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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Evolutionary multiobjective feature selection for sentiment analysis(Institute of Electrical and Electronics Engineers (IEEE), 2021) Pelin Angın; Deniz, Ayça; Department of International Relations; Angın, Merih; Faculty Member; Department of International Relations; College of Administrative Sciences and Economics; 308500Sentiment analysis is one of the prominent research areas in data mining and knowledge discovery, which has proven to be an effective technique for monitoring public opinion. The big data era with a high volume of data generated by a variety of sources has provided enhanced opportunities for utilizing sentiment analysis in various domains. In order to take best advantage of the high volume of data for accurate sentiment analysis, it is essential to clean the data before the analysis, as irrelevant or redundant data will hinder extracting valuable information. In this paper, we propose a hybrid feature selection algorithm to improve the performance of sentiment analysis tasks. Our proposed sentiment analysis approach builds a binary classification model based on two feature selection techniques: an entropy-based metric and an evolutionary algorithm. We have performed comprehensive experiments in two different domains using a benchmark dataset, Stanford Sentiment Treebank, and a real-world dataset we have created based on World Health Organization (WHO) public speeches regarding COVID-19. The proposed feature selection model is shown to achieve significant performance improvements in both datasets, increasing classification accuracy for all utilized machine learning and text representation technique combinations. Moreover, it achieves over 70% reduction in feature size, which provides efficiency in computation time and space.Publication Open Access Autophagy and cancer dormancy(Frontiers, 2021) Akçay, Arzu; Akkoç, Yunus; Peker, Nesibe; Gözüaçık, Devrim; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; N/A; N/A; 40248Metastasis and relapse account for the great majority of cancer-related deaths. Most metastatic lesions are micro metastases that have the capacity to remain in a non-dividing state called "dormancy" for months or even years. Commonly used anticancer drugs generally target actively dividing cancer cells. Therefore, cancer cells that remain in a dormant state evade conventional therapies and contribute to cancer recurrence. Cellular and molecular mechanisms of cancer dormancy are not fully understood. Recent studies indicate that a major cellular stress response mechanism, autophagy, plays an important role in the adaptation, survival and reactivation of dormant cells. In this review article, we will summarize accumulating knowledge about cellular and molecular mechanisms of cancer dormancy, and discuss the role and importance of autophagy in this context.Publication Open Access The structural basis of Akt PH domain interaction with calmodulin(Elsevier, 2021) Jang, Hyunbum; Nussinov, Ruth; N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Weako, Jackson; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 26605; 8745Akt plays a key role in the Ras/PI3K/Akt/mTOR signaling pathway. In breast cancer, Akt translocation to the plasma membrane is enabled by the interaction of its pleckstrin homology domain (PHD) with calmodulin (CaM). At the membrane, the conformational change promoted by PIP3 releases CaM and facilitates Thr308 and Ser473 phosphorylation and activation. Here, using modeling and molecular dynamics simulations, we aim to figure out how CaM interacts with Akt's PHD at the atomic level. Our simulations show that CaM-PHD interaction is thermodynamically stable and involves a beta-strand rather than an alpha-helix, in agreement with NMR data, and that electrostatic and hydrophobic interactions are critical. The PHD interacts with CaM lobes; however, multiple modes are possible. IP4, the polar head of PIP3, weakens the CaM-PHD interaction, implicating the release mechanism at the plasma membrane. Recently, we unraveled the mechanism of PI3K alpha activation at the atomistic level and the structural basis for Ras role in the activation. Here, our atomistic structural data clarify the mechanism of how CaM interacts, delivers, and releases Akt-the next node in the Ras/PI3K pathway-at the plasma membrane.Publication Open Access Low complexity adaptation for reconfigurable intelligent surface-based MIMO systems(Institute of Electrical and Electronics Engineers (IEEE), 2020) Yiğit, Zehra; Altunbaş, İbrahim; Department of Electrical and Electronics Engineering; Başar, Ertuğrul; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 149116Reconfigurable intelligent surface (RIS)-based transmission technology offers a promising solution to enhance wireless communication performance cost-effectively through properly adjusting the parameters of a large number of passive reflecting elements. This letter proposes a cosine similarity theorem-based low-complexity algorithm for adapting the phase shifts of an RIS that assists a multiple-input multiple-output (MIMO) transmission system. A semi-analytical probabilistic approach is developed to derive the theoretical average bit error probability (ABEP) of the system. Furthermore, the validity of the theoretical analysis is supported through extensive computer simulations.Publication Open Access Fundamental sensitivity limitations of nanomechanical resonant sensors due to thermomechanical noise(Institute of Electrical and Electronics Engineers (IEEE), 2020) Hanay, M. Selim; Department of Electrical and Electronics Engineering; Demir, Alper; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 3756Nanomechanical resonators are used as high performance sensors of physical stimuli such as force and mass changes. Any such physical stimulus produces a shift in the resonance frequency of the nanomechanical structure, which can be measured accurately by using a feedback system that locks the frequency of a signal generator to the resonance. Closed-loop frequency tracking is the most prevalent technique in the fields of nanomechanical sensors and non-contact atomic force microscopy. Ultimate performance of sensors is limited by various nonideal effects such as temperature variations, radiation, electromagnetic interference, and noise arising from inherent physical mechanisms. Here, we consider the noise performance of nanomechanical resonant sensors, which has so far eluded explanation with conflicting results reported in the literature. We present a precise theory for these ubiquitous sensors based on nanomechanical resonators under feedback in order to decipher the fundamental sensitivity limitations due to thermomechanical noise. The results we obtain, when the performance is limited by the thermomechanical noise of the resonator, are in complete agreement with the ones from stochastic simulations. Our findings shed light on recent results in the literature and resolve a critical problem regarding the frequency noise of nanomechanical sensors under feedback. Our results have applications in nanomechanics, atomic force microscopy, microwave and suspended microchannel resonators.Publication Open Access Al2O3 micro- and nanostructures affect vascular cell response(Royal Society of Chemistry (RSC), 2016) Kiefer, Karin; Akpınar, Gürler; Haidar, Ayman; Ikier, Tuba; Akkan, Çağrı Kaan; Akman, Erhan; Lee, Juseok; Miro, Marina Martinez; Kaçar, Elif; Demir, Arif; Veith, Michael; Kasap, Murat; Kesmez, Mehmet; Abdul-Khaliq, Hashim; Aktaş, Cenk; N/A; Ural, Dilek; Faculty Member; School of Medicine; 1057In-stent restenosis (ISR) is one of the most common and serious complications observed after stent implantation. ISR is characterized by the inordinate proliferation of smooth muscle cells (SMC) that leads to narrowing of the blood vessels. To achieve a healthy endothelium, it is critical to selectively enhance the growth of endothelial cells (EC) while suppressing the growth of smooth muscle cells, which is still a major challenge and yet to be achieved. In this study, novel surfaces have been developed to support the selective growth of endothelial cells. Micro-and nanostructured Al2O3 surfaces with unique topographical features were fabricated and tested. Surface characterization and cellular response of endothelial cells (HUVEC) as well as smooth muscle cells (HUVSMC) has been investigated at cellular and molecular levels. A topography driven selective cell response of ECs over SMCs was demonstrated successfully. This selective response of ECs was also analyzed at protein levels in order to understand the basic mechanism.Publication Open Access Chaotic spin correlations in frustrated Ising hierarchical lattices(American Physical Society (APS), 2009) Berker, A. Nihat; Department of Physics; Aral, Neşe; Department of Physics; College of SciencesSpin-spin correlations are calculated in frustrated hierarchical Ising models that exhibit chaotic renormalization-group behavior. The spin-spin correlations, as a function of distance, behave chaotically. The far correlations, but not the near correlations, are sensitive to small changes in temperature or frustration, with temperature changes having a larger effect. On the other hand, the calculated free energy, internal energy, and entropy are smooth functions of temperature. The recursion-matrix calculation of thermodynamic densities in a chaotic band is demonstrated. The leading Lyapunov exponents are calculated as a function of frustration.Publication Open Access Transcriptomic response of yeast cells to ATX1 deletion under different copper levels(BioMed Central, 2016) Cankorur-Çetinkaya, Ayça; Eraslan, Serpil; Kırdar, Betül; Eraslan, Serpil; Other; Koç University HospitalBackground: Iron and copper homeostatic pathways are tightly linked since copper is required as a cofactor for high affinity iron transport. Atx1p plays an important role in the intracellular copper transport as a copper chaperone transferring copper from the transporters to Ccc2p for its subsequent insertion into Fet3p, which is required for high affinity iron transport. Results: In this study, genome-wide transcriptional landscape of ATX1 deletants grown in media either lacking copper or having excess copper was investigated. ATX1 deletants were allowed to recover full respiratory capacity in the presence of excess copper in growth environment. The present study revealed that iron ion homeostasis was not significantly affected by the absence of ATX1 either at the transcriptional or metabolic levels, suggesting other possible roles for Atx1p in addition to its function as a chaperone in copper-dependent iron absorption. The analysis of the transcriptomic response of atx1 Delta/atx1 Delta and its integration with the genetic interaction network highlighted for the first time, the possible role of ATX1 in cell cycle regulation, likewise its mammalian counterpart ATOX1, which was reported to play an important role in the copper-stimulated proliferation of non-small lung cancer cells. Conclusions: The present finding revealed the dispensability of Atx1p for the transfer of copper ions to Ccc2p and highlighted its possible role in the cell cycle regulation. The results also showed the potential of Saccharomyces cerevisiae as a model organism in studying the capacity of ATOX1 as a therapeutic target for lung cancer therapy.Publication Open Access CdTe quantum dot sensitized hexaniobate nanoscrolls and their photoelectrochemical properties(Royal Society of Chemistry (RSC), 2012) Department of Chemistry; Öztuna, Feriha Eylül Saraç; Akkaya, Ceren Yılmaz; Acar, Havva Funda Yağcı; Ünal, Uğur; PhD Student; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Sciences; N/A; N/A; 178902; N/AWe have constructed hybrid quantum dot-layered niobate films with an electrophoretic deposition method. The structure and photoelectrochemical behaviour were demonstrated.Publication Open Access Multiple shape correspondence by dynamic programming(Wiley, 2014) Sahillioğlu, Y.; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of EngineeringWe present a multiple shape correspondence method based on dynamic programming, that computes consistent bijective maps between all shape pairs in a given collection of initially unmatched shapes. As a fundamental distinction from previous work, our method aims to explicitly minimize the overall distortion, i.e., the average isometric distortion of the resulting maps over all shape pairs. We cast the problem as optimal path finding on a graph structure where vertices are maps between shape extremities. We exploit as much context information as possible using a dynamic programming based algorithm to approximate the optimal solution. Our method generates coarse multiple correspondences between shape extremities, as well as denser correspondences as by-product. We assess the performance on various mesh sequences of (nearly) isometric shapes. Our experiments show that, for isometric shape collections with non-uniform triangulation and noise, our method can compute relatively dense correspondences reasonably fast and outperform state of the art in terms of accuracy.