Multi-study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures

Sung, Jaeyun,Kim, Pan-Jun,Ma, Shuyi,Funk, Cory C.,Magis, Andrew T.,Wang, Yuliang,Hood, Leroy,Geman, Donald,Price, Nathan D. Public Library of Science 2013 PLoS computational biology Vol.9 No.7

<▼1><P>We utilized abundant transcriptomic data for the primary classes of brain cancers to study the feasibility of separating all of these diseases simultaneously based on molecular data alone. These signatures were based on a new method reported herein – Identification of Structured Signatures and Classifiers (ISSAC) – that resulted in a brain cancer marker panel of 44 unique genes. Many of these genes have established relevance to the brain cancers examined herein, with others having known roles in cancer biology. Analyses on large-scale data from multiple sources must deal with significant challenges associated with heterogeneity between different published studies, for it was observed that the variation among individual studies often had a larger effect on the transcriptome than did phenotype differences, as is typical. For this reason, we restricted ourselves to studying only cases where we had at least two independent studies performed for each phenotype, and also reprocessed all the raw data from the studies using a unified pre-processing pipeline. We found that learning signatures across multiple datasets greatly enhanced reproducibility and accuracy in predictive performance on truly independent validation sets, even when keeping the size of the training set the same. This was most likely due to the meta-signature encompassing more of the heterogeneity across different sources and conditions, while amplifying signal from the repeated global characteristics of the phenotype. When molecular signatures of brain cancers were constructed from all currently available microarray data, 90% phenotype prediction accuracy, or the accuracy of identifying a particular brain cancer from the background of all phenotypes, was found. Looking forward, we discuss our approach in the context of the eventual development of organ-specific molecular signatures from peripheral fluids such as the blood.</P></▼1><▼2><P><B>Author Summary</B></P><P>From a multi-study, integrated transcriptomic dataset, we identified a marker panel for differentiating major human brain cancers at the gene-expression level. The ISSAC molecular signatures for brain cancers, composed of 44 unique genes, are based on comparing expression levels of pairs of genes, and phenotype prediction follows a diagnostic hierarchy. We found that sufficient dataset integration across multiple studies greatly enhanced diagnostic performance on truly independent validation sets, whereas signatures learned from only one dataset typically led to high error rate. Molecular signatures of brain cancers, when obtained using all currently available gene-expression data, achieved 90% phenotype prediction accuracy. Thus, our integrative approach holds significant promise for developing organ-level, comprehensive, molecular signatures of disease.</P></▼2>

AN APPROXIMATE RIEMANN SOLVER FOR CHEMICAL EQUILIBRIUM FLOWS IN ROCKET ENGINES

V. Magi,A. Dadone,A. Perrini 대한기계학회 1992 International Conference on Fluid Machinery Vol.1 No.1

Hibiscus sabdariffa L.: phytoconstituents, nutritive, and pharmacological applications

Mohamed A. Salem,Ahmed Zayed,Magy E. Beshay,Mesih Mirna M. Abdel,Khayal Reem F. Ben,Fady A. George,Shahira M. Ezzat 경희대학교 융합한의과학연구소 2022 Oriental Pharmacy and Experimental Medicine Vol.22 No.3

Hibiscus sabdariffa L. (HS) calyx extracts have been well-documented for the treatment of hypertension, liver dysfunctions, and diabetes among others. An updated concise review of HS regarding phytoconstituents, and involved putative mechanisms of potential biological activities is presented. HS showed other food and other industrial applications, including the preparation of metallic nanoparticles. These activities were explained by the presence of a broad spectrum of valuable phytochemicals, including the red pigments anthocyanins, phenolic, and organic acids and polyphenolics (e.g., flavonoids and tannins). Most of the bioactivities were found to be associated with anthocyanins-rich extracts. Anthocyanins were found to have various mechanisms for the treatment of hypertension, including direct vasodilation and inhibition of angiotensinconverting enzyme (ACE). However, leaves and seeds showed also other potential applications in food industry, owing to the significant amounts of phenolic antioxidant compounds. Therefore, valorization and optimization of bioactive constituents’ extraction from plant biowastes should be considered for maximizing the benefits of HS extracts.

An Efficient Maintenance Plan Using Proposed Framework of RCM Made Simple Approach

Eman K. Abd Elhalim,Ragab K. Abdel-Magied,Islam H. Afefy,Mohamed F. Aly 대한산업공학회 2019 Industrial Engineeering & Management Systems Vol.18 No.2

Reliability Centered Maintenance (RCM) is an effective maintenance strategy and a powerful tool for industrial system enhancement. In this paper, a Framework of RCM is proposed. RCM Made Simple approach is adopted instead of classical RCM to overcome its complexity. A comprehensive analysis is carried out using the proposed Framework which generates a maintenance plane for industrial systems. This analysis is applied on a real case study. The results revealed which component could be critical, potentially critical, commitment, or run to failure. Moreover, it presented the function of each component, failure modes, failure effects and its consequence on the system, failure causes, PM task required, PM frequency for each task, and how to prevent each failure cause. The Framework that proposed in this paper could be adopted as a simple approach to enhance the Reliability, Availability, and Maintainability (RAM) of the industrial systems.

Industrial by-product utilized synthesis of mesoporous aluminum silicate sorbent for thorium removal

Sarah Alharthi,Mahmoud Osman Abd El-Magied 한국화학공학회 2021 Korean Journal of Chemical Engineering Vol.38 No.11

Recently, there has been an increasing concern in finding sorbents for radionuclide removal from natural sources. AS-BFS sorbent (aluminum silicate composites derived from blast furnace slag) is a suitable candidate for this purpose; due to economic and environmental reasons. Blast furnace slag (BFS) is a by-product of the iron and steel industry plants. The development of a cost-effective route for recycling and utilization assessment of BFS is an urgent task. AS-BFS was prepared from BFS and its physicochemical properties were determined. The elemental composition of the AS-BFS is mainly oxygen (44%), Si (34%), and Al (19%), with traces of titanium, iron, chloride, and calcium. Experimental potentiality regarding sorption characteristics of AS-BFS to thorium ions was explored via the batch method. AS-BFS showed good adsorption capacity for thorium (obtained after 240 min) from aqueous streams (39.7 mg/g). The sorption process is fitted to the mono-layer adsorption model at optimum conditions. It was also proved that adsorption kinetics follows the pseudo-second-order model. The desorption results revealed that thorium ions (93%) could be eluted using 1M HNO3. Hence, the research work indicates that the thorium sorption method with AS-BFS is cost-effective, efficient, and recommended for thorium removal from natural sources.

High-Grade Prostatic Intraepithelial Neoplasia

Joseph C Klink,Ranko Miocinovic,Cristina Magi Galluzzi,Eric A Klein 대한비뇨의학회 2012 Investigative and Clinical Urology Vol.53 No.5

High-grade prostatic intraepithelial neoplasia (HGPIN) has been established as a precursor to prostatic adenocarcinoma. HGPIN shares many morphological, genetic, and molecular signatures with prostate cancer. Its predictive value for the development of future adenocarcinoma during the prostate-specific antigen screening era has decreased, mostly owing to the increase in prostate biopsy cores. Nevertheless, a literature review supports that large-volume HGPIN and multiple cores of involvement at the initial biopsy should prompt a repeat biopsy of the prostate within 1 year. No treatment is recommended for HGPIN to slow its progression to cancer.

Tissue CA125 and HE4 Gene Expression Levels Offer Superior Accuracy in Discriminating Benign from Malignant Pelvic Masses

Fawzy, Amal,Mohamed, Mohamed R,Ali, Mohamed AM,El-Magied, Mohamed H Abd,Helal, Amany M Asian Pacific Journal of Cancer Prevention 2016 Asian Pacific journal of cancer prevention Vol.17 No.1

Background: Ovarian cancer remains a major worldwide health care issue due to the lack of satisfactory diagnostic methods for early detection of the disease. Prior studies on the role of serum cancer antigen 125 (CA125) and human epididymis protein 4 (HE4) in detecting ovarian cancer presented conflicting results. New tools to improve the accuracy of identifying malignancy are urgently needed. We here aimed to evaluate the diagnostic utility of tissue CA125 and HE4 gene expression in comparison to serum CA125 and HE4 in discriminating benign from malignant pelvic masses. Materials and Methods: One-hundred Egyptian women were enrolled in this study, including 60 epithelial ovarian cancer (EOC) patients and 20 benign ovarian tumor patients, as well as 20 apparently healthy women. Preoperative serum levels of CA125 and HE4 were measured by immunoassays. Tissue expression levels of genes encoding CA125 and HE4 were determined by quantitative real time polymerase chain reaction (qRT-PCR). The diagnostic performance of CA125 and HE4, measured either as mRNA or protein levels, was evaluated by receiver operating characteristic (ROC) curves. Results: The serum CA125+HE4 combination and serum HE4, with area under the curve (AUC) values of 0.935 and 0.932, respectively, performed significantly better than serum CA125 (AUC=0.592; P<0.001). Tissue CA125 and HE4 (AUC=1) performed significantly better than serum CA125 (P<0.001), serum HE4 (P=0.016) and the serum CA125+HE4 combination (P=0.018). Conclusions: Measurement of tissue CA125 and HE4 gene expression not only improves discriminatory performance, but also broadens the range of differential diagnostic possibilities in distinguishing EOC from benign ovarian tumors.

Infusing the axioms of clinical reasoning while designing clinical anatomy case vignettes teaching for novice medical students: a randomised cross over study

Dinesh Kumar,V,Rajprasath R,N,A,Priyadharshini,Magi Murugan,Rema Devi 대한해부학회 2020 Anatomy & Cell Biology Vol.53 No.2

The clinical reasoning skills is often gained when the biomedical knowledge is broadened and deepened alongside exposure to patients. The ‘ideal’ blend of axioms of clinical reasoning and case based learning would establish the pedagogical bridges right from the first year of medical education. So this study aimed to investigate the perceived importance and efficacy of teaching clinical reasoning skills among first year medical students, as this has not previously been described. As a priori, two clinical reasoning skill sessions were conducted using clinico-anatomical case vignettes designed according to the literature regarding clinical reasoning (‘serial cue’ approach and hypothetico-deduction). Students were divided into intervention and control group and crossed over in subsequent sessions. Analysis was done by mixed method approach including measuring proof of benefit using post-test comparison, quantitative survey and qualitative analysis by nominal group discussion. Post test scores were compared using student’s t-test. Feedbacks were analysed using descriptive statistics. The results showed that post test scores were significantly higher in intervention group than the control group in both sessions (P<0.001, 0.016). A total of 66% students felt, diagnostic skills and lateral thinking abilities were improved and It helped in developing problem-solving abilities for 67% students. clinico-anatomical case vignettes helped in understanding anatomical basis of clinical conditions for 61% students. To conclude, introducing clinical reasoning has considerable effect in improving the decision making ability of the students and if incorporated right from the first year, would better prepare the students in successful transition to clinical learning environment.

Heterologous prime-boost with the mRNA-1273 vaccine among CoronaVac-vaccinated healthcare workers in Indonesia

Theresia Santi,Veli Sungono,Lina Kamarga,Baringin De Samakto,Ferry Hidayat,Feronica Kusuma Hidayat,Magy Satolom,Anita Permana,Irawan Yusuf,Ivet Marita Suriapranata,Juandy Jo 대한백신학회 2022 Clinical and Experimental Vaccine Research Vol.11 No.2

Purpose: This study was performed to investigate humoral immune response and adverse events upon the heterologous prime-boost with a single dose of the mRNA-1273 vaccine among fully CoronaVac-vaccinated, infection-naïve healthcare workers in Indonesia. Materials and Methods: One hundred twenty-five eligible healthcare workers were recruited from one hospital for this prospective cohort study. Blood collection was conducted twice, i.e., on 7 days before and 28 days after the booster vaccination. The titer of anti-SARS-CoV-2 receptor-binding domain (RBD) antibodies was quantified accordingly. The post-vaccination adverse event was recorded for both CoronaVac and mRNA-1273 vaccinations. Any breakthrough infection was monitored during the follow-up period. Wilcoxon matched-pairs signed rank test was used to test differences between groups. Results: A significant increase was observed in the titer of anti-SARS-CoV-2 RBD antibodies upon receiving the mRNA-1273 booster (geometric mean titers of 65.57 and 47,445 U/mL in pre- and post-booster, respectively), supporting the argument to use heterologous prime-boost vaccination to improve the protection against COVID-19 in a high-risk population. The mRNA-1273 vaccine, however, caused a higher frequency of adverse events than the CoronaVac vaccine. Nonetheless, the adverse events were considered minor medical events and temporary as all subjects were not hospitalized and fully recovered. Of note, no breakthrough infection was observed during the follow-up to 12 weeks post-booster. Conclusion: The heterologous prime-boost vaccination of healthcare workers with a single dose of the mRNA-1273 vaccine generated a significant elevation in humoral immune response towards RBD of SARS-CoV-2 and was associated with a higher frequency, but minor and transient, adverse events.