. The study aimed to identify and compare the physico-chemical and microbial quality of sugarcane juice. The chemical qualities of juices including moisture, PH, ash, total soluble solid, total sugar, reducing sugar and titrable acidity were found slightly different in Mymensingh, Gazipur and Narayangonj areas. The highest and lowest value of moisture, ash, PH, total soluble solids, total sugar, reducing sugar and titrable acidity were found in 84.33% - 79.26% (Gazipur-Mymensingh), 0.57% - 0.04% (Mymensingh-Gazipur), 5.9 - 2.9 (Gazipur-Narayangonj), 17.48% - 4.98% (Mymensingh-Narayangonj), 21.9% - 6.56% (Mymensingh-Gazipur), 3.7 - 2.1 (Gazipur-Mymensingh) and 0.523% - 0.007% (Narayangonj-Gazipur) respectively. For microbiological analysis, the total viable count of sugar cane juice in Mymensingh, Gazipur and Narayangonj were ranged from 0.6 × 105 - 43.6 × 105 cfu/ml, 4.6 × 105 - 21.6 × 105 cfu/ml and 3.6 × 105 - 36.6 × 105 cfu/ml respectively, where the permitted value is 1.0 × 104 cfu/ml, whereas the total coliform count was ranged from 0.4 × 105 - 6.4 × 105 cfu/ml, 0.6 × 105 - 8.4 × 105 cfu/ml and 0.00 - 8.4 × 105 cfu/ml, where the permitted value is 100 cfu/ml and total fungal count was ranged from 5.5 × 105 - 56.5 × 105 cfu/ml, 21.5 × 105 - 54.5 × 105 cfu/ml and 32.5 × 105 - 68.5 × 105 cfu/ml, where the permitted value is 1000 cfu/ml. Ac

关键词： Sugarcane Street Vendors Microbial Quality Reducing Sugar

Rural Resilience: A Comprehensive Study on Water Supply, Sanitation, Disease Patterns, and Hygiene Practices in Munshiganj, Bangladesh

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Journal of Environmental Protection 2024年第1期15卷 63-75页

作者： Jubayer Hoque Rifat Islam md. Mustafizur Rahman md. Golam Rabbani md. selim Reja Saifur Rahman Soykat Saim Raiyan md. Shafiqul Ahsan Emon Sakil Khan Department of Environmental Science and Disaster Management Bangabandhu Sheikh Mujibur Rahman Science and Technology University Gopalgnj Bangladesh Department of Political Science Bangabandhu Sheikh Mujibur Rahman Science and Technology University GopalgnjBangladesh Department of Statistics Bangabandhu Sheikh Mujibur Rahman Science and Technology University Gopalgnj Bangladesh

This research project investigates the current status of water supply, sanitation, and hygiene practices in Munshiganj District, Bangladesh. Data collection involved a structured questionnaire and a reconnaissance survey. Findings reveal that 30% of individuals rely on surface water (hand-tube wells, rivers, and ponds), prioritized as canal > river > pond, while 70% depend on groundwater (subterranean electric motor, deep tube-well). Drinking water is generally sufficient, with 95% reporting adequacy throughout the year. About 45% use hand tube-well water, 28% use deep tube-well water, and 11% use supply tap water for various purposes. Bathing trends include underground water through electric motor > pond > hand tube-well water > river, while for cooking, the order is underground water through electric motor > pond > hand tube-well water > river. Toilet water supply ranks as supply tap water > hand tube-well water > deep tube-well water. Although sanitation awareness is high, some lack knowledge of good hygiene practices. After defecating, handwashing methods include soap, ash, soil, or water. Children’s waste disposal varies, with some discarding it in open areas. Approximately 40% suffer from diseases like Diarrhoea due to unsafe water, primarily affecting children and elders. Training exists, but a significant portion lacks sanitation education. Dry skin or exposure to cold water may cause temporary irritation. Local government involvement in sanitation efforts is less active compared to non-governmental organizations. Results emphasize the need to enhance community awareness of safe water supplies and sanitation practices. .

关键词： Water Supply Sanitation Practices Hygiene Awareness Groundwater Dependency Community Health Intervention

A Comparative Study of 3D Virtual Pattern and Traditional Pattern Making

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Journal of Textile Science and Technology 2024年第1期10卷 1-24页

作者： md. Ahshan Habib md. Shamsul Alam Department of Fashion Design & Technology Sonargaon University Dhaka Bangladesh Department of Apparel Manufacture & Technology Sonargaon University Dhaka Bangladesh

Pattern making plays a key role in the aspect of fashion design and garment production, as it serves as the transformative process that turns a simple drawing into a consistent accumulation of garments. The process of creating conventional or manual patterns requires a significant amount of time and a specialized skill set in various areas such as grading, marker planning, and fabric utilization. This study examines the potential of 3D technology and virtual fashion designing software in optimizing the efficiency and cost-effectiveness of pattern production processes. The proposed methodology is characterized by a higher level of comprehensiveness and reliability, resulting in time efficiency and providing a diverse range of design options. The user is not expected to possess comprehensive knowledge of traditional pattern creation procedures prior to engaging in the task. The software offers a range of capabilities including draping, 3D-to-2D and 2D-to-3D unfolding, fabric drivability analysis, ease allowance calculation, add-fullness manipulation, style development, grading, and virtual garment try-on. The strategy will cause a shift in the viewpoints and methodologies of business professionals when it comes to the use of 3D fashion design software. Upon recognizing the potential time, financial, and resource-saving benefits associated with the integration of 3D technology into their design development process, individuals will be motivated to select for its utilization over conventional pattern making methods. Individuals will possess the capacity to transfer their cognitive processes and engage in introspection regarding their professional endeavors and current activities through the utilization of 3D virtual pattern-making and fashion design technologies. To enhance the efficacy and ecological sustainability of designs, designers have the potential to integrate 3D technology with virtual fashion software, thereby compliant advantages for both commercial enterprises and the environment.

关键词： Pattern-Making 3D Pattern Making Virtual Fashion 3D-to-2D Unfolding Sustainable Designs

Insights into Manipulation: Unveiling Tampered Images Using Modified ELA, Deep Learning, and Explainable AI

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Journal of Computer and Communications 2024年第6期12卷 135-151页

作者： md. Mehedi Hasan md. Masud Rana Abu Sayed md. Mostafizur Rahaman Department of Information and Communication Technology Bangladesh University of Professionals Dhaka Bangladesh Department of Computer Science and Engineering Jahangirnagar University Dhaka Bangladesh

Digital image forgery (DIF) is a prevalent issue in the modern age, where malicious actors manipulate images for various purposes, including deception and misinformation. Detecting such forgeries is a critical task for maintaining the integrity of digital content. This thesis explores the use of Modified Error Level Analysis (ELA) in combination with a Convolutional Neural Network (CNN), as well as, Feedforward Neural Network (FNN) model to detect digital image forgeries. Additionally, incorporation of Explainable Artificial Intelligence (XAI) to this research provided insights into the process of decision-making by the models. The study trains and tests the models on the CASIA2 dataset, emphasizing both authentic and forged images. The CNN model is trained and evaluated, and Explainable AI (SHapley Additive exPlanation— SHAP) is incorporated to explain the model’s predictions. Similarly, the FNN model is trained and evaluated, and XAI (SHAP) is incorporated to explain the model’s predictions. The results obtained from the analysis reveals that the proposed approach using CNN model is most effective in detecting image forgeries and provides valuable explanations for decision interpretability.

关键词： IFD DIF ELA CNN FNN XAI SHAP CASIA2.0

Exploring the Role of Serum Cystatin C in Early Detection of Acute Kidney Injury among On-Pump Cardiac Surgery Patients: A Single-Center Investigation in Bangladesh

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World Journal of Cardiovascular Diseases 2024年第6期14卷 363-373页

作者： md. Ahaduzzaman md. Abir Tazim Chowdhury Munama Magdum md. Saiful Islam Khan Satyajit Sharma Monoj Tiwari md. Abul Bashar Maruf md. Alauddin Omar Sadeque Khan md. Mostafizur Rahman Mirza md. Nazmus Saquib Department of Cardiothoracic and Vascular Surgery Evercare Hospital Dhaka Dhaka Bangladesh Department of Preventive and Social Medicine National Institute of Preventive and Social Medicine Dhaka Bangladesh Department of Cardiothoracic Anesthesia Evercare Hospital Dhaka Dhaka Bangladesh Department of Cardiac Surgery National Heart Foundation Hospital & Research Institute Dhaka Bangladesh Department of Cardiovascular and Thoracic Surgery B.P. Koirala Memorial Cancer Hospital Bharatpur Chitwan Nepal Department of Cardiac Surgery United Hospital Limited Dhaka Bangladesh Department of Cardiac Surgery Bangabandhu Sheikh Mujib Medical University Dhaka Bangladesh Department of Cardiac Surgery Ibrahim Cardiac Hospital & Research Institute Dhaka Bangladesh

Background: Acute Kidney Injury (AKI) stands as a prominent postoperative complication in on-pump cardiac surgery, with repercussions on morbidity, mortality, and hospitalization duration. Current diagnostic criteria relying on serum creatinine levels exhibit a delayed identification of AKI, prompting an exploration of alternative biomarkers. Aims and Objectives: This study is designed to overcome diagnostic constraints and explore the viability of serum Cystatin C as an early predictor of Acute Kidney Injury (AKI) in individuals undergoing on-pump cardiac surgery. The investigation aims to establish the relationship between serum Cystatin C levels and the onset of AKI in patients subjected to on-pump cardiac surgery. Primary objectives involve the assessment of the diagnostic effectiveness of serum Cystatin C, its comparison with serum creatinine, and the exploration of its potential for the early identification and treatment of AKI. Methodology: Conducted as a single-center study at the cardiac surgery department of BSMMU in Bangladesh from September 2020 to August 2022, a comparative cross-sectional analysis involved 31 participants categorized into No AKI and AKI groups based on Kidney Disease: Improving Global Outcomes (KDIGO) criteria. Data collection encompassed preoperative, post-CBP (cardiopulmonary bypass) conclusion at 2 hours, postoperative day 1, and postoperative day 2 intervals. Statistical analyses included Chi-squared tests, independent Student’s t-tests, and one-sample t-tests. Significance was set at P Results: The study revealed no significant differences in baseline characteristics between the No AKI and AKI groups, except for CPB time and cross-clamp time. Serum Cystatin C levels in the AKI group exhibited statistical significance at various time points, highlighting its potential as an early detector. Conversely, Serum Creatinine levels in the AKI group showed no statistical significance. The Receiver Operating Characteristic (ROC) curve analysis further supported the efficacy of serum Cyst

关键词： Acute Kidney Injury (AKI) On-Pump Cardiac Surgery Serum Cystatin C Serum Creatinine Diagnostic Biomarkers Early Detection Cardiopulmonary Bypass Single-Center Study Bangladesh