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
Recently, detecting dynamic patterns for growing communities in social networks have attracted significant attention. The objective of dynamic community detection is to analyze and identify clusters in complex networks that change over time. Different optimization algorithms, including both single-objective and multi-objective approaches, have been employed to address the challenge of dynamic community detection. Although current evolutionary algorithms for identifying community structure can traverse extensive areas of partition space, they often become stuck in local minima. In addition, limited studies have addressed this issue by integrating local search strategies with evolutionary algorithms for community identification. This paper in
... Show MoreNon uniform channelization is a crucial task in cognitive radio receivers for obtaining separate channels from the digitized wideband input signal at different intervals of time. The two main requirements in the channelizer are reconfigurability and low complexity. In this paper, a reconfigurable architecture based on a combination of Improved Coefficient Decimation Method (ICDM) and Coefficient Interpolation Method (CIM) is proposed. The proposed Hybrid Coefficient Decimation-Interpolation Method (HCDIM) based filter bank (FB) is able to realize the same number of channels realized using (ICDM) but with a maximum decimation factor divided by the interpolation factor (L), which leads to less deterioration in stop band at
... Show MoreThe petroleum industry, which is one of the pillars of the national economy, has the potential to generate vast wealth and employment possibilities. The transportation of petroleum products is complicated and changeable because of the hazards caused by the corrosion consequences. Hazardous chemical leaks caused by natural disasters may harm the environment, resulting in significant economic losses. It significantly threatens the aim for sustainable development. When a result, determining the likelihood of leakage and the potential for environmental harm, it becomes a top priority for decision-makers as they develop maintenance plans. This study aims to provide an in-depth understanding of the risks associated with oil and gas pipeli
... Show MoreA robust video-bitrate adaptive scheme at client-aspect plays a significant role in keeping a good quality of video streaming technology experience. Video quality affects the amount of time the video has turned off playing due to the unfilled buffer state. Therefore to maintain a video streaming continuously with smooth bandwidth fluctuation, a video buffer structure based on adapting the video bitrate is considered in this work. Initially, the video buffer structure is formulated as an optimal control-theoretic problem that combines both video bitrate and video buffer feedback signals. While protecting the video buffer occupancy from exceeding the limited operating level can provide continuous video str
... Show MoreA new synthesis of Schiff (K) 6 and Mannich bases (Q) 7 had formed compound (Q) 7 by reacting compound (K) with N-methylaniline at the presence of formalin 35% to given Mannich base (Q). Additionally, new complexes were formed by reacting Schiff base (K) with metal salts CuCl2·2H2O, PdCl2·2H2O, and PtCl6·6H2O by 2:1 of M:L ratio. New ligands and their complexes were characterized, exanimated, and confirmed through several techniques, including FTIR, UV-visible, 1H-NMR, 13C-NMR spectroscopy, CHN analysis, FAA, TG, molar conductivity, and magnetic susceptibility. These compounds and their complexes were screened against breast cancer cells. It was determined that several of these compounds had a significant anti-breast cancer effec
... Show MoreBackground: CYP1A1 gene polymorphisms and tobacco smoking are among several risk factors for various types of cancers, but their influence on breast cancer remains controversial. We analyzed the possible association of CYP1A1 gene polymorphisms and tobacco smoking-related breast cancer in women from Iraq. Materials and methods: In this case-control study, gene polymorphism of CYP1A1 gene (CYP1A1m1, T6235C and CYP1A1m2, A4889G) of 199 histologically verified breast cancer patients' and 160 cancer-free control women's specimens were performed by using PCR-based restriction fragment length polymorphism. Results: Three genotype frequencies (TT, TC, and CC) of CYP1A1m1T/C appeared in 16.1, 29.6, and 54.3% of women with breast cancer, respectiv
... Show MoreBackground: Colorectal cancer, the most common gastrointestinal cancer, is a significant health issue globally. Mucin 16 plays a critical role in cancer signal transduction pathways and is a potential glycoprotein target for cancer therapy. The miRNA-200 family also regulates the expression of numerous genes that play vital roles in cancer cells. This study aimed to investigate the changes in mucin 16 and miRNA-200a in patients with colorectal cancer (CRC). Subjects and Methods: Fifty-six patients with CRC, including 26 in stage 3 and 30 in stage 4, were included in this study, along with 38 healthy volunteers as a control group. Parameters such as mucin 16, miRNA-200a, total protein, albumin, globulin, and the albumin/globulin rati
... Show MoreProxy-based sliding mode control PSMC is an improved version of PID control that combines the features of PID and sliding mode control SMC with continuously dynamic behaviour. However, the stability of the control architecture maybe not well addressed. Consequently, this work is focused on modification of the original version of the proxy-based sliding mode control PSMC by adding an adaptive approximation compensator AAC term for vibration control of an Euler-Bernoulli beam. The role of the AAC term is to compensate for unmodelled dynamics and make the stability proof more easily. The stability of the proposed control algorithm is systematically proved using Lyapunov theory. Multi-modal equation of motion is derived using the Galerkin metho
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