A network-biology approach for identification of key genes and pathways involved in malignant peritoneal mesothelioma

Mahfuz, A.M.U.B.,Zubair-Bin-Mahfuj, A.M.,Podder, Dibya Joti Korea Genome Organization 2021 Genomics & informatics Vol.19 No.2

Even in the current age of advanced medicine, the prognosis of malignant peritoneal mesothelioma (MPM) remains abysmal. Molecular mechanisms responsible for the initiation and progression of MPM are still largely not understood. Adopting an integrated bioinformatics approach, this study aims to identify the key genes and pathways responsible for MPM. Genes that are differentially expressed in MPM in comparison with the peritoneum of healthy controls have been identified by analyzing a microarray gene expression dataset. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of these differentially expressed genes (DEG) were conducted to gain a better insight. A protein-protein interaction (PPI) network of the proteins encoded by the DEGs was constructed using STRING and hub genes were detected analyzing this network. Next, the transcription factors and miRNAs that have possible regulatory roles on the hub genes were detected. Finally, survival analyses based on the hub genes were conducted using the GEPIA2 web server. Six hundred six genes were found to be differentially expressed in MPM; 133 are upregulated and 473 are downregulated. Analyzing the STRING generated PPI network, six dense modules and 12 hub genes were identified. Fifteen transcription factors and 10 miRNAs were identified to have the most extensive regulatory functions on the DEGs. Through bioinformatics analyses, this work provides an insight into the potential genes and pathways involved in MPM.

Can Gravity Model Explain BIMSTEC`s Trade?

( Mahfuz Kabir ),( Ruhul Salim ) 세종대학교 경제통합연구소 (구 세종대학교 국제경제연구소) 2010 Journal of Economic Integration Vol.25 No.1

This paper examines the trading pattern of Bay of Bengal Initiative for Multi-Sectoral Technical and Economic Cooperation (BIMSTEC) by employing an augmented gravity model. The econometric specification followed Egger (2000, 2002), Baltagi et al. (2003) and Serlenga and Shin (2007). Diagnostic checks imply the presence of serial correlation, heteroscedasticity and contemporaneous correlation in both import and export panels, which are allowed for in the Prais-Winsten regression with panel-specific AR(1). Regression estimates show that BIMSTEC`s imports follow the Linder hypothesis, while the exports exhibit Heckscher-Ohlin-Samuelson prototype. Results also suggest that distance elasticity is negative and significant. Real depreciation is import-reducing and export enhancing. Common language and bilateral trade agreement are found to be import and export enhancing, respectively. Governance of both local and destination countries impact trade of the bloc positively. Finally, belonging to the bloc accounts for about 29% of its exports, which is an indication of good prospect if trade policies are liberalised within the bloc. Thus, gravity model can successfully explain the pattern of the bloc`s trade.

Bangladeshi Science Lecturers’ Beliefs and Self-reported Actions on Universal Design for Learning

Mahfuz, Md Shohag,김용욱,차정호 대구대학교 한국특수교육문제연구소 2019 특수교육저널 : 이론과 실천 Vol.20 No.4

[Purpose] In this research, the authors surveyed Bangladeshi university science lecturers’ beliefs and self-reported actions on diversified students’ disability-related topics and on inclusive teaching practices and their implementation. [Method] For this purpose, we use the Inclusive Teaching Strategies Inventory (ITSI), which is comprised of the following six subscales: a) Accommodation, b) Accessible Course Materials, c) Course Modification, d) Inclusive Lecture Strategies, e) Inclusive Class, and f) Inclusive Assessment. The ITSI contains two feedback categories that evaluate both lectures’ beliefs and self-reported actions on UDL in the six areas. We conducted SPSS-24 for a series of analyses to determine the Bangladeshi science lecturers’ beliefs and self-reported actions on UDL by lecturers’ gender and teaching experience, as well as the differences with equivalent data from the U.S., Spain and Canada. [Results] The results revealed that Bangladeshi science lecturers’ belief levels were higher than their self-reported actions. There were some significant differences among lecturers’ gender and teaching experience in both belief and action of UDL. Bangladeshi lecturers’ self-reported actions were significantly lower than that of the three other countries, although their beliefs were higher. [Conclusion] Professional development for Bangladeshi lecturers are needed in future to help them utilize UDL guidelines in their classes.

Effect of golden needle mushroom (Flammulina velutipes) stem waste on laying performance, calcium utilization, immune response and serum immunity at early phase of production

Mahfuz, Shad,Song, Hui,Liu, Zhongjun,Liu, Xinyu,Diao, Zipeng,Ren, Guihong,Guo, Zhixin,Cui, Yan Asian Australasian Association of Animal Productio 2018 Animal Bioscience Vol.31 No.5

Objective: This experiment was conducted to evaluate the effects of golden needle mushroom (Flammulina velutipes) stem waste (FVW), on organic eggs production, calcium utilization, antibody response, serum immunoglobulin, and serum cytokine concentration at early phase of production in laying hens. Methods: A total 210, 19 weeks old aged ISA Brown layers were randomly assigned into 5 equal treatment groups, with 7 replications of 6 hens each. Dietary treatment included a standard basal diet as control; antibiotic (0.05% flavomycin); 2% FVW; 4% FVW; and 6% FVW. The experimental duration was 10 weeks. Results: There was no significant differences (p>0.05) on hen day egg production, egg weight, egg mass, feed intake, and feed conversion ratio (FCR) among experimental groups. Unmarketable eggs were significantly lower (p<0.05) both in 4% FVW and 6% FVW fed groups than control group. The calcium retention and calcium in egg shell deposition were significantly higher (p<0.05) in FVW inclusion groups than control and antibiotic groups. Antibody titers against Newcastle diseases were significantly higher (p<0.05) in 6% FVW fed group (except combined with 4% FVW at day 147) and infectious bronchitis were significantly higher (p<0.05) in FVW fed groups (except 2% FVW and 4% FVW at day 161) than control and antibiotic groups. Serum immunoglobulin sIgA was significantly higher (p<0.05) in all levels of FVW and IgG was significantly higher (p<0.05) in 4% FVW than control and antibiotic groups. Serum cytokine concentration interleukin-2 (IL-2) was significantly higher (p<0.05) in 6% FVW; IL-6 and tumor necrotic $factor-{\alpha}$ were significantly higher (p<0.05) both in 4% FVW and 6% FVW than control and antibiotic groups; IL-4 was significantly higher (p<0.05) in antibiotic, 2% FVW and 4% FVW fed groups than control. Conclusion: F. velutipes mushroom waste can be used as a novel substitute for antibiotic for organic egg production and sound health status in laying hens.

A Physiologically Based Pharmacokinetic Model for Absorption and Distribution of Imatinib in Human Body

Mohammad Mahfuz Chowdhury,김도현,안정근 대한화학회 2011 Bulletin of the Korean Chemical Society Vol.32 No.11

A whole body physiologically based pharmacokinetic (PBPK) model was applied to investigate absorption,distribution, and physiologic variations on pharmacokinetics of imatinib in human body. Previously published pharmacokinetic data of the drug after intravenous (i.v.) infusion and oral administration were simulated by the PBPK model. Oral dose absorption kinetics were analyzed by adopting a compartmental absorption and transit model in gut section. Tissue/plasma partition coefficients of drug after i.v. infusion were also used for oral administration. Sensitivity analysis of the PBPK model was carried out by taking parameters that were commonly subject to variation in human. Drug concentration in adipose tissue was found to be higher than those in other tissues, suggesting that adipose tissue plays a role as a storage tissue for the drug. Variations of metabolism in liver, body weight, and blood/plasma partition coefficient were found to be important factors affecting the plasma concentration profile of drug in human body.

Bangladeshi Science Lecturers’ Belief and perception of their Practices on Universal Design for Learning

( Md Shohag Mahfuz ),( Jeongho Cha ) 대구대학교 한국특수교육문제연구소 2018 한국특수교육문제연구소 학술대회발표자료집 Vol.2018 No.1

Nowadays in Bangladesh students with diversified learners are increasing in prevalence to higher education settings, and there is no single method of teaching that can meet the needs of all students. Instead, multiple, flexible methods of instruction are needed. Thus, it is very important for university teachers specially science lecturers to give a broad awareness to students with disability and inclusive teaching practices based on the reliance of Universal Design for Learning (UDL) strategies. In this research, we surveyed Bangladeshi University Science Lecturers belief and perception toward their practices on diversified students’ disability related topics and inclusive teaching practices and their implementation of mentioned practices by using the Inclusive Teaching Strategies Inventory (ITST). The ITSI consist of six subscales representing the following items: a) Accommodations (ACC), b) Accessible Course Materials (ACM), c) Course Modifications (CM), d) Inclusive Lecture Strategies (ILS), e) Inclusive Class(IC), and f) Inclusive Assessment (IA). The ITSI contains two feedback categories which allow for an evaluation of both belief and perception of lectures’ practice on UDL in the six areas. From the analysis it was revealed that in the subscale ILS Lectures’ belief and their self-reported actions were the highest. Followed by ILS they had given more emphasis on the subscale ACC, where their level of belief and actions were comparatively higher than other subscales. Although Bangladeshi science lecturers’ belief and their self-reported action were almost same on the subscales ACM, IC and IA but the lowest perceptions were found in the subscale CM and in general, it was revealed that lecturers’ belief comparatively higher than their action in all the items.

On the Performance of Indoor Path Loss for Ultra Wideband Communications

Mohammad Upal Mahfuz,Kazi M. Ahmed 한국통신학회 2005 한국통신학회 학술대회 및 강연회 Vol.2005 No.4

A Physiologically Based Pharmacokinetic Model for Absorption and Distribution of Imatinib in Human Body

Chowdhury, Mohammad Mahfuz,Kim, Do-Hyun,Ahn, Jeong-Keun Korean Chemical Society 2011 Bulletin of the Korean Chemical Society Vol.32 No.11

A whole body physiologically based pharmacokinetic (PBPK) model was applied to investigate absorption, distribution, and physiologic variations on pharmacokinetics of imatinib in human body. Previously published pharmacokinetic data of the drug after intravenous (i.v.) infusion and oral administration were simulated by the PBPK model. Oral dose absorption kinetics were analyzed by adopting a compartmental absorption and transit model in gut section. Tissue/plasma partition coefficients of drug after i.v. infusion were also used for oral administration. Sensitivity analysis of the PBPK model was carried out by taking parameters that were commonly subject to variation in human. Drug concentration in adipose tissue was found to be higher than those in other tissues, suggesting that adipose tissue plays a role as a storage tissue for the drug. Variations of metabolism in liver, body weight, and blood/plasma partition coefficient were found to be important factors affecting the plasma concentration profile of drug in human body.

Assessment of radionuclides from coal-fired brick kilns on the outskirts of Dhaka city and the consequent hazards on human health and the environment

Siraz M.M. Mahfuz,Rakib M.D.A.,Alam M.S.,Al Mahmud Jubair,Rashid Md Bazlar,Khandaker Mayeen Uddin,Islam Md. Shafiqul,Yeasmin S. 한국원자력학회 2023 Nuclear Engineering and Technology Vol.55 No.8

In a first-of-its-kind study, terrestrial radionuclide concentrations were measured in 35 topsoil samples from the outskirts of Dhaka using HPGe gamma-ray spectrometry to assess the radiological consequences of such a vast number of brick kilns on the plant workers, general as well as dwelling environment. The range of activity concentrations of 226Ra, 232Th, and 40K is found at 19 ± 3.04 to 38 ± 4.94, 39 ± 5.85 to 57 ± 7.41, and (430 ± 51.60 to 570 ± 68.40) Bq/kg, respectively. 232Th and 40K concentrations were higher than the global averages. Bottom ash deposition in lowlands, fly ash buildup in soils, and the fallout of micro-particles are all probable causes of the elevated radioactivity levels. 137Cs was found in the sample, which indicates the migration of 137Cs from nuclear accidents or nuclear fallout, or the contamination of feed coal. Although the effective dose received by the general public was below the recommended dose limit but, most estimates of hazard parameters surpass their respective population weighted global averages, indicating that brick kiln workers and nearby residents are not safe due to prolonged exposures to terrestrial radiation. In addition, the soil around sampling sites is found to be unsuitable for agricultural purposes.

Deep convolutional neural networks based ECG beats classifi cation to diagnose cardiovascular conditions

Md. Rashed-Al-Mahfuz,Mohammad Ali Moni,Pietro Lio’,Sheikh Mohammed Shariful Islam,Shlomo Berkovsky,Matloob Khushi,Julian M. W. Quinn 대한의용생체공학회 2021 Biomedical Engineering Letters (BMEL) Vol.11 No.2

Medical practitioners need to understand the critical features of ECG beats to diagnose and identify cardiovascular conditionsaccurately. This would be greatly facilitated by identifying the signifi cant features of frequency components in temporalECG wave-forms using computational methods. In this study, we have proposed a novel ECG beat classifi er based ona customized VGG16-based Convolution Neural Network (CNN) that uses the time-frequency representation of temporalECG, and a method to identify the contribution of interpretable ECG frequencies when classifying based on the SHapleyAdditive exPlanations (SHAP) values. We applied our model to the MIT-BIH arrhythmia dataset to classify the ECG beatsand to characterise of the beats frequencies. This model was evaluated with two advanced time-frequency analysis methods. Our results indicated that for 2-4 classes our proposed model achieves a classifi cation accuracy of 100% and for 5 classes itachieves a classifi cation accuracy of 99.90%. We have also tested the proposed model using premature ventricular contractionbeats from the American Heart Association (AHA) database and normal beats from Lobachevsky University Electrocardiographydatabase (LUDB) and obtained a classifi cation accuracy of 99.91% for the 5-classes case. In addition, SHAP valueincreased the interpretability of the ECG frequency features. Thus, this model could be applicable to the automation of thecardiovascular diagnosis system and could be used by clinicians.