Cancer is in general not a result of an abnormality of a single gene but a consequence of changes in many genes, it is therefore of great importance to understand the roles of different oncogenic and tumor suppressor pathways in tumorigenesis. In recent years, there have been many computational models developed to study the genetic alterations of different pathways in the evolutionary process of cancer. However, most of the methods are knowledge-based enrichment analyses and inflexible to analyze user-defined pathways or gene sets. In this paper, we develop a nonparametric and data-driven approach to testing for the dynamic changes of pathways over the cancer progression. Our method is based on an expansion and refinement of the pathway being studied, followed by a graph-based multivariate test, which is very easy to implement in practice. The new test is applied to the rich Cancer Genome Atlas data to study the (epi)genetic alterations of 186 KEGG pathways in the development of serous ovarian cancer. To make use of the comprehensive data, we incorporate three data types in the analysis representing gene expression level, copy number and DNA methylation level. Our analysis suggests a list of nine pathways that are closely associated with serous ovarian cancer progression, including cell cycle, ERBB, JAK-STAT signaling and p53 signaling pathways. By pairwise tests, we found that most of the identified pathways contribute only to a particular transition step. For instance, the cell cycle and ERBB pathways play key roles in the early-stage transition, while the ECM receptor and apoptosis pathways contribute to the progression from stage III to stage IV. The proposed computational pipeline is powerful in detecting important pathways and gene sets that drive cancers at certain stage(s). It offers new insights into the understanding of molecular mechanism of cancer initiation and progression. © 2020 Elsevier Ltd
Professional learning societies (PLS) are a systematic method for improving teaching and learning performance through designing and building professional learning societies. This leads to overcoming a culture of isolation and fragmenting the work of educational supervisors. Many studies show that constructing and developing strong professional learning societies - focused on improving education, curriculum and evaluation will lead to increased cooperation and participation of educational supervisors and teachers, as well as increases the application of effective educational practices in the classroom.
The roles of the educational supervisor to ensure the best and optimal implementation and activation of professional learning soci
... Show MorePhotonic crystal fiber interferometers are widely used for sensing applications. In this work, solid core-Photonic crystal fiber based on Mach-Zehnder modal interferometer for sensing refractive index was presented. The general structure of sensor applied by splicing short lengths of PCF in both sides with conventional single mode fiber (SMF-28). To apply modal interferometer theory; collapsing technique based on fusion splicing used to excite higher order modes (LP01 and LP11). Laser diode (1550 nm) has been used as a pump light source. Where a high sensitive optical spectrum analyzer (OSA) was used to monitor and record the transmitted. The experimental work shows that the interference spectrum of Photonic crystal fiber interferometer
... Show MoreA Strength Pareto Evolutionary Algorithm 2 (SPEA 2) approach for solving the multi-objective Environmental / Economic Power Dispatch (EEPD) problem is presented in this paper. In the past fuel cost consumption minimization was the aim (a single objective function) of economic power dispatch problem. Since the clean air act amendments have been applied to reduce SO2 and NOX emissions from power plants, the utilities change their strategies in order to reduce pollution and atmospheric emission as well, adding emission minimization as other objective function made economic power dispatch (EPD) a multi-objective problem having conflicting objectives. SPEA2 is the improved version of SPEA with better fitness assignment, density estimation, an
... Show MoreThis study employs wavelet transforms to address the issue of boundary effects. Additionally, it utilizes probit transform techniques, which are based on probit functions, to estimate the copula density function. This estimation is dependent on the empirical distribution function of the variables. The density is estimated within a transformed domain. Recent research indicates that the early implementations of this strategy may have been more efficient. Nevertheless, in this work, we implemented two novel methodologies utilizing probit transform and wavelet transform. We then proceeded to evaluate and contrast these methodologies using three specific criteria: root mean square error (RMSE), Akaike information criterion (AIC), and log
... Show MoreThe present study aims to investigate the various request constructions used in Classical Arabic and Modern Arabic language by identifying the differences in their usage in these two different genres. Also, the study attempts to trace the cases of felicitous and infelicitous requests in the Arabic language. Methodologically, the current study employs a web-based corpus tool (Sketch Engine) to analyze different corpora: the first one is Classical Arabic, represented by King Saud University Corpus of Classical Arabic, while the second is The Arabic Web Corpus “arTenTen” representing Modern Arabic. To do so, the study relies on felicity conditions to qualitatively interpret the quantitative data, i.e., following a mixed mode method
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