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  1. Article ; Online: Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects

    Rima Hajjo / Dima A. Sabbah / Alexander Tropsha

    Pathogens, Vol 11, Iss 743, p

    2022  Volume 743

    Abstract: COVID-19 vaccines have been instrumental tools in reducing the impact of SARS-CoV-2 infections around the world by preventing 80% to 90% of hospitalizations and deaths from reinfection, in addition to preventing 40% to 65% of symptomatic illnesses. ... ...

    Abstract COVID-19 vaccines have been instrumental tools in reducing the impact of SARS-CoV-2 infections around the world by preventing 80% to 90% of hospitalizations and deaths from reinfection, in addition to preventing 40% to 65% of symptomatic illnesses. However, the simultaneous large-scale vaccination of the global population will indubitably unveil heterogeneity in immune responses as well as in the propensity to developing post-vaccine adverse events, especially in vulnerable individuals. Herein, we applied a systems biology workflow, integrating vaccine transcriptional signatures with chemogenomics, to study the pharmacological effects of mRNA vaccines. First, we derived transcriptional signatures and predicted their biological effects using pathway enrichment and network approaches. Second, we queried the Connectivity Map (CMap) to prioritize adverse events hypotheses. Finally, we accepted higher-confidence hypotheses that have been predicted by independent approaches. Our results reveal that the mRNA-based BNT162b2 vaccine affects immune response pathways related to interferon and cytokine signaling, which should lead to vaccine success, but may also result in some adverse events. Our results emphasize the effects of BNT162b2 on calcium homeostasis, which could be contributing to some frequently encountered adverse events related to mRNA vaccines. Notably, cardiac side effects were signaled in the CMap query results. In summary, our approach has identified mechanisms underlying both the expected protective effects of vaccination as well as possible post-vaccine adverse effects. Our study illustrates the power of systems biology approaches in improving our understanding of the comprehensive biological response to vaccination against COVID-19.
    Keywords COVID-19 ; mRNA vaccine ; informatics workflow ; SARS-CoV-2 ; systems biology ; vaccine adverse events ; Medicine ; R
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Unlocking the Potential of the Human Microbiome for Identifying Disease Diagnostic Biomarkers

    Rima Hajjo / Dima A. Sabbah / Abdel Qader Al Bawab

    Diagnostics, Vol 12, Iss 1742, p

    2022  Volume 1742

    Abstract: The human microbiome encodes more than three million genes, outnumbering human genes by more than 100 times, while microbial cells in the human microbiota outnumber human cells by 10 times. Thus, the human microbiota and related microbiome constitute a ... ...

    Abstract The human microbiome encodes more than three million genes, outnumbering human genes by more than 100 times, while microbial cells in the human microbiota outnumber human cells by 10 times. Thus, the human microbiota and related microbiome constitute a vast source for identifying disease biomarkers and therapeutic drug targets. Herein, we review the evidence backing the exploitation of the human microbiome for identifying diagnostic biomarkers for human disease. We describe the importance of the human microbiome in health and disease and detail the use of the human microbiome and microbiota metabolites as potential diagnostic biomarkers for multiple diseases, including cancer, as well as inflammatory, neurological, and metabolic diseases. Thus, the human microbiota has enormous potential to pave the road for a new era in biomarker research for diagnostic and therapeutic purposes. The scientific community needs to collaborate to overcome current challenges in microbiome research concerning the lack of standardization of research methods and the lack of understanding of causal relationships between microbiota and human disease.
    Keywords biomarkers ; diagnostic biomarkers ; metagenomics ; microbial metabolites ; microbiome ; microbiome biomarkers ; Medicine (General) ; R5-920
    Subject code 610
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: A cross-sectional study confirms temporary post-COVID-19 vaccine menstrual irregularity and the associated physiological changes among vaccinated women in Jordan

    Ensaf Y. Almomani / Rima Hajjo / Ahmad Qablan / Dima A. Sabbah / Abass Al-Momany

    Frontiers in Medicine, Vol

    2023  Volume 10

    Abstract: BackgroundCOVID-19 vaccines continue to save people’s lives around the world; however, some vaccine adverse events have been a major concern which slowed down vaccination campaigns. Anecdotal evidence pointed to the vaccine effect on menstruation but ... ...

    Abstract BackgroundCOVID-19 vaccines continue to save people’s lives around the world; however, some vaccine adverse events have been a major concern which slowed down vaccination campaigns. Anecdotal evidence pointed to the vaccine effect on menstruation but evidence from the adverse event reporting systems and the biomedical literature was lacking. This study aimed to investigate the physiological changes in women during menstruation amid the COVID-19 vaccination.MethodsA cross-sectional online survey was distributed to COVID-19 vaccinated women from Nov 2021 to Jan 2022. The results were analyzed using the SPSS software.ResultsAmong the 564 vaccinated women, 52% experienced significant menstrual irregularities post-vaccination compared to before regardless of the vaccine type. The kind of menstrual irregularity varied among the vaccinated women, for example, 33% had earlier menstruation, while 35% reported delayed menstruation. About 31% experienced heavier menstruation, whereas 24% had lighter menstrual flow. About 29% had menstruation last longer, but 13% had it shorter than usual. Noteworthy, the menstrual irregularities were more frequent after the second vaccine shot, and they disappeared within 3 months on average. Interestingly, 24% of the vaccinated women reported these irregularities to their gynecologist.ConclusionThe COVID-19 vaccine may cause physiological disturbances during menstruation. Luckily, these irregularities were short-termed and should not be a reason for vaccine hesitancy in women. Further studies are encouraged to unravel the COVID-19 vaccine adverse effect on women’s health.
    Keywords COVID-19 vaccine ; adverse events ; menstrual cycle irregularity ; vaccinated women ; Jordan ; Medicine (General) ; R5-920
    Subject code 300
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Chemocentric Informatics Analysis

    Rima Hajjo / Dima A. Sabbah / Sanaa K. Bardaweel

    ACS Omega, Vol 5, Iss 46, Pp 29765-

    Dexamethasone Versus Combination Therapy for COVID-19

    2020  Volume 29779

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Shedding the Light on Post-Vaccine Myocarditis and Pericarditis in COVID-19 and Non-COVID-19 Vaccine Recipients

    Rima Hajjo / Dima A. Sabbah / Sanaa K. Bardaweel / Alexander Tropsha

    Vaccines, Vol 9, Iss 1186, p

    2021  Volume 1186

    Abstract: Myocarditis and pericarditis have been linked recently to COVID-19 vaccines without exploring the underlying mechanisms, or compared to cardiac adverse events post-non-COVID-19 vaccines. We introduce an informatics approach to study post-vaccine adverse ... ...

    Abstract Myocarditis and pericarditis have been linked recently to COVID-19 vaccines without exploring the underlying mechanisms, or compared to cardiac adverse events post-non-COVID-19 vaccines. We introduce an informatics approach to study post-vaccine adverse events on the systems biology level to aid the prioritization of effective preventive measures and mechanism-based pharmacotherapy by integrating the analysis of adverse event reports from the Vaccine Adverse Event Reporting System (VAERS) with systems biology methods. Our results indicated that post-vaccine myocarditis and pericarditis were associated most frequently with mRNA COVID-19 vaccines followed by live or live-attenuated non-COVID-19 vaccines such as smallpox and anthrax vaccines. The frequencies of cardiac adverse events were affected by vaccine, vaccine type, vaccine dose, sex, and age of the vaccinated individuals. Systems biology results suggested a central role of interferon-gamma (INF-gamma) in the biological processes leading to cardiac adverse events, by impacting MAPK and JAK-STAT signaling pathways. We suggest that increasing the time interval between vaccine doses minimizes the risks of developing inflammatory adverse reactions. We also propose glucocorticoids as preferred treatments based on system biology evidence. Our informatics workflow provides an invaluable tool to study post-vaccine adverse events on the systems biology level to suggest effective mechanism-based pharmacotherapy and/or suitable preventive measures.
    Keywords COVID-19 ; myocarditis ; pericarditis ; SARS-CoV-2 ; systems biology ; vaccine ; Medicine ; R
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Identification of Tumor-Specific MRI Biomarkers Using Machine Learning (ML)

    Rima Hajjo / Dima A. Sabbah / Sanaa K. Bardaweel / Alexander Tropsha

    Diagnostics, Vol 11, Iss 742, p

    2021  Volume 742

    Abstract: The identification of reliable and non-invasive oncology biomarkers remains a main priority in healthcare. There are only a few biomarkers that have been approved as diagnostic for cancer. The most frequently used cancer biomarkers are derived from ... ...

    Abstract The identification of reliable and non-invasive oncology biomarkers remains a main priority in healthcare. There are only a few biomarkers that have been approved as diagnostic for cancer. The most frequently used cancer biomarkers are derived from either biological materials or imaging data. Most cancer biomarkers suffer from a lack of high specificity. However, the latest advancements in machine learning (ML) and artificial intelligence (AI) have enabled the identification of highly predictive, disease-specific biomarkers. Such biomarkers can be used to diagnose cancer patients, to predict cancer prognosis, or even to predict treatment efficacy. Herein, we provide a summary of the current status of developing and applying Magnetic resonance imaging (MRI) biomarkers in cancer care. We focus on all aspects of MRI biomarkers, starting from MRI data collection, preprocessing and machine learning methods, and ending with summarizing the types of existing biomarkers and their clinical applications in different cancer types.
    Keywords biomarkers ; imaging ; machine learning ; MRI ; oncology ; Medicine (General) ; R5-920
    Subject code 610
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: N- Phenyl-6-Chloro-4-Hydroxy-2-Quinolone-3-CarboxAmides

    Dima A. Sabbah / Rawan A. Haroon / Sanaa K. Bardaweel / Rima Hajjo / Kamal Sweidan

    Molecules, Vol 26, Iss 73, p

    Molecular Docking, Synthesis, and Biological Investigation as Anticancer Agents

    2021  Volume 73

    Abstract: Cancer is a multifactorial disease and the second leading cause of death worldwide. Diverse factors induce carcinogenesis, such as diet, smoking, radiation, and genetic defects. The phosphatidylinositol 3-kinase (PI3Kα) has emerged as an attractive ... ...

    Abstract Cancer is a multifactorial disease and the second leading cause of death worldwide. Diverse factors induce carcinogenesis, such as diet, smoking, radiation, and genetic defects. The phosphatidylinositol 3-kinase (PI3Kα) has emerged as an attractive target for anticancer drug design. Eighteen derivatives of N- phenyl-6-chloro-4-hydroxy-2-quinolone-3-carboxamide were synthesized and characterized using FT-IR, NMR ( 1 H and 13 C), and high-resolution mass spectra (HRMS). The series exhibited distinct antiproliferative activity (IC 50 µM) against human epithelial colorectal adenocarcinoma (Caco-2) and colon carcinoma (HCT-116) cell lines, respectively: compounds 16 (37.4, 8.9 µM), 18 (50.9, 3.3 µM), 19 (17.0, 5.3 µM), and 21 (18.9, 4.9 µM). The induced-fit docking (IFD) studies against PI3Kαs showed that the derivatives occupy the PI3Kα binding site and engage with key binding residues.
    Keywords anticancer ; colon cancer ; PI3Kα ; AKT ; docking ; quinolone-3-carboxamide ; Organic chemistry ; QD241-441
    Subject code 540
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Salivary Microbiome and Cigarette Smoking

    Walid Al-Zyoud / Rima Hajjo / Ahmed Abu-Siniyeh / Sarah Hajjaj

    International Journal of Environmental Research and Public Health, Vol 17, Iss 1, p

    A First of Its Kind Investigation in Jordan

    2019  Volume 256

    Abstract: There is accumulating evidence in the biomedical literature suggesting the role of smoking in increasing the risk of oral diseases including some oral cancers. Smoking alters microbial attributes of the oral cavity by decreasing the commensal microbial ... ...

    Abstract There is accumulating evidence in the biomedical literature suggesting the role of smoking in increasing the risk of oral diseases including some oral cancers. Smoking alters microbial attributes of the oral cavity by decreasing the commensal microbial population and increasing the pathogenic microbes. This study aims to investigate the shift in the salivary microbiota between smokers and non-smokers in Jordan. Our methods relied on high-throughput next-generation sequencing (NGS) experiments for V3-V4 hypervariable regions of the 16S rRNA gene, followed by comprehensive bioinformatics analysis including advanced multidimensional data visualization methods and statistical analysis approaches. Six genera— Streptococcus , Prevotella , Vellionella , Rothia , Neisseria , and Haemophilus —predominated the salivary microbiota of all samples with different percentages suggesting the possibility for the salivary microbiome to restored after quitting smoking. Three genera— Streptococcus , Prevotella , and Veillonella —showed significantly elevated levels among smokers at the expense of Neisseria in non-smokers. In conclusion, smoking has a definite impact on shifting the salivary microbiota in smokers. We can suggest that there is microbial signature at the genera level that can be used to classify smokers and non-smokers by Linear Discriminant Analysis Effect Size (LEfSe) based on the salivary abundance of genera. Proteomics and metabolomics studies are highly recommended to fully understand the effect of bacterial endotoxin release and xenobiotic metabolism on the bacterial interrelationships in the salivary microbiome and how they affect the growth of each other in the saliva of smokers.
    Keywords saliva ; microbiome ; microbiota ; smoking ; 16s rrna ; next-generation sequencing ; operational taxonomic unit (otu) ; bioinformatics ; jordan ; Medicine ; R
    Subject code 616
    Language English
    Publishing date 2019-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Molecular Modeling, Synthesis and Biological Evaluation of N -Phenyl-4-Hydroxy-6-Methyl-2-Quinolone-3-CarboxAmides as Anticancer Agents

    Dima A. Sabbah / Shaima’ E. Hasan / Reema Abu Khalaf / Sanaa K. Bardaweel / Rima Hajjo / Khalid M. Alqaisi / Kamal A. Sweidan / Aya M. Al-Zuheiri

    Molecules, Vol 25, Iss 5348, p

    2020  Volume 5348

    Abstract: The emergence of phosphatidylinositol 3-kinase (PI3Kα) in cancer development has accentuated its significance as a potential target for anticancer drug design. Twenty one derivatives of N -phenyl-4-hydroxy-6-methyl-2-quinolone-3-carboxamide were ... ...

    Abstract The emergence of phosphatidylinositol 3-kinase (PI3Kα) in cancer development has accentuated its significance as a potential target for anticancer drug design. Twenty one derivatives of N -phenyl-4-hydroxy-6-methyl-2-quinolone-3-carboxamide were synthesized and characterized using NMR ( 1 H and 13 C) and HRMS. The derivatives displayed inhibitory activity against human epithelial colorectal adenocarcinoma (Caco-2) and human colon cancer (HCT-116) cell lines: compounds 8 (IC 50 Caco-2 = 98 µM, IC 50 HCT-116 = 337 µM) and 16 (IC 50 Caco-2 = 13 µM, IC 50 HCT-116 = 240.2 µM). Results showed that compound 16 significantly affected the gene encoding AKT, BAD, and PI3K. The induced-fit docking (IFD) studies against PI3Kα demonstrated that the scaffold accommodates the kinase domains and forms H-bonds with significant binding residues.
    Keywords anticancer ; colon cancer ; PI3Kα ; AKT ; docking ; quinolone-3-carboxamide ; Organic chemistry ; QD241-441
    Subject code 540
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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