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Article ; Online: Introducing the f

Gamal, Mahmoud / Ibrahim, Marwa A

2024 Volume 25, Issue 1, Page(s) 17

Abstract: Background: qPCR is a widely used technique in scientific research as a basic tool in gene expression analysis. Classically, the quantitative endpoint of qPCR is the threshold cycle (C: Results: The performance of the new f: Conclusions: We ... ...

Abstract	Background: qPCR is a widely used technique in scientific research as a basic tool in gene expression analysis. Classically, the quantitative endpoint of qPCR is the threshold cycle (C Results: The performance of the new f Conclusions: We recommend using the f
Language	English
Publishing date	2024-01-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-024-05630-y
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Article ; Online: Exploring the composition of protein-ligand binding sites for cancerous inhibitor of PP2A (CIP2A) by inhibitor guided binding analysis: paving a new way for the Discovery of drug candidates against triple negative breast cancer (TNBC).

Ibitoye, Oluwayimika / Ibrahim, Mahmoud A A / Soliman, Mahmoud E S

Journal of receptor and signal transduction research

2024 Volume 43, Issue 6, Page(s) 133–143

Abstract: Triple-negative breast cancer (TNBC) is associated with high-grade invasive carcinoma leading to a 10% to 15% death rate in younger premenopausal women. Targeting cancerous inhibitors of protein phosphatase (CIP2A) has been a highly effective approach ... ...

Abstract	Triple-negative breast cancer (TNBC) is associated with high-grade invasive carcinoma leading to a 10% to 15% death rate in younger premenopausal women. Targeting cancerous inhibitors of protein phosphatase (CIP2A) has been a highly effective approach for exploring therapeutic drug candidates. Lapatinib, a dual tyrosine kinase inhibitor, has shown promising inhibition properties by inducing apoptosis in TNBC carcinogenesis
MeSH term(s)	Female ; Humans ; Lapatinib/therapeutic use ; Triple Negative Breast Neoplasms/drug therapy ; Triple Negative Breast Neoplasms/metabolism ; Triple Negative Breast Neoplasms/pathology ; Ligands ; Intracellular Signaling Peptides and Proteins/metabolism ; Membrane Proteins/metabolism ; Transcription Factors ; Binding Sites ; Carcinogenesis ; Cell Line, Tumor
Chemical Substances	Lapatinib (0VUA21238F) ; Ligands ; Intracellular Signaling Peptides and Proteins ; Membrane Proteins ; Transcription Factors
Language	English
Publishing date	2024-02-13
Publishing country	England
Document type	Journal Article
ZDB-ID	1230969-2
ISSN	1532-4281 ; 1079-9893
ISSN (online)	1532-4281
ISSN	1079-9893
DOI	10.1080/10799893.2023.2298903
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Article ; Online: Introducing the f 0% method

Mahmoud Gamal / Marwa A. Ibrahim

BMC Bioinformatics, Vol 25, Iss 1, Pp 1-

a reliable and accurate approach for qPCR analysis

2024 Volume 18

Abstract: Abstract Background qPCR is a widely used technique in scientific research as a basic tool in gene expression analysis. Classically, the quantitative endpoint of qPCR is the threshold cycle (CT) that ignores differences in amplification efficiency among ... ...

Abstract	Abstract Background qPCR is a widely used technique in scientific research as a basic tool in gene expression analysis. Classically, the quantitative endpoint of qPCR is the threshold cycle (CT) that ignores differences in amplification efficiency among many other drawbacks. While other methods have been developed to analyze qPCR results, none has statistically proven to perform better than the CT method. Therefore, we aimed to develop a new qPCR analysis method that overcomes the limitations of the CT method. Our f 0% [eff naught percent] method depends on a modified flexible sigmoid function to fit the amplification curve with a linear part to subtract the background noise. Then, the initial fluorescence is estimated and reported as a percentage of the predicted maximum fluorescence (f 0%). Results The performance of the new f 0% method was compared against the CT method along with another two outstanding methods—LinRegPCR and Cy0. The comparison regarded absolute and relative quantifications and used 20 dilution curves obtained from 7 different datasets that utilize different DNA-binding dyes. In the case of absolute quantification, f 0% reduced CV%, variance, and absolute relative error by 1.66, 2.78, and 1.8 folds relative to CT; and by 1.65, 2.61, and 1.71 folds relative to LinRegPCR, respectively. While, regarding relative quantification, f 0% reduced CV% by 1.76, 1.55, and 1.25 folds and variance by 3.13, 2.31, and 1.57 folds regarding CT, LinRegPCR, and Cy0, respectively. Finally, f 0% reduced the absolute relative error caused by LinRegPCR by 1.83 folds. Conclusions We recommend using the f 0% method to analyze and report qPCR results based on its reported advantages. Finally, to simplify the usage of the f 0% method, it was implemented in a macro-enabled Excel file with a user manual located on https://github.com/Mahmoud0Gamal/F0-perc/releases .
Keywords	Real-time PCR ; Delta CT ; PCR efficiency ; Calibration curve ; Performance indicators ; Variation between replicates ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	518
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Inhibition of both NOX and TNF-α exerts substantial renoprotective effects in renal ischemia reperfusion injury rat model.

Bayoumi, Amina A / Ahmad, Enssaf Ahmad / Ibrahim, Islam A A E-H / Mahmoud, Mona F / Elbatreek, Mahmoud H

European journal of pharmacology

2024 Volume 970, Page(s) 176507

Abstract: Background and aims: Acute kidney injury (AKI) due to renal ischemia-reperfusion injury (RIRI) is associated with high morbidity and mortality, with no renoprotective drug available. Previous research focused on single drug targets, yet this approach ... ...

Abstract	Background and aims: Acute kidney injury (AKI) due to renal ischemia-reperfusion injury (RIRI) is associated with high morbidity and mortality, with no renoprotective drug available. Previous research focused on single drug targets, yet this approach has not reached translational success. Given the complexity of this condition, we aimed to identify a disease module and apply a multitarget network pharmacology approach. Methods: Identification of a disease module with potential drug targets was performed utilizing Disease Module Detection algorithm using NADPH oxidases (NOXs) as seeds. We then assessed the protective effect of a multitarget network pharmacology targeting the identified module in a rat model of RIRI. Rats were divided into five groups; sham, RIRI, and RIRI treated with setanaxib (NOX inhibitor, 10 mg/kg), etanercept (TNF-α inhibitor, 10 mg/kg), and setanaxib and etanercept (5 mg/kg each). Kidney functions, histopathological changes and oxidative stress markers (MDA and reduced GSH) were assessed. Immunohistochemistry of inflammatory (TNF-α, NF-κB) apoptotic (cCasp-3, Bax/Bcl 2), fibrotic (α-SMA) and proteolysis (MMP-9) markers was performed. Results: Our in-silico analysis yielded a disease module with TNF receptor 1 (TNFR1A) as the closest target to both NOX1 and NOX2. Targeting this module by a low-dose combination of setanaxib, and etanercept, resulted in a synergistic effect and ameliorated ischemic AKI in rats. This was evidenced by improved kidney function and reduced expression of inflammatory, apoptotic, proteolytic and fibrotic markers. Conclusions: Our findings show that applying a multitarget network pharmacology approach allows synergistic renoprotective effect in ischemic AKI and might pave the way towards translational success.
MeSH term(s)	Rats ; Animals ; Tumor Necrosis Factor-alpha/pharmacology ; Etanercept/pharmacology ; Kidney ; Reperfusion Injury/complications ; Reperfusion Injury/drug therapy ; Reperfusion Injury/prevention & control ; Ischemia/pathology ; Acute Kidney Injury/drug therapy ; Acute Kidney Injury/prevention & control
Chemical Substances	Tumor Necrosis Factor-alpha ; Etanercept (OP401G7OJC)
Language	English
Publishing date	2024-03-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80121-5
ISSN	1879-0712 ; 0014-2999
ISSN (online)	1879-0712
ISSN	0014-2999
DOI	10.1016/j.ejphar.2024.176507
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Article: Autologous Nanofat Injection Combined with Fractional CO2 Laser in the Treatment of Atrophic Acne Scars.

Rageh, Mahmoud A / Ibrahim, Shady Mahmoud Attia / Abdallah, Noha / Tawfik, Abeer Attia

Clinical, cosmetic and investigational dermatology

2024 Volume 17, Page(s) 697–705

Abstract: Background: Atrophic acne scarring is a widely prevalent condition and one of the most distressing complications of acne vulgaris. Numerous options with variable outcomes are available for the treatment of acne scarring. Laser is considered a first-line ...

Abstract	Background: Atrophic acne scarring is a widely prevalent condition and one of the most distressing complications of acne vulgaris. Numerous options with variable outcomes are available for the treatment of acne scarring. Laser is considered a first-line therapy for acne scars, and recently there has been a growing interest in using stem cells and their derivatives for treating acne scars. In addition, combined therapeutic modalities often achieve more satisfactory results than a single treatment. Objective: We tried to evaluate the role of nanofat and fractional CO2 laser as a combined treatment approach for atrophic acne scarring. Methods: Twenty-five patients with atrophic acne scarring were enrolled. They received a single session of intradermal nanofat injection, at different points 1 cm apart, for acne scars. Two weeks later, they were treated with three sessions of fractional CO2 laser at monthly intervals. Patients were evaluated three months after the last session using the quantitative Goodman and Baron scoring system. Pain, side effects, and patients' satisfaction were also evaluated. Results: There were two males and 23 females with a mean age of 25.96 years. Their skin type ranged between Fitzpatrick skin type III, IV, and V. Boxcar scars were the most common scar type in 13 patients (52%). After treatment, there was a significant reduction (p <0.05) in the quantitative Goodman and Baron scores. The improvement was more evident in rolling scars. Seven patients reported significant improvement, and 12 reported marked improvement. Conclusion: This study showed that combining nanofat and fractional CO2 laser is a safe and effective treatment modality for atrophic acne scars.
Language	English
Publishing date	2024-03-20
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2494852-4
ISSN	1178-7015
ISSN	1178-7015
DOI	10.2147/CCID.S454514
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Article ; Online: New strategies for sterilization and preservation of fresh fish skin grafts.

Ibrahim, Ahmed / Fahmy, Hossam M / Mahmoud, Ghada Abd-Elmonsef / Soliman, Mahmoud / Elshahawy, Abdelnaby M

Scientific reports

2024 Volume 14, Issue 1, Page(s) 1253

Abstract: The introduction of fish skin as a biological dressing for treating burns and wounds holds great promise, offering an alternative to existing management strategies. However, the risk of disease transmission is a significant concern. Therefore, this study ...

Abstract	The introduction of fish skin as a biological dressing for treating burns and wounds holds great promise, offering an alternative to existing management strategies. However, the risk of disease transmission is a significant concern. Therefore, this study aimed to examine how established sterilization and preservation procedures affected fish skin grafts' microbiological and histological properties for long-term usage. Lyophilization of the fish skin graft followed by rehydration in normal saline for 15 min did not change the collagen content. Furthermore, gamma irradiation of the lyophilized fish skin graft at different lengths 5, 10, and 25 KGy showed a significant reduction in microbial growth (aerobic bacteria, aerobic yeasts, and fungi) at 15- and 30 days after the irradiation. However, exposure to 10 KGy was found to be the most effective intensity among the different gamma irradiation lengths since it preserved the collagen fiber content and intensity in the lyophilized fish skin grafts at 15- and 30 days after the irradiation. These findings provide efficient preservation and sterilization methods for long-term usage of the fresh Tilapia skin grafts used for biological dressings.
MeSH term(s)	Animals ; Skin Transplantation ; Preservation, Biological ; Freeze Drying ; Collagen ; Fishes ; Sterilization/methods ; Ichthyosis, Lamellar
Chemical Substances	Collagen (9007-34-5)
Language	English
Publishing date	2024-01-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-51608-4
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Article ; Online: Cr(VI) and doxorubicin adsorptive capture by a novel bionanocomposite of Ti-MOF@TiO

Mahmoud, Mohamed E / Ibrahim, Ghada A A

International journal of biological macromolecules

2023 Volume 253, Issue Pt 1, Page(s) 126489

Abstract: Biodegradable polymers, biochars and metal organic frameworks (MOFs) have manifested as top prospects for elimination of harmful pollutants. In the current study, Ti-MOF was synthesized and decorated with ... ...

Abstract	Biodegradable polymers, biochars and metal organic frameworks (MOFs) have manifested as top prospects for elimination of harmful pollutants. In the current study, Ti-MOF was synthesized and decorated with TiO
MeSH term(s)	Hydrogels ; Chitosan/chemistry ; Titanium/chemistry ; Adsorption ; Water Pollutants, Chemical/chemistry ; Chromium/chemistry ; Water/chemistry ; Kinetics ; Hydrogen-Ion Concentration
Chemical Substances	chromium hexavalent ion (18540-29-9) ; biochar ; Hydrogels ; Chitosan (9012-76-4) ; titanium dioxide (15FIX9V2JP) ; Titanium (D1JT611TNE) ; Water Pollutants, Chemical ; Chromium (0R0008Q3JB) ; Water (059QF0KO0R)
Language	English
Publishing date	2023-08-23
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.2023.126489
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Article ; Online: Mathematical Modeling of SARS-CoV-2 Transmission between Minks and Humans Considering New Variants and Mink Culling.

Ibrahim, Mahmoud A / Dénes, Attila

Tropical medicine and infectious disease

2023 Volume 8, Issue 8

Abstract: We formulated and studied mathematical models to investigate control strategies for the outbreak of the disease caused by SARS-CoV-2, considering the transmission between humans and minks. Two novel models, namely SEIR and SVEIR, are proposed to ... ...

Abstract	We formulated and studied mathematical models to investigate control strategies for the outbreak of the disease caused by SARS-CoV-2, considering the transmission between humans and minks. Two novel models, namely SEIR and SVEIR, are proposed to incorporate human-to-human, human-to-mink, and mink-to-human transmission. We derive formulas for the reproduction number R0 for both models using the next-generation matrix technique. We fitted our model to the daily number of COVID-19-infected cases among humans in Denmark as an example, and using the best-fit parameters, we calculated the values of R0 to be 1.58432 and 1.71852 for the two-strain and single-strain models, respectively. Numerical simulations are conducted to investigate the impact of control measures, such as mink culling or vaccination strategies, on the number of infected cases in both humans and minks. Additionally, we investigated the possibility of the mutated virus in minks being transmitted to humans. Our results indicate that to control the disease and spread of SARS-CoV-2 mutant strains among humans and minks, we must minimize the transmission and contact rates between mink farmers and other humans by quarantining such individuals. In order to reduce the virus mutation rate in minks, culling or vaccination strategies for infected mink farms must also be implemented. These measures are essential in managing the spread of SARS-CoV-2 and its variants, protecting public health, and mitigating the potential risks associated with human-to-mink transmission.
Language	English
Publishing date	2023-08-03
Publishing country	Switzerland
Document type	Journal Article
ISSN	2414-6366
ISSN (online)	2414-6366
DOI	10.3390/tropicalmed8080398
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Article: A mathematical model for the spread of Varroa mites in honeybee populations: two simulation scenarios with seasonality.

Ibrahim, Mahmoud A / Dénes, Attila

Heliyon

2022 Volume 8, Issue 9, Page(s) e10648

Abstract: We formulate and study a mathematical model for a honeybee colony infected ... ...

Abstract	We formulate and study a mathematical model for a honeybee colony infected with
Language	English
Publishing date	2022-09-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2022.e10648
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Article: Investigation and Tailoring of Rotating Squares' and Rectangles' Auxetic Structure Behavior through Computational Simulations of 6082T6 Aluminum Alloy Structures.

Elsamanty, Mahmoud / Elshokrofy, Hassan / Ibrahim, Abdelkader / Järvenpää, Antti / Khedr, Mahmoud

Materials (Basel, Switzerland)

2023 Volume 16, Issue 24

Abstract: Auxetic structures, renowned for their unique lateral expansion under longitudinal strain, have attracted significant research interest due to their extraordinary mechanical characteristics, such as enhanced toughness and shear resistance. This study ... ...

Abstract	Auxetic structures, renowned for their unique lateral expansion under longitudinal strain, have attracted significant research interest due to their extraordinary mechanical characteristics, such as enhanced toughness and shear resistance. This study provides a systematic exploration of these structures, constructed from rigid rotating square or rectangular unit cells. Incremental alterations were applied to key geometrical parameters, including the angle (θ) between connected units, the side length (
Language	English
Publishing date	2023-12-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2487261-1
ISSN	1996-1944
ISSN	1996-1944
DOI	10.3390/ma16247597
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