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Article ; Online: Bovine serum albumin prevents human hemoglobin aggregation and retains its chaperone-like activity.

Khan, Sadaf / Naeem, Aabgeena

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 1, Page(s) 346–361

Abstract: This study investigates the ability of bovine serum albumin (BSA) to act as an extracellular chaperone (EC) on human hemoglobin (Hb) at a pH of 7.4. The best temperature for studying this behavior was determined by analyzing Hb's aggregation kinetics at ... ...

Abstract	This study investigates the ability of bovine serum albumin (BSA) to act as an extracellular chaperone (EC) on human hemoglobin (Hb) at a pH of 7.4. The best temperature for studying this behavior was determined by analyzing Hb's aggregation kinetics at multiple temperatures. 55 °C was chosen as the optimal temperature for forming Hb amyloids. BSA was then tested at various concentrations (20-100 μM) to assess its chaperone-like activity on Hb at 55 °C. At a concentration of 100 μM, BSA exhibits chaperone-like activity with a client protein:BSA ratio of 1:10. The high ratio implies that the chaperone activity of BSA is favored by the effects of macromolecular crowding. The results showed that BSA has the potential to inhibit Hb's dissociation into alpha and beta subunits and protein aggregation by inhibiting secondary nucleation. BSA also causes the depolymerization of fibrils over time. The results were validated using molecular docking and all-atom molecular dynamics simulations. MD analysis such as RMSD, RMSF, Rg, SASA, Hydrogen bond, PCA, Free energy landscape (FEL) revealed that the stability of hemoglobin is greater when it is bound to BSA compared to unbound state. The study suggests that BSA can potentially bind to Hb dimers and reduce excitonic interactions, which reduces Hb aggregation. These results are consistent with the aggregation kinetics experiments.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Binding Sites ; Protein Binding ; Molecular Docking Simulation ; Serum Albumin, Bovine/chemistry ; Amyloid/metabolism ; Hemoglobins/metabolism ; Thermodynamics
Chemical Substances	Serum Albumin, Bovine (27432CM55Q) ; Amyloid ; Hemoglobins
Language	English
Publishing date	2023-03-28
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2192802
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Article ; Online: Protective role of chlorogenic acid in preserving cytochrome-c stability against HFIP-induced molten globule state at physiological pH.

Khan, Sadaf / Ansari, Bushra / Ansari, Neha Kausar / Naeem, Aabgeena

International journal of biological macromolecules

2024 Volume 261, Issue Pt 2, Page(s) 129845

Abstract: Numerous neurodegenerative disorders are characterized by protein misfolding and aggregation. The mechanism of protein aggregation is intricate, and it is very challenging to study at cellular level. Inhibition of protein aggregation by interfering with ... ...

Abstract	Numerous neurodegenerative disorders are characterized by protein misfolding and aggregation. The mechanism of protein aggregation is intricate, and it is very challenging to study at cellular level. Inhibition of protein aggregation by interfering with its pathway is one of the ways to prevent neurodegenerative diseases. In the present work, we have evaluated the protective effect of a polyphenol compound chlorogenic acid (CGA) on the native and molten globule state of horse heart cytochrome c (cyt c). A molten globule state of this heme protein was achieved in the presence of fluorinated alcohol 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) at physiological pH, as studied by UV-Vis absorption, circular dichroism, intrinsic and ANS fluorescence. We found that at 50 % (v/v) HFIP, the native cyt c transformed into a molten globule state. The same techniques were also used to analyze the protective effect of CGA on the molten globule state of cyt c, and the results show that the CGA prevented the molten globular state and retained the protein close to the native state at 1:1 protein:CGA sub molar ratio. Molecular dynamics study also revealed that CGA retains the stability of cyt c in HFIP medium by preserving it in an intermediate state close to native conformation.
MeSH term(s)	Animals ; Horses ; Cytochromes c/chemistry ; Chlorogenic Acid ; Protein Folding ; Protein Aggregates ; Circular Dichroism ; Hydrogen-Ion Concentration ; Protein Conformation ; Protein Denaturation ; Hydrocarbons, Fluorinated ; Propanols
Chemical Substances	hexafluoroisopropanol (3D632GYQ50) ; Cytochromes c (9007-43-6) ; Chlorogenic Acid (318ADP12RI) ; Protein Aggregates ; Hydrocarbons, Fluorinated ; Propanols
Language	English
Publishing date	2024-02-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.129845
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Article: Adaptation of Research Project Requirement at Pharmacy Undergraduate Studies: Students' Perception, Attitude, and Experiences.

Rahim, Najia / Rafiq, Kiran / Nesar, Shagufta / Naeem, Sadaf / Anjum, Fakhsheena / Mughal, Muhammad Azhar

Scientifica

2024 Volume 2024, Page(s) 8144325

Abstract: Objective: To determine the final year pharmacy undergraduate students' attitudes toward research after completing a research project.: Methods: A research project was introduced in the final year of the PharmD program in January 2022. After a period ...

Abstract	Objective: To determine the final year pharmacy undergraduate students' attitudes toward research after completing a research project. Methods: A research project was introduced in the final year of the PharmD program in January 2022. After a period of one year, in Janurary 2023, students submitted their final research to the faculty members. The survey was conducted from 1st March to 30st April 2023 using a study tool that contained items asking students' demographic, their research perceptions, attitude and experience, and also motivation/barriers faced during the research project. Descriptive and Results: Majority of the students (93.8%) agreed regarding the significance of research in the pharmacy profession. Students were found to have their projects a worthwhile learning opportunity (94.2%). Students' motivation to execute research project stems from mandatory curriculum courses, improving clinical or hospital pharmacist training and fulfilling research skills (90%). Barriers hindered include lack of training, time, and patient follow-up (approximately 70%). Conclusion: The current study's finding was concluded with the fact that research is a valuable component of a well-rounded education and can enhance a pharmacist's skills. However, they need a combination of formal education and practical experience to pursue a profession in pharmacy.
Language	English
Publishing date	2024-04-02
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	2672321-9
ISSN	2090-908X
ISSN	2090-908X
DOI	10.1155/2024/8144325
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Article ; Online: Molecular Dynamic Simulations Unravel the Underlying Impact of Missense Mutation in Autoimmunity Gene

Pasha, Usman / Nisar, Haseeb / Nisar, Hajira / Abid, Rizwan / Ashraf, Naeem Mahmood / Sadaf, Saima

Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research

2023 Volume 43, Issue 3, Page(s) 121–132

Abstract: Genetic mutations in various proteins have been implicated with increased risk or severity of rheumatoid arthritis (RA) in different population groups. In the present case-control study, we have investigated the risk association of single nucleotide ... ...

Abstract	Genetic mutations in various proteins have been implicated with increased risk or severity of rheumatoid arthritis (RA) in different population groups. In the present case-control study, we have investigated the risk association of single nucleotide mutations present in some of the highly reported anti-inflammatory proteins and/or cytokines, with RA susceptibility in the Pakistani subjects. The study involves 310 ethnically and demographically similar participants from whom blood samples were taken and processed for DNA extraction. Through extensive data mining, 5 hotspot mutations reported in 4 genes, that is, interleukin (
MeSH term(s)	Humans ; Arthritis, Rheumatoid/genetics ; Autoimmune Diseases ; Autoimmunity/genetics ; Case-Control Studies ; DNA ; Gene Frequency ; Genetic Predisposition to Disease ; Genotype ; Interleukin-10/genetics ; Molecular Dynamics Simulation ; Mutation, Missense ; Nucleotides ; Polymorphism, Single Nucleotide ; Protein Tyrosine Phosphatase, Non-Receptor Type 22/genetics
Chemical Substances	DNA (9007-49-2) ; Interleukin-10 (130068-27-8) ; Nucleotides ; Protein Tyrosine Phosphatase, Non-Receptor Type 22 (EC 3.1.3.48) ; PTPN22 protein, human (EC 3.1.3.48)
Language	English
Publishing date	2023-02-22
Publishing country	United States
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1226675-9
ISSN	1557-7465 ; 1079-9907
ISSN (online)	1557-7465
ISSN	1079-9907
DOI	10.1089/jir.2022.0216
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Article: Molecular docking analysis of fluoroquinolones and other natural and synthetic compounds with the HCV NS3 helicase.

Ul Haq, Ahtesham / Sheikh, Alisalman / Naeem, Sadaf / Abidi, Syed Hani

Bioinformation

2022 Volume 18, Issue 3, Page(s) 147–154

Abstract: It is of an interest to document the molecular docking analysis of fluoroquinolones and other natural and synthetic compounds with the HCV NS3 helicase. Data shows that three fluoroquinolones interacted with the NS3 helicase in the catalytic region, ... ...

Abstract	It is of an interest to document the molecular docking analysis of fluoroquinolones and other natural and synthetic compounds with the HCV NS3 helicase. Data shows that three fluoroquinolones interacted with the NS3 helicase in the catalytic region, targeting some of the amino acids known to play a crucial role in NS3 helicase activity. Similarly, binding energy shows that the fluoroquinolones were comparable to the thiazolpiperazinyl derivatives, while superior to several of the synthetic and natural derivatives. The results show three fluoroquinolones to be potent helicase inhibitors that can be repurposed as supplemental therapy against HCV especially in cases non-responsive to DAAAs.
Language	English
Publishing date	2022-03-31
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2203786-X
ISSN	0973-2063
ISSN	0973-2063
DOI	10.6026/97320630018147
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Article ; Online: Combined effect of endophytic Bacillus mycoides and rock phosphate on the amelioration of heavy metal stress in wheat plants.

Shahzad, Asim / Aslam, Uzma / Ferdous, Shazia / Qin, Mingzhou / Siddique, Anam / Billah, Motsim / Naeem, Muhammad / Mahmood, Zahid / Kayani, Sadaf

BMC plant biology

2024 Volume 24, Issue 1, Page(s) 125

Abstract: Background: Zinc (Zn) and nickel (Ni) are nutrients that are crucial for plant growth; however, when they are present at higher concentrations, they can cause toxicity in plants. The present study aimed to isolate plant growth promoting endophytic ... ...

Abstract	Background: Zinc (Zn) and nickel (Ni) are nutrients that are crucial for plant growth; however, when they are present at higher concentrations, they can cause toxicity in plants. The present study aimed to isolate plant growth promoting endophytic bacteria from Viburnum grandiflorum and assess its plant and defense promoting potential alone and in combination with RP in zinc (Zn) and nickel (Ni) toxic soil. The isolated endophytic bacteria were identified using 16s rRNA gene sequencing. For the experiment, twelve different treatments were applied using Zn, Ni, isolated endophytic Bacillus mycoides (Accession # MW979613), and rock phosphate (RP). The Ni, Zn and RP were used at the rate of (100 mg/kg) and (0.2 g/kg) respectively. A pot experiment with three replicates of each treatment was conducted using a complete randomized design (CRD). Results: The results indicated that Ni (T5 = seed + 100 mg/kg Ni and T9 = seed + 100 mg/kg Zn) and Zn concentrations inhibited plant growth, but the intensity of growth inhibition was higher in Ni-contaminated soil. Bacillus mycoides and RP at 100 mg/Kg Zn (T12 = inoculated seed + 100 mg/kg Zn + RP0.2 g/kg.) increased the shoot length, leaf width, protein and sugar content by 57%, 13%, 20% and 34%, respectively, compared to the control. The antioxidant enzymes superoxide dismutases (SOD), peroxidase (POD) were decreased in contaminated soil. Furthermore, Ni and Zn accumulation was inhibited in T11 (seed + 100 mg/kg Zn + RP0.2 g/Kg) and T12 (inoculated seed + 100 mg/kg Zn + RP0.2 g/Kg) by 62 and 63% respectively. The Cu, Ca, and K, contents increased by 128, 219 and 85, Mn, Na, and K by 326, 449, and 84% in (T3 = inoculated seed) and (T4 = inoculated seed + RP 0.2 g/Kg) respectively. Conclusions: Ni was more toxic to plants than Zn, but endophytic bacteria isolated from Viburnum grandiflorum, helped wheat (Triticum aestivum) plants and reduced the toxic effects of Ni and Zn. The effect of Bacillus mycoides was more prominent in combination with RP which promoted and suppressed heavy-metal toxicity. The reported combination of Bacillus mycoides and RP may be useful for improving plant growth and overcoming metal stress.
MeSH term(s)	Triticum/genetics ; Nickel/toxicity ; Nickel/metabolism ; Phosphates/metabolism ; RNA, Ribosomal, 16S/genetics ; Metals, Heavy/toxicity ; Metals, Heavy/metabolism ; Zinc/metabolism ; Bacteria/metabolism ; Soil ; Soil Pollutants/metabolism ; Bacillus
Chemical Substances	Nickel (7OV03QG267) ; Phosphates ; RNA, Ribosomal, 16S ; Metals, Heavy ; Zinc (J41CSQ7QDS) ; Soil ; Soil Pollutants
Language	English
Publishing date	2024-02-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2059868-3
ISSN	1471-2229 ; 1471-2229
ISSN (online)	1471-2229
ISSN	1471-2229
DOI	10.1186/s12870-024-04812-3
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Article ; Online: The beneficial effect of Allium Cepa bulb extract on reproduction of rats; A two-generation study on fecundity and sex hormones.

Suri, Sadia / Khan, Saira Saeed / Naeem, Sadaf / Nisa, Zeb Un / Alam, Nausheen / Majeed, Saba / Kumar, Suresh / Khan, Rafeeq Alam

PloS one

2024 Volume 19, Issue 3, Page(s) e0294999

Abstract: Allium Cepa Linn. (Onions) has extensively been used in traditional medicine, is one of the important Allium species regularly used in our daily diet, and has been the source of robust phenolic compounds. The current study is intended to evaluate the ... ...

Abstract	Allium Cepa Linn. (Onions) has extensively been used in traditional medicine, is one of the important Allium species regularly used in our daily diet, and has been the source of robust phenolic compounds. The current study is intended to evaluate the fecundity-enhancing effect of A. Cepa on the reproductive performance of two successive generations of rats; F0 and F1. A. Cepa extract was initially tested for in vitro antioxidant assay via DPPH and ROS, followed by in vivo toxicity testing. In the fecundity assessment, eighteen pairs of male and female rats (n = 36, 1:1, F0 generation) were divided into three groups and dosed with 75mg/kg and 150 mg/kg daily of A. Cepa extract and saline respectively, up to pre-cohabitation, cohabitation, gestation and lactation period. The reproductive performance, including body weight, live birth index, fertility index, and litter size, was assessed. Various parameters like Hematological, Hormonal (FSH, LH, Testosterone, estradiol), antioxidant markers (SOD, Glutathione peroxidase) and lipid profile of F0 and F1 generations were assessed with evaluation of histopathology of male and female organs. Ethanolic extract of A. Cepa showed the greatest antioxidant potential in DPPH and ROS methods. The continued exposure of the F0 and F1 generations to A. Cepa extract did not affect body weight, fertility index, litter size, and survival index. However, semen pH, sperm motility, sperm count, sperm viability, and semen volume were significantly improved in both generations. We have found pronounced fecundity outcomes in both genders of F0 and F1 generations with A. Cepa 150mg/kg/day extract as compared to control. Results showed that A. Cepa significantly increased (P < 0.05) hemoglobin, follicular stimulating hormone (FSH), luteinizing hormone (LH), plasma testosterone and glutathione peroxidase activities, while total lipid, LDL, and cholesterol were significantly decreased (P < 0.05) in both generations. Histology of both generations of animals reveals enhanced spermatogenesis and enhanced folliculogenesis with improved architecture. Altogether, the present results suggest that A. Cepa extract improved fecundity in both male and female rats by improving hormonal activities and oxidative stress.
MeSH term(s)	Rats ; Male ; Female ; Animals ; Onions ; Reactive Oxygen Species/pharmacology ; Antioxidants/pharmacology ; Sperm Motility ; Seeds ; Reproduction ; Fertility ; Body Weight ; Testosterone ; Luteinizing Hormone/pharmacology ; Follicle Stimulating Hormone/pharmacology ; Glutathione Peroxidase ; Lipids/pharmacology
Chemical Substances	Reactive Oxygen Species ; Antioxidants ; Testosterone (3XMK78S47O) ; Luteinizing Hormone (9002-67-9) ; Follicle Stimulating Hormone (9002-68-0) ; Glutathione Peroxidase (EC 1.11.1.9) ; Lipids
Language	English
Publishing date	2024-03-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0294999
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Article ; Online: Validation of questionnaire regarding online teaching (QOT) during Covid-19 in Karachi, Pakistan.

Rahim, Najia / Nesar, Shagufta / Mumtaz, Tayyaba / Naeem, Sadaf / Ali, Muhammad

PloS one

2022 Volume 17, Issue 9, Page(s) e0274268

Abstract: The present study involved an extra-cultural adaptation and validation of questionnaire regarding online teaching (QOT) to know faculty perception, attitude and experiences of online teaching. Cronbach's alpha was determined for assessing internal ... ...

Abstract	The present study involved an extra-cultural adaptation and validation of questionnaire regarding online teaching (QOT) to know faculty perception, attitude and experiences of online teaching. Cronbach's alpha was determined for assessing internal reliability of QOT and found to be 0.886, confirmed that the scale have good reliability. Factor Analysis of the scale (Principal Component Analysis) was used to examine factor structure and then trailed by varimax rotation. The items were allocated four sub scales. A survey technique was used for the validation of QOT and the survey was conducted during September-December' 2020 in private and public universities of Karachi to determine the pharmacy faculty's perception and experience regarding online teaching. Approximately 35% responded that "It is very easy to prepare and deliver an online course" and 45% opined that "The universities offering Pharm.D should adopt the use of e-learning for teaching in future to complement traditional teaching". Majority of the faculty were in favor of starting online teaching during pandemic to complete semester on time (72%). However, in-campus courses contribute more to students' learning than online courses in pharmaceutical sciences (65.5%). The present study summarizes that academic staff did opt online teaching over one-to-one teaching in the lock down situation during Covid-19 pandemic however, they agreed not to replace traditional teaching to online teaching. Teachers recognized some difficulties and challenges during online teaching including difficulty in preparing lecture for online teaching than traditional classroom teaching, shortage of long time training sessions. Female teachers were inclined to online teaching than male and lecturers tend to prefer online teaching compared to senior teachers. Universities and administration should take imperative acts for improving online teaching for better learning during lock down or any other situation where social distancing is required.
MeSH term(s)	COVID-19/epidemiology ; Communicable Disease Control ; Education, Distance/methods ; Female ; Humans ; Male ; Pakistan ; Pandemics ; Reproducibility of Results ; Surveys and Questionnaires
Language	English
Publishing date	2022-09-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0274268
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Article: Harnessing the Phytase Production Potential of Soil-Borne Fungi from Wastewater Irrigated Fields Based on Eco-Cultural Optimization under Shake Flask Method

Sadaf, Naila / Haider, Muhammad Zulqurnain / Iqbal, Naeem / Abualreesh, Muyassar H. / Alatawi, Aishah

Agriculture (Basel). 2022 Jan. 12, v. 12, no. 1

2022

Abstract: Indigenous fungi present in agricultural soils could have synchronized their inherent potentials to the local climatic conditions. Therefore, the fungi resident in the untreated wastewater irrigated agricultural field might develop their potential for ... ...

Abstract	Indigenous fungi present in agricultural soils could have synchronized their inherent potentials to the local climatic conditions. Therefore, the fungi resident in the untreated wastewater irrigated agricultural field might develop their potential for producing various enzymes to handle the induced full organic load from domestic wastewater and toxic chemicals from the textile industry. Around 53 various fungal isolates were grown and separated from the soil samples from these sites through soil dilution, soil-culture plate, and soil-culture plate methods. All the purified fungi were subjected to a phosphatase production test, and only 13 fungal strains were selected as phosphatase producers. Among them, only five fungi identified as Aspergillus niger, Aspergillus flavus, Aspergillus fumigatus, Penicillium purourogenum, and Mucor rouxii based on morphological similarities, showing higher phosphate solubilizing indices, were utilized for eco-cultural fine-tuning to harness their full production potential under shake flask (SF) method. Among various media, orchestral tuning, 200 µM sodium phytate as substrate with 1.5 mL of inoculum size of the fungi, pH 7, temperature 30 °C, glucose, and ammonium nitrate as carbon and nitrogen additive with seven days of incubation were found to be the most appropriate cultural conditions to harness the phytase production potential of the selected fungi. Aspergillus niger and Aspergillus flavus showed initial phytase activity (5.2 Units/mL, 4.8 Units/mL) and phytase specific activity (2.85, 2.65 Units/mL per mg protein) during screening to be enhanced up to 17 ± 0.033 (Units/mL), 16 ± 0.033 (Units/mL) and (13 ± 0.012), 10 ± 0.066 (Units/mL per mg protein), respectively, with the above-mentioned conditions. The phytase enzyme produced from these fungi were found to be almost stable for a wide range of pH (4–8); temperature (20–60 °C); insensitive to Ca²⁺ and Mg²⁺ ions, and EDTA, Ni²⁺, and Ba²⁺ inhibitors but highly sensitive to Mn²⁺, Cu²⁺, and Zn²⁺ ions, and Co²⁺, Cr³⁺, Al³⁺, Fe²⁺ and Ag¹⁺ inhibitors. It was suggested that both phytase-producing strains of A. niger and A. flavus or their crude phytase enzymes might be good candidates for application in soils to release phosphates from phytate and a possible valuable substitute of phosphate fertilizers.
Keywords	Aspergillus flavus ; Aspergillus fumigatus ; Aspergillus niger ; Mucor ; Penicillium ; agricultural land ; agriculture ; ammonium nitrate ; calcium ; carbon ; culture flasks ; glucose ; inoculum ; municipal wastewater ; nitrogen ; pH ; phosphates ; phytases ; phytic acid ; solubilization ; temperature ; textile industry ; toxicity
Language	English
Dates of publication	2022-0112
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2651678-0
ISSN	2077-0472
ISSN	2077-0472
DOI	10.3390/agriculture12010103
Database	NAL-Catalogue (AGRICOLA)

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Article: In silico

Azmi, Muhammad Bilal / Sultana, Saleha / Naeem, Sadaf / Qureshi, Shamim Akhtar

Saudi journal of biological sciences

2020 Volume 28, Issue 1, Page(s) 731–737

Abstract: Present work aimed to investigate ... ...

Abstract	Present work aimed to investigate the
Language	English
Publishing date	2020-11-05
Publishing country	Saudi Arabia
Document type	Journal Article
ZDB-ID	2515206-3
ISSN	2213-7106 ; 1319-562X
ISSN (online)	2213-7106
ISSN	1319-562X
DOI	10.1016/j.sjbs.2020.10.066
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