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Article ; Online: Integrated bioinformatics analysis reveals upregulated extracellular matrix hub genes in pancreatic cancer: Implications for diagnosis, prognosis, immune infiltration, and therapeutic strategies.

Mogal, Md Roman / Jame, Jasmin Akter / Sohel, Md / Mozibullah, Md / Mahmod, Md Rashel / Junayed, Asadullah / Kar, Newton / Arbia, Lubatul / Al Mamun, Abdullah / Sikder, Md Asaduzzaman

Cancer reports (Hoboken, N.J.)

2024 Volume 7, Issue 4, Page(s) e2059

Abstract: Background: Pancreatic cancer (PC) stands out as one of the most formidable malignancies and exhibits an exceptionally unfavorable clinical prognosis due to the absence of well-defined diagnostic indicators and its tendency to develop resistance to ... ...

Abstract	Background: Pancreatic cancer (PC) stands out as one of the most formidable malignancies and exhibits an exceptionally unfavorable clinical prognosis due to the absence of well-defined diagnostic indicators and its tendency to develop resistance to therapeutic interventions. The primary objective of this present study was to identify extracellular matrix (ECM)-related hub genes (HGs) and their corresponding molecular signatures, with the intent of potentially utilizing them as biomarkers for diagnostic, prognostic, and therapeutic applications. Methods: Three microarray datasets were sourced from the NCBI database to acquire upregulated differentially expressed genes (DEGs), while MatrisomeDB was employed for filtering ECM-related genes. Subsequently, a protein-protein interaction (PPI) network was established using the STRING database. The created network was visually inspected through Cytoscape, and HGs were identified using the CytoHubba plugin tool. Furthermore, enrichment analysis, expression pattern analysis, clinicopathological correlation, survival analysis, immune cell infiltration analysis, and examination of chemical compounds were carried out using Enrichr, GEPIA2, ULCAN, Kaplan Meier plotter, TIMER2.0, and CTD web platforms, respectively. The diagnostic and prognostic significance of HGs was evaluated through the ROC curve analysis. Results: Ten genes associated with ECM functions were identified as HGs among 131 DEGs obtained from microarray datasets. Notably, the expression of these HGs exhibited significantly (p < 0.05) higher in PC, demonstrating a clear association with tumor advancement. Remarkably, higher expression levels of these HGs were inversely correlated with the likelihood of patient survival. Moreover, ROC curve analysis revealed that identified HGs are promising biomarkers for both diagnostic (AUC > 0.75) and prognostic (AUC > 0.64) purposes. Furthermore, we observed a positive correlation between immune cell infiltration and the expression of most HGs. Lastly, our study identified nine compounds with significant interaction profiles that could potentially act as effective chemical agents targeting the identified HGs. Conclusion: Taken together, our findings suggest that COL1A1, KRT19, MMP1, COL11A1, SDC1, ITGA2, COL1A2, POSTN, FN1, and COL5A1 hold promise as innovative biomarkers for both the diagnosis and prognosis of PC, and they present as prospective targets for therapeutic interventions aimed at impeding the progression PC.
MeSH term(s)	Humans ; Gene Expression Profiling ; Biomarkers, Tumor/analysis ; Prognosis ; Pancreatic Neoplasms/diagnosis ; Pancreatic Neoplasms/genetics ; Pancreatic Neoplasms/therapy ; Computational Biology ; Extracellular Matrix/genetics
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2024-04-18
Publishing country	United States
Document type	Journal Article
ISSN	2573-8348
ISSN (online)	2573-8348
DOI	10.1002/cnr2.2059
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Development and characterization of eco-friendly starch-based plastic reinforcing tea for packaging applications

Sikder Muhammad Khalid Hossain / Md Ruhul Amin / Md Arefin Kowser / Mohammad Asaduzzaman Chowdhury / Nayem Hossain

Current Research in Green and Sustainable Chemistry, Vol 7, Iss , Pp 100374- (2023)

2023

Abstract: Petrochemical-based plastics are posing a threat to human existence because of their toxic nature and slow biodegradation rate. However, biodegradable plastics manufactured from natural ingredients are showing hope. The current work deals with developing ...

Abstract	Petrochemical-based plastics are posing a threat to human existence because of their toxic nature and slow biodegradation rate. However, biodegradable plastics manufactured from natural ingredients are showing hope. The current work deals with developing and characterising starch-based bio-plastic where white vinegar and glycerol have been used as matrix materials and tea has been used as filler material. The developed bio-plastic samples were characterized by soil biodegradation test, Mechanical test, Fourier Transformed Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM), Thermogravimetric analysis (TGA) and Differential Scanning Calorimetry (DSC) analyses. More than 60% of degradation occurred within 28 days. The results proved that the bio-plastic synthesized using used tea has higher tensile strength than those synthesized using black tea. Higher melting point and glass transition temperature were also obtained from the sample synthesized using used tea, confirmed by TGA and DSC analysis. The FTIR analysis confirmed the presence of various organic functional groups. The obtained results were compared with the results available in the literature. Based on the results, the developed bio-plastic samples can be successfully used in packaging applications.
Keywords	Bioplastic ; Used tea leaves ; Degradable ; Environmental impact ; Morphology ; Chemistry ; QD1-999
Subject code	621
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Common genetic aspects between COVID-19 and sarcoidosis: A network-based approach using gene expression data.

Mogal, Md Roman / Sompa, Sagarika Adhikary / Junayed, Asadullah / Mahmod, Md Rashel / Abedin, Md Zainul / Sikder, Md Asaduzzaman

Biochemistry and biophysics reports

2022 Volume 29, Page(s) 101219

Abstract: The pandemic situation of novel coronavirus disease 2019 (COVID-19) is a global threat on our current planet, with its rapid spread and high mortality rate. Sarcoidosis patients are at high risk to COVID-19 severity for having lung injuries as well as ... ...

Abstract	The pandemic situation of novel coronavirus disease 2019 (COVID-19) is a global threat on our current planet, with its rapid spread and high mortality rate. Sarcoidosis patients are at high risk to COVID-19 severity for having lung injuries as well as treating with immunosuppressive agents. So, physicians are in dilemma whether they should use immunosuppressive agents or not for the patients with sarcoidosis history and COVID-19 infection. Therefore, common factors should be identified to provide effective treatment. For determining the common genes between COVID-19 and sarcoidosis, GSE164805 and GSE18781 were retrieved from the Gene Expression Omnibus (GEO) database. Common upregulated genes were identified by using R language to investigate their involved pathways and gene ontologies (GO). With the aid of the STRING Cytoscape plugin tool, protein-protein interactions (PPIs) network was constructed. From the PPIs network, Hub genes and essential modules were detected by using Cytohubba, and MCODE respectively. For hub genes, TFs, TFs-miRNA, and drug, interaction networks were built through the NetworkAnalyst web platform. A total of 34 common upregulated genes were identified and among them, five hub genes, including TET2, MUC5AC, VDR, NFE2L2, and BCL6 were determined. In addition, a cluster having VDR and NFE2L2 was detected from the PPIs network. Moreover, 32 transcription factors and 9 miRNA were recognized for hub genes. Furthermore, vitamin D and some of its analogous compounds were obtained from the drug interaction network. In conclusion, hub genes identified in this study might have potential roles in modulating COVID-19 infection and sarcoidosis. However, further studies are required to corroborate this study.
Language	English
Publishing date	2022-02-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2831046-9
ISSN	2405-5808 ; 2405-5808
ISSN (online)	2405-5808
ISSN	2405-5808
DOI	10.1016/j.bbrep.2022.101219
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Article ; Online: Common genetic aspects between COVID-19 and sarcoidosis

Md. Roman Mogal / Sagarika Adhikary Sompa / Asadullah Junayed / Md. Rashel Mahmod / Md. Zainul Abedin / Md. Asaduzzaman Sikder

Biochemistry and Biophysics Reports, Vol 29, Iss , Pp 101219- (2022)

A network-based approach using gene expression data

2022

Abstract	The pandemic situation of novel coronavirus disease 2019 (COVID-19) is a global threat on our current planet, with its rapid spread and high mortality rate. Sarcoidosis patients are at high risk to COVID-19 severity for having lung injuries as well as treating with immunosuppressive agents. So, physicians are in dilemma whether they should use immunosuppressive agents or not for the patients with sarcoidosis history and COVID-19 infection. Therefore, common factors should be identified to provide effective treatment. For determining the common genes between COVID-19 and sarcoidosis, GSE164805 and GSE18781 were retrieved from the Gene Expression Omnibus (GEO) database. Common upregulated genes were identified by using R language to investigate their involved pathways and gene ontologies (GO). With the aid of the STRING Cytoscape plugin tool, protein-protein interactions (PPIs) network was constructed. From the PPIs network, Hub genes and essential modules were detected by using Cytohubba, and MCODE respectively. For hub genes, TFs, TFs-miRNA, and drug, interaction networks were built through the NetworkAnalyst web platform. A total of 34 common upregulated genes were identified and among them, five hub genes, including TET2, MUC5AC, VDR, NFE2L2, and BCL6 were determined. In addition, a cluster having VDR and NFE2L2 was detected from the PPIs network. Moreover, 32 transcription factors and 9 miRNA were recognized for hub genes. Furthermore, vitamin D and some of its analogous compounds were obtained from the drug interaction network. In conclusion, hub genes identified in this study might have potential roles in modulating COVID-19 infection and sarcoidosis. However, further studies are required to corroborate this study.
Keywords	COVID-19 ; Sarcoidosis ; Protein-protein interaction ; Hub genes ; Drug network ; Vitamin D ; Biology (General) ; QH301-705.5 ; Biochemistry ; QD415-436
Subject code	572 ; 570
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Human tissue banking in Bangladesh: hope for the patients of massive burns, surgical wound and bone associated complications.

Rahman, Md Shaifur / Akhtar, Naznin / Hasan, Md Zahid / Asaduzzaman, Sikder M

International journal of burns and trauma

2019 Volume 9, Issue 2, Page(s) 23–27

Abstract: Each year throughout Bangladesh, thousands of people suffering from massive burns and surgical wounds require amniotic grafts for transplantation. Additionally, the stricken persons of the country have to embrace bone associated disability for the whole ... ...

Abstract	Each year throughout Bangladesh, thousands of people suffering from massive burns and surgical wounds require amniotic grafts for transplantation. Additionally, the stricken persons of the country have to embrace bone associated disability for the whole life due to traumatic complications need bone graft to treat. As a result, these two problems are the largest financial burden as this situation not only affect the family of patients but also cripple down national economy. However, institute of tissue banking in Bangladesh has undertaken the service program on the processing, preservation and clinical applications of amnion membrane and bone graft for rehabilitative surgery. Importantly, in recent years, this institute has started cranial bone autograft processing and transplantation. In accidental cases such as head injury, it is difficult to provide suitable cranial bone allograft according to demand. In this situation, injured cranial bone of the patient is being transported to the lab of the institute, where the scientist, tissue banker and medic work together immediately to process the cranial bone and sterilize by gamma radiation; and after quality assurance, the processed cranial bone autograft is being supplied for replacement surgery. The use of irradiated amnion and bone allografts and cranial bone autograft in reconstructive surgery restore normalcy to lives of many patients from disabilities. This tissue bank is based on finding and obtaining qualified donors from the community and a demand for tissue grafts from the hospitals. Although growing needs for tissue transplantation but raw and processed tissue grafts preservation and banking braces enormous logistical limitations. The only human tissue bank in Bangladesh, however, ensures the availability of tissue allografts of high quality and acceptability to the recipients for rehabilitative surgery for a decade, regardless patients' socio-economic status.
Language	English
Publishing date	2019-04-15
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2664425-3
ISSN	2160-2026
ISSN	2160-2026
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Article ; Online: A Computational Approach to Justifying Stratifin as a Candidate Diagnostic and Prognostic Biomarker for Pancreatic Cancer.

Mogal, Md Roman / Junayed, Asadullah / Mahmod, Md Rashel / Sompa, Sagarika Adhikary / Lima, Suzana Afrin / Kar, Newton / TasminaTarin / Khatun, Marina / Zubair, Md Abu / Sikder, Md Asaduzzaman

BioMed research international

2022 Volume 2022, Page(s) 1617989

Abstract: Pancreatic cancer (PC) is considered a silent killer because it does not show specific symptoms at an early stage. Thus, identifying suitable biomarkers is important to avoid the burden of PC. Stratifin (SFN) encodes the 14-3- ... ...

Abstract	Pancreatic cancer (PC) is considered a silent killer because it does not show specific symptoms at an early stage. Thus, identifying suitable biomarkers is important to avoid the burden of PC. Stratifin (SFN) encodes the 14-3-3
MeSH term(s)	Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Computational Biology ; Gene Expression Regulation, Neoplastic ; Humans ; Pancreatic Neoplasms/diagnosis ; Pancreatic Neoplasms/genetics ; Prognosis ; Pancreatic Neoplasms
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2022-05-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2022/1617989
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Development and Characterization of Bioplastic Synthesized from Ginger and Green Tea for Packaging Applications

Md. Arefin Kowser / Sikder Muhammad Khalid Hossain / Md. Ruhul Amin / Mohammad Asaduzzaman Chowdhury / Nayem Hossain / Osama Madkhali / Md. Rezaur Rahman / Muhammad Tariq Saeed Chani / Abdullah M. Asiri / Jamal Uddin / Mohammed M. Rahman

Journal of Composites Science, Vol 7, Iss 107, p

2023 Volume 107

Abstract: The world is suffering from heavy pollution because of synthetic petrochemical plastic used in our daily activities. A possible solution is the use of bioplastic synthesized from natural renewable resources. The present work investigates the development ... ...

Abstract	The world is suffering from heavy pollution because of synthetic petrochemical plastic used in our daily activities. A possible solution is the use of bioplastic synthesized from natural renewable resources. The present work investigates the development and characterization of polymer bioplastic using ginger tea and green tea to decrease the adverse effect of petrochemical plastic waste for versatile applications. Two kinds of bioplastic samples were produced with two types of tea, ginger tea and green tea, using glycerol, vinegar, starch, and water. SEM (scanning electron microscopy), FTIR (Fourier transformed infrared spectroscopy), mechanical (tensile), TGA (thermogravimetric analysis), DSC (differential scanning calorimetry), and time tests of bioplastic degradation analysis were carried out to evaluate the morphological, mechanical, and thermal behaviors of the synthesized tea bioplastics. The research result showed ginger tea bioplastic had a maximum tensile strength of 2.9 MPa and a minimum elongation of 7.46 mm. More than 78% of degradation occurred in ginger bioplastic within 30 days. Compatible thermal and morphological characteristics are also observed in the prepared bioplastic samples.
Keywords	bioplastic ; ginger tea ; green tea ; environmental remediation ; morphology ; Technology ; T ; Science ; Q
Subject code	669
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The impact of wood dust on pulmonary function and blood immunoglobulin E, erythrocyte sedimentation rate, and C- reactive protein: A cross-sectional study among sawmill workers in Tangail, Bangladesh.

Mogal, Md Roman / Islam, Md Didarul / Hasan, Md Ikbal / Junayed, Asadullah / Sompa, Sagarika Adhikary / Mahmod, Md Rashel / Akter, Aklima / Abedin, Md Zainul / Sikder, Md Asaduzzaman

Health science reports

2022 Volume 5, Issue 3, Page(s) e646

Abstract: Background and aims: Occupational exposure to wood dust leads to lung function abnormalities that are prominent causes of morbidity and disability of sawmill workers. The adverse respiratory effects of wood dust in sawmills have not been studied ... ...

Abstract	Background and aims: Occupational exposure to wood dust leads to lung function abnormalities that are prominent causes of morbidity and disability of sawmill workers. The adverse respiratory effects of wood dust in sawmills have not been studied thoroughly in Bangladesh. This study aimed to investigate the effect of wood dust on the respiratory health of sawmill workers compared to controls as well as to determine the association of wood dust-exposing effects with inflammatory blood biomarkers, such as immunoglobulin E (IgE), erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP). Methods: This cross-sectional study included 100 sawmill workers from 25 distinct sawmills in various areas of Tangail, Bangladesh as well as 100 healthy volunteers who were adopted as a control group. Questionaries' survey and pulmonary function tests were performed face to face. Furthermore, after performing lung function tests, blood was drawn for further IgE, ESR, and CRP analyses. Results: Respiratory symptoms including breathlessness (32%), coughing (39%), sneezing (43%), chest tightness (30%), and itching (40%) were significantly higher in sawmill workers compared with control. Besides, sawmill workers' exposure to wood dust revealed a significantly lower level of spirometry parameters (forced vital capacity [FVC], FVC (%), forced expiratory volume in 1 s [FEV1], FEV1 (%), peak expiratory flow [PEF], PEF (%), FEV1/FVC (%), FEF25, FEF75, and FEF2575) compared with control and these spirometry parameters decreased with the increasing length of service. Moreover, a significantly higher level of IgE was observed in sawmill workers (290.90 ± 39.49) than in the control (120.95 ± 23.00). The high level of IgE suggests that the lower pulmonary function may be linked to allergic responses to wood dust among sawmill workers. Conclusion: This study suggested that exposure to wood dust can cause impairment of respiratory function along with high IgE levels.
Language	English
Publishing date	2022-05-22
Publishing country	United States
Document type	Journal Article
ISSN	2398-8835
ISSN (online)	2398-8835
DOI	10.1002/hsr2.646
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Article ; Online: Association between ankyrin 2 gene and breast cancer progression

Md. Roman Mogal / Md. Rashel Mahmod / Sagarika Adhikary Sompa / Asadullah Junayed / Md. Zainul Abedin / Md. Asaduzzaman Sikder

Informatics in Medicine Unlocked, Vol 25, Iss , Pp 100663- (2021)

A preliminary computational assessment using the database approach

2021

Abstract: Breast cancer (BC) is considered the second leading cause of cancer-related death in women. Accurate diagnosis is thus of utmost importance to avoid the burden of BC. Ankyrin 2 (ANK2) encodes the structural membrane adapter protein ankyrin-B, which is ... ...

Abstract	Breast cancer (BC) is considered the second leading cause of cancer-related death in women. Accurate diagnosis is thus of utmost importance to avoid the burden of BC. Ankyrin 2 (ANK2) encodes the structural membrane adapter protein ankyrin-B, which is ubiquitously expressed in the human body. In this study, bioinformatics tools were used to determine whether ANK2 could be used as a diagnostic and prognostic biomarker in BC. ANK2 expression was analyzed using ONCOMINE, UALCAN, GEPIA2, and GENT2. Data from these servers showed the downregulated expression of ANK2 in BC relative to that in normal tissue. Further, downregulated ANK2 expression was found in such conditions as estrogen receptor-negative, human epidermal growth factor receptor 2-positive, positive nodal status, basal-like tumor, and triple-negative breast cancer, according to the data from the bc-GenExMiner v4.5 server. Analysis of 18 BC studies retrieved from the cBioPortal database revealed 88 missense mutations with 0.46%–5.09% copy number alterations in the ANK2 gene sequence. Additionally, a positive correlation between downregulated ANK2 expression and reduced survival probability of BC patients was revealed by a Kaplan–Meier plotter. Moreover, chordin-like 1, a tumor suppressor, was highly co-expressed with ANK2, as shown by the ONCOMINE, UCSC Xena, and GEPIA2 tools. The signaling pathways and gene ontologies of ANK2 and its co-expressed genes were identified using the Enrichr platform. The present results suggest that the ANK2 may serve as a biomarker for diagnosis, prognosis, and therapeutic purposes in BC.
Keywords	ANK2 ; Biomarker ; Breast cancer ; CHRDL1 ; Bioinformatics tools ; Gene downregulation ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	616
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Amnion and collagen-based blended hydrogel improves burn healing efficacy on a rat skin wound model in the presence of wound dressing biomembrane.

Rana, Md Masud / Rahman, Md Shaifur / Ullah, Md Akib / Siddika, Ayesha / Hossain, Md Liakat / Akhter, Md Shamim / Hasan, Md Zahid / Asaduzzaman, Sikder M

Bio-medical materials and engineering

2020 Volume 31, Issue 1, Page(s) 1–17

Abstract: Background: A burn wound is one of the most frequent and devastating injuries for patients which requires extensive care. Early treatment of burn wounds improves healing significantly.: Objective: This study was designed to investigate the efficacy ... ...

Abstract	Background: A burn wound is one of the most frequent and devastating injuries for patients which requires extensive care. Early treatment of burn wounds improves healing significantly. Objective: This study was designed to investigate the efficacy of amnion and collagen-based hydrogels on cutaneous burn wound healing in rats with covering membrane. Methods: We prepared a novel cell free hydrogel comprising human amnion, rabbit collagen, carboxymethyl cellulose sodium salt, citric acid, methyl paraben, propyl paraben, glycerin and triethanol amine. The wound covering membrane was developed from rabbit collagen and prawn shell chitosan. Beside swelling ratio, water absorption, equilibrium water content, gel fraction and spreadability analysis, in vitro cytotoxicity and biocompatibility tests were performed for the formulated hydrogels. Following the skin irritation study, second-degree burns were created on the dorsal region of the rats and the gels were applied with/without covering membrane to study the wound contraction and re-epithelialization period. Results: The formulated hydrogels were observed non-cytotoxic and compatible with human blood cells. No erythema and edema were found in skin irritation assay confirming the safety and applicability. Hydrogel consisting in a combination of amnion and collagen demonstrated significantly rapid wound healing, driven by complete re-epithelialization (16.75 ± 0.96 days) and closure by wound contraction (72 ± 3.27%, P < 0.0000009) when wound dressing membrane was used, whereas this gel alone healed about 62.5 ± 4.43% (P < 0.00001) and required 18.75 ± 0.50 days to complete re-epithelialization. Additionally, the gel with covering membrane treated group had maximum average body weight, food and water intake. Conclusion: The amnion and collagen-based blended gel offers alternative possibilities to treat skin wounds when covered with film, which could overcome the limitations associated with modern therapeutic products such as high costs, long manufacturing times, complexities, storing, and presence of living biomaterials.
MeSH term(s)	Amnion/chemistry ; Animals ; Bandages ; Biocompatible Materials/chemistry ; Biocompatible Materials/therapeutic use ; Biological Dressings ; Burns/pathology ; Burns/therapy ; Collagen/chemistry ; Disease Models, Animal ; Female ; Humans ; Hydrogels/chemistry ; Hydrogels/therapeutic use ; Materials Testing ; Pregnancy ; Rabbits ; Rats ; Rats, Wistar ; Wound Healing
Chemical Substances	Biocompatible Materials ; Hydrogels ; Collagen (9007-34-5)
Language	English
Publishing date	2020-03-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1066216-9
ISSN	1878-3619 ; 0959-2989
ISSN (online)	1878-3619
ISSN	0959-2989
DOI	10.3233/BME-201076
Database	MEDical Literature Analysis and Retrieval System OnLINE

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