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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Multifunctional alginate-based hydrogel with reversible crosslinking for controlled therapeutics delivery(Elsevier, 2020) Ekinci, Duygu; N/A; Department of Chemical and Biological Engineering; Batool, Syeda Rubab; Nazeer, Muhammad Anwaar; Kızılel, Seda; Şahin, Afsun; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; N/A; 28376; 171267Glycan-based alginate hydrogels have great potential in creating new vehicles with responsive behavior and tunable properties for biomedicine. However, precise control and tunability in properties present major barrier for clinical translation of these materials. Here, we report the synthesis of pH responsive anthracene modified glycan-based hydrogels for selective release of therapeutic molecules. Hydrogels were crosslinked through simultaneous photopolymerization of vinyl groups and photodimerization of anthracene. Incorporation of anthracene into these gels leads to reversible control on crosslinking and transition between gel/sol states through dimerization/dedimerization of anthracene groups. Chemotherapeutic drug doxorubicin-loaded hydrogels were then tested in a cancer mimetic microenvironment where 85% of the drug was released from anthracene-conjugated hydrogels at pH 2 for 6 days. Control on gelation with anthracene incorporation was observed through alterations in modulus, where storage modulus was increased two-fold with anthracene conjugation during photopolymerization and photodimerization. Furthermore, cell survival analysis revealed that anthracene conjugation could selectively compromise cancer cell viability without inducing significant toxicity on healthy fibroblasts. This study combines light-induced control of crosslink density due to anthracene and pH-triggered therapeutics delivery with alginate. The approach would be applicable for systems where multiple control is required with high precision.Publication Open Access User interface paradigms for visually authoring mid-air gestures: a survey and a provocation(CEUR-WS, 2014) Department of Media and Visual Arts; Department of Computer Engineering; Baytaş, Mehmet Aydın; Yemez, Yücel; Özcan, Oğuzhan; Faculty Member; Faculty Member; Department of Media and Visual Arts; Department of Computer Engineering; College of Social Sciences and Humanities; College of Engineering; N/A; N/A; 12532Gesture authoring tools enable the rapid and experiential prototyping of gesture-based interfaces. We survey visual authoring tools for mid-air gestures and identify three paradigms used for representing and manipulating gesture information: graphs, visual markup languages and timelines. We examine the strengths and limitations of these approaches and we propose a novel paradigm to authoring location-based mid-air gestures based on space discretization.Publication Open Access Engagement rewarded actor-critic with conservative Q-learning for speech-driven laughter backchannel generation(Association for Computing Machinery (ACM), 2021) Department of Computer Engineering; Bayramoğlu, Öykü Zeynep; Erzin, Engin; Sezgin, Tevfik Metin; Yemez, Yücel; Faculty Member; Faculty Member; Faculty Member; Department of Computer Engineering; Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); College of Engineering; Graduate School of Sciences and Engineering; N/A; 34503; 18632; 107907We propose a speech-driven laughter backchannel generation model to reward engagement during human-agent interaction. We formulate the problem as a Markov decision process where speech signal represents the state and the objective is to maximize human engagement. Since online training is often impractical in the case of human-agent interaction, we utilize the existing human-to-human dyadic interaction datasets to train our agent for the backchannel generation task. We address the problem using an actor-critic method based on conservative Q-learning (CQL), that mitigates the distributional shift problem by suppressing Q-value over-estimation during training. The proposed CQL based approach is evaluated objectively on the IEMOCAP dataset for laughter generation task. When compared to the existing off-policy Q-learning methods, we observe an improved compliance with the dataset in terms of laugh generation rate. Furthermore, we show the effectiveness of the learned policy by estimating the expected engagement using off-policy policy evaluation techniques.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 Conditional law and occupation times of two-sided sticky Brownian motion(Elsevier, 2020) Department of Mathematics; Çağlar, Mine; Can, Buğra; Faculty Member; Department of Mathematics; College of Sciences; 105131; N/ASticky Brownian motion on the real line can be obtained as a weak solution of a system of stochastic differential equations. We find the conditional distribution of the process given the driving Brownian motion, both at an independent exponential time and at a fixed time t>0. As a classical problem, we find the distribution of the occupation times of a half-line, and at 0, which is the sticky point for the process.Publication Open Access An information theoretical analysis of broadcast networks and channel routing for FRET-based nanoscale communications(Institute of Electrical and Electronics Engineers (IEEE), 2012) Kuşcu, Murat; Malak, Derya; Akan, Özgür Barış; Faculty Member; College of EngineeringNanoscale communication based on Forster Resonance Energy Transfer (FRET) enables nanomachines to communicate with each other using the excited state of the fluorescent molecules as the information conveyer. In this study, FRET-based nanoscale communication is further extended to realize FRET-based nanoscale broadcast communication with one transmitter and many receiver nanomachines, and the performance of the broadcast channel is analyzed information theoretically. Furthermore, an electrically controllable routing mechanism is proposed exploiting the Quantum Confined Stark Effect (QCSE) observed in quantum dots. It is shown that by appropriately selecting the employed molecules on the communicating nanomachines, it is possible to control the route of the information flow by externally applying electric field in FRET-based nanonetworks.Publication Open Access Compressed training based massive MIMO(Institute of Electrical and Electronics Engineers (IEEE), 2019) Yılmaz, Baki Berkay; Department of Electrical and Electronics Engineering; Erdoğan, Alper Tunga; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 41624Massive multiple-input-multiple-output (MIMO) scheme promises high spectral efficiency through the employment of large scale antenna arrays in base stations. In time division duplexed implementations, co-channel mobile terminals transmit training information such that base stations can estimate and exploit channel state information to spatially multiplex these users. In the conventional approach, the optimal choice for training length was shown to be equal to the number of users, K. In this paper, we propose a new semiblind framework, named as "MIMO Compressed Training," which utilizes information symbols in addition to training symbols for adaptive spatial multiplexing. We show that this framework enables us to reduce (compress) the training length down to a value close to log(2) (K), i.e., the logarithm of the number of users, without any sparsity assumptions on the channel matrix. We also derive a prescription for the required packet length for proper training. The framework is built upon some convex optimization settings that enable efficient and reliable algorithm implementations. The numerical experiments demonstrate the strong potential of the proposed approach in terms of increasing the number of users per cell and improving the link quality.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.