Possible Prognostic Role of HER2/Neu in Ductal Carcinoma In Situ and Atypical Ductal Proliferative Lesions of the Breast

Daoud, Sahar Aly,Ismail, Wesam Maghawri,Abdelhamid, Mohamed Salah,Nabil, Tamer Mohamed,Daoud, Sahar Aly Asian Pacific Journal of Cancer Prevention 2016 Asian Pacific journal of cancer prevention Vol.17 No.8

HER2/neu is a well-established prognostic and predictive factor for invasive breast cancer. However, the role of HER2/neu in ductal breast carcinoma in situ (DCIS) is debated and recent data have suggested that it is mainly linked to in situ local recurrence. Although molecular data suggest that atypical ductal hyperplasia (ADH) and duct carcinoma in situ (DCIS) are related lesions, albeit with vastly different clinical implications, the role of HER2/neu expression in atypical ductal hyperplasia is not well defined either. The aim of this study was to evaluate over expression of HER2/neu in DCIS and cases of ADH in comparison with invasive breast carcinoma. Archival primary breast carcinoma paraffin blocks (n=15), DCIS only (n=10) and ductal epithelial hyperplasia and other breast benign lesions (n=25) were analyzed for HER2/neu immunoexpression. Follow up was available for 40% of the patients. HER2/neu was positive in 80%of both DCIS and invasive carcinoma, and 67% of atypical ductal hyperplasia (ADH) cases. Thus at least a subset of patients with preinvasive breast lesions were positive, which strongly suggests a role for Her2/neu in identifying high-risk patients for malignant transformation. Although these are preliminary data, which need further studies of gene amplification within these patients as well as a larger patient cohort with longer periods of follow up, they support the implementation of routine Her2/neu testing in patients diagnosed as pure DCIS and in florid ADH.

Evaluation of refined theories for multilayered shells via Axiomatic/Asymptotic method

Daoud S. Mashat,E. Carrera,Ashraf M. Zenkour,Sadah A. Al Khateeb,A. Lamberti 대한기계학회 2014 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.28 No.11

This paper is devoted to refined shell theories for the analysis of isotropic and laminated shells. Refined theories are built by assuminghigher expansion order for the displacement field in the shell thickness directions. The implementation of these theories is made accordingto the Carrera unified formulation (CUF) which makes it possible to obtain shell governing equations in terms of fundamental nucleiwhose form is independent of the chosen theory shell. Equivalent single layer and layer wise schemes are used. The axiomatic/asymptotic technique is employed to evaluate the effectiveness of each displacement variable in the adopted displacement expansion. The error introduced by each term deactivation is evaluated with respect to a reference solution and according to a given error criterion; ifthe error computed does not exceed an a priori defined threshold the term is considered as not relevant and discarded. In this way it ispossible to construct reduced models for each stress/displacement component. Attention has been restricted to closed form Navier typesolutions and simply supported orthotropic shells are considered in the numerical investigation. Analysis of the displacement variablesrelevance is performed considering the influence of the kind of material and of the geometry, specifically isotropic and laminated materialsand thick and thin shells. “Best”' reduced models are proposed and related distributions are discussed.

Detecting outliers in segmented genomes of flu virus using an alignment-free approach

Daoud, Mosaab Korea Genome Organization 2020 Genomics & informatics Vol.18 No.1

In this paper, we propose a new approach to detecting outliers in a set of segmented genomes of the flu virus, a data set with a heterogeneous set of sequences. The approach has the following computational phases: feature extraction, which is a mapping into feature space, alignment-free distance measure to measure the distance between any two segmented genomes, and a mapping into distance space to analyze a quantum of distance values. The approach is implemented using supervised and unsupervised learning modes. The experiments show robustness in detecting outliers of the segmented genome of the flu virus.

The extension of the largest generalized-eigenvalue based distance metric D_ij(γ₁) in arbitrary feature spaces to classify composite data points

Daoud, Mosaab Korea Genome Organization 2019 Genomics & informatics Vol.17 No.4

Analyzing patterns in data points embedded in linear and non-linear feature spaces is considered as one of the common research problems among different research areas, for example: data mining, machine learning, pattern recognition, and multivariate analysis. In this paper, data points are heterogeneous sets of biosequences (composite data points). A composite data point is a set of ordinary data points (e.g., set of feature vectors). We theoretically extend the derivation of the largest generalized eigenvalue-based distance metric D<SUB>ij</SUB>(γ<SUB>1</SUB>) in any linear and non-linear feature spaces. We prove that D<SUB>ij</SUB>(γ<SUB>1</SUB>) is a metric under any linear and non-linear feature transformation function. We show the sufficiency and efficiency of using the decision rule $\bar{{\delta}}_{{\Xi}i}$(i.e., mean of D<SUB>ij</SUB>(γ<SUB>1</SUB>)) in classification of heterogeneous sets of biosequences compared with the decision rules min<SUB>𝚵i</SUB>and median<SUB>𝚵i</SUB>. We analyze the impact of linear and non-linear transformation functions on classifying/clustering collections of heterogeneous sets of biosequences. The impact of the length of a sequence in a heterogeneous sequence-set generated by simulation on the classification and clustering results in linear and non-linear feature spaces is empirically shown in this paper. We propose a new concept: the limiting dispersion map of the existing clusters in heterogeneous sets of biosequences embedded in linear and nonlinear feature spaces, which is based on the limiting distribution of nucleotide compositions estimated from real data sets. Finally, the empirical conclusions and the scientific evidences are deduced from the experiments to support the theoretical side stated in this paper.

A note on the distance distribution paradigm for Mosaab-metric to process segmented genomes of influenza virus

Daoud, Mosaab Korea Genome Organization 2020 Genomics & informatics Vol.18 No.1

In this paper, we present few technical notes about the distance distribution paradigm for Mosaab-metric using 1, 2, and 3 grams feature extraction techniques to analyze composite data points in high dimensional feature spaces. This technical analysis will help the specialist in bioinformatics and biotechnology to deeply explore the biodiversity of influenza virus genome as a composite data point. Various technical examples are presented in this paper, in addition, the integrated statistical learning pipeline to process segmented genomes of influenza virus is illustrated as sequential-parallel computational pipeline.

Insights of window-based mechanism approach to visualize composite biodata point in feature spaces

Daoud, Mosaab Korea Genome Organization 2019 Genomics & informatics Vol.17 No.1

In this paper, we propose a window-based mechanism visualization approach as an alternative way to measure the seriousness of the difference among data-insights extracted from a composite biodata point. The approach is based on two components: undirected graph and Mosaab-metric space. The significant application of this approach is to visualize the segmented genome of a virus. We use Influenza and Ebola viruses as examples to demonstrate the robustness of this approach and to conduct comparisons. This approach can provide researchers with deep insights about information structures extracted from a segmented genome as a composite biodata point, and consequently, to capture the segmented genetic variations and diversity (variants) in composite data points.

Stromal Modulation and its Role in the Diagnosis of Papillary Patterned Thyroid Lesions

Daoud, Sahar Aly,Esmail, Reham Shehab El Nemr,Hareedy, Amal Ahmed,Khalil, Abdullah Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.8

The papillary patterned lesion of thyroid may be challenging with many diagnostic pitfalls. Tumor stroma plays an important part in the determination of the tumor phenotype. CD34 is thought to be involved in the modulation of cell adhesion and signal transduction as CD34(+) fibrocytes are potent antigen-presenting cells. Smooth muscle actin (SMA) positivity could be diagnostic for fibroblast activation during tumorigenesis. We aimed to examine the expression of CD34 and alphaSMA in the stroma of papillary thyroid hyperplasia, papillary thyroid carcinoma and papillary tumors of uncertain malignant potential in order to elucidate their possible differential distribution and roles. A total number of 54 cases with papillary thyroid lesions were studied by routine H&E staining, CD34 and ASMA immunostaining. ASMA was not expressed in benign papillary hyperplastic lesions while it was expressed in papillary carcinoma, indicating that tumors have modulated stroma. Although the stroma was not well developed in papillary lesions with equivocal features of uncertain potentiality, CD34 was notable in such cases with higher incidence in malignant cases. So ASMA as well as CD34 could predict neoplastic behavior, pointing to the importance of the stromal role. Differences between groups suggest that the presence of CD34 + stromal cells is an early event in carcinogensis and is associated with neoplasia, however ASMA+ cells are more likely to be associated with malignant behavior and metastatic potential adding additional tools to the light microscopic picture helping in diagnosis of problematic cases with H&E.

Hybrid-Boost Modular Multilevel Converter-Based Medium-Voltage Multiphase Induction Motor Drive for Subsea Applications

Daoud, Mohamed,Elserougi, Ahmed,Massoud, Ahmed,Bojoi, Radu,Abdel-Khalik, Ayman,Ahmed, Shehab The Korean Institute of Power Electronics 2019 JOURNAL OF POWER ELECTRONICS Vol.19 No.3

This paper proposes a hybrid-boost Modular Multilevel Converter (MMC) for the Medium-Voltage (MV) Variable Speed Drives (VSDs) employed in subsea applications, such as oil and gas recovery. In the presented architecture, a hybrid-boost MMC with a reduced number of semiconductor devices driving a multiphase Induction Machine (IM) is investigated. The stepped output voltage generated by the MMC reduces or eliminates the filtering requirements. Moreover, the boosting capability of the proposed architecture eliminates the need for bulky low-frequency transformers at the converter output terminals. A detailed illustration of the hybrid-boost MMC operation, the expected limitations/constraints, and the voltage balancing technique are presented. A simulation model of the proposed MV hybrid-boost MMC-based five-phase IM drive has been built to investigate the system performance. Finally, a downscaled prototype has been constructed for experimental verification.

Transcriptome Analysis of the Barley-Rhynchosporium secalis Interaction

Al-Daoude, Antonious,Shoaib, Amina,Al-Shehadah, Eyad,Jawhar, Mohammad,Arabi, Mohammad Imad Eddin The Korean Society of Plant Pathology 2014 Plant Pathology Journal Vol.30 No.4

Leaf scald caused by the infection of Rhynchosporium secalis, is a worldwide crop disease resulting in significant loss of barley yield. In this study, a systematic sequencing of expressed sequence tags (ESTs) was chosen to obtain a global picture of the assembly of genes involved in pathogenesis. To identify a large number of plant ESTs, which are induced at different time points, an amplified fragment length polymorphism (AFLP) display of complementary DNA (cDNA) was utilized. Transcriptional changes of 140 ESTs were observed, of which 19 have no previously described function. Functional annotation of the transcripts revealed a variety of infection-induced host genes encoding classical pathogenesis-related (PR) or genes that play a role in the signal transduction pathway. The expression analyses by a semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) revealed that Rar1 and Rpg4 are defense inducible genes, and were consistent with the cDNA-AFLP data in their expression patterns. Hence, the here presented transcriptomic approach provides novel global catalogue of genes not currently represented in the EST databases.

Insights of window-based mechanism approach to visualize composite biodata point in feature spaces

Mosaab Daoud 한국유전체학회 2019 Genomics & informatics Vol.17 No.1

In this paper, we propose a window-based mechanism visualization approach as an alternative way to measure the seriousness of the difference among data-insights extracted from a composite biodata point. The approach is based on two components: undirected graph and Mosaab-metric space. The significant application of this approach is to visualize the segmented genome of a virus. We use Influenza and Ebola viruses as examples to demonstrate the robustness of this approach and to conduct comparisons. This approach can provide researchers with deep insights about information structures extracted from a segmented genome as a composite biodata point, and consequently, to capture the segmented genetic variations and diversity (variants) in composite data points.