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Publication Open Access 1899 yılı Osmanlı İmparatorluğu için jeomekansal ve çok modlu bir ulaşım ağı oluşturma denemesi(Koç University Research Center for Anatolian Civilizations (ANAMED) / Koç Üniversitesi Anadolu Medeniyetleri Araştırma Merkezi (ANAMED), 2020) Gerrits, Piet; Department of History; Kabadayı, Mustafa Erdem; Özkan, Osman; Koçak, Turgay; Faculty Member; Teaching Faculty; Department of History; College of Social Sciences and Humanities; 33267; N/A; N/APublication Open Access 3D bioprinted organ?on?chips(Wiley, 2022) Mustafaoğlu, Nur; Zhang, Yu Shrike; Department of Mechanical Engineering; N/A; N/A; Dabbagh, Sajjad Rahmani; Sarabi, Misagh Rezapour; Birtek, Mehmet Tuğrul; Taşoğlu, Savaş; Faculty Member; Department of Mechanical Engineering; KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); 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 Social Sciences and Humanities; Graduate School of Sciences and Engineering; N/A; N/A; N/A; 291971Organ-on-a-chip (OOC) platforms recapitulate human in vivo-like conditions more realistically compared to many animal models and conventional two-dimensional cell cultures. OOC setups benefit from continuous perfusion of cell cultures through microfluidic channels, which promotes cell viability and activities. Moreover, microfluidic chips allow the integration of biosensors for real-time monitoring and analysis of cell interactions and responses to administered drugs. Three-dimensional (3D) bioprinting enables the fabrication of multicell OOC platforms with sophisticated 3D structures that more closely mimic human tissues. 3D-bioprinted OOC platforms are promising tools for understanding the functions of organs, disruptive influences of diseases on organ functionality, and screening the efficacy as well as toxicity of drugs on organs. Here, common 3D bioprinting techniques, advantages, and limitations of each method are reviewed. Additionally, recent advances, applications, and potentials of 3D-bioprinted OOC platforms for emulating various human organs are presented. Last, current challenges and future perspectives of OOC platforms are discussed.Publication Open Access 3D printed personalized magnetic micromachines from patient blood-derived biomaterials(American Association for the Advancement of Science (AAAS), 2021) Ceylan, Hakan; Doğan, Nihal Olcay; Yaşa, İmmihan Ceren; Department of Mechanical Engineering; Sitti, Metin; Musaoğlu, Miraç Nur; Kulalı, Zeynep Umut; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 297104; N/A; N/AWhile recent wireless micromachines have shown increasing potential for medical use, their potential safety risks concerning biocompatibility need to be mitigated. They are typically constructed from materials that are not intrinsically compatible with physiological environments. Here, we propose a personalized approach by using patient blood-derivable biomaterials as the main construction fabric of wireless medical micromachines to alleviate safety risks from biocompatibility. We demonstrate 3D printed multiresponsive microswimmers and microrollers made from magnetic nanocomposites of blood plasma, serum albumin protein, and platelet lysate. These micro-machines respond to time-variant magnetic fields for torque-driven steerable motion and exhibit multiple cycles of pH-responsive two-way shape memory behavior for controlled cargo delivery and release applications. Their proteinaceous fabrics enable enzymatic degradability with proteinases, thereby lowering risks of long-term toxicity. The personalized micromachine fabrication strategy we conceptualize here can affect various future medical robots and devices made of autologous biomaterials to improve biocompatibility and smart functionality.Publication Open Access 3D-printed microneedles in biomedical applications(Elsevier, 2021) Rahbarghazi, Reza; Yetişen, Ali Kemal; N/A; Department of Mechanical Engineering; Dabbagh, Sajjad Rahmani; Sarabi, Misagh Rezapour; Sokullu, Emel; Taşoğlu, Savaş; Faculty Member; Faculty Member; Department of Mechanical Engineering; KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Social Sciences and Humanities; Graduate School of Sciences and Engineering; School of Medicine; College of Engineering; N/A; N/A; 163024; 291971Conventional needle technologies can be advanced with emerging nano- and micro-fabrication methods to fabricate microneedles. Nano-/micro-fabricated microneedles seek to mitigate penetration pain and tissue damage, as well as providing accurately controlled robust channels for administrating bioagents and collecting body fluids. Here, design and 3D printing strategies of microneedles are discussed with emerging applications in biomedical devices and healthcare technologies. 3D printing offers customization, cost-efficiency, a rapid turnaround time between design iterations, and enhanced accessibility. Increasing the printing resolution, the accuracy of the features, and the accessibility of low-cost raw printing materials have empowered 3D printing to be utilized for the fabrication of microneedle platforms. The development of 3D-printed microneedles has enabled the evolution of pain-free controlled release drug delivery systems, devices for extracting fluids from the cutaneous tissue, biosignal acquisition, and point-of-care diagnostic devices in personalized medicine.Publication Open Access A 2D MEMS stage for optical applications(Society of Photo-optical Instrumentation Engineers (SPIE), 2006) Ataman, Çağlar; Petremand, Yves; Noell, Wilfried; Epitaux, Marc; de Rooij, Nico F.; Department of Electrical and Electronics Engineering; Ürey, Hakan; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 8579A 2D MEMS platform for a microlens scanner application is reported. The platform is fabricated on an SOI wafer with 50/μm thick device layer. Entire device is defined with a single etching step on the same layer. Through four S-shaped beams, the device is capable of producing nonlinear 2D motion from linear ID translation of two pairs of comb actuator sets. The device has a clear aperture of 2mm by 2mm, which is hallowed from the backside for micro-optics assembly. In this paper, a numerical device model and its validation via experimental characterization results are presented. Integration of the micro-optical components with the stage is also discussed. Additionally, a new driving scheme to minimize the settling time of the device in DC operation is explored.Publication Open Access A comprehensive ınvestigation of associations of objective and subjective socioeconomic status with perceived health and subjective well-being(Ubiquity Press, 2020) Department of Psychology; Cemalcılar, Zeynep; Kezer, Murat; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; Graduate School of Social Sciences and Humanities; 40374; N/ASocioeconomic status (SES) accounts for disparities in health and well-being. Recent studies consider the effects of individuals' subjective standing in society (i.e., subjective SES) as well as the traditional (objective) indicators of SES (i.e., income, education, occupational status), in predominantly Western samples. This study presents a comprehensive investigation of associations of objective and subjective SES with individuals' perceived health and well-being in a representative sample of young adults (aged 18-35; N = 3016) from a non-WEIRD (Western, Educated, Industrialized, Rich and Democratic) population (i.e., Turkey), employing polynomial regressions and plotting the results onto a three-dimensional plane. Findings confirmed the value of polynomial regression to understanding the relationship of different types of SES with perceived health and well-being. For instance, while perceived overall health was descriptively greater when objective-SES exceeded subjective-SES, the reverse was the case for happiness, one indicator of well-being. Our findings also suggest an additive effect of the two types of socioeconomic status on majority of the outcome variables; individuals' perceptions of overall health, life satisfaction, happiness, and financial satisfaction were enhanced when they reported higher scores on both objective and subjective SES.Publication Open Access A cross-layer design for QoS support in cognitive radio sensor networks for smart grid applications(Institute of Electrical and Electronics Engineers (IEEE), 2012) Güngör, Vehbi C.; Shah, Ghalib Asadullah; Akan, Özgür Barış; Faculty Member; College of EngineeringIn this paper, we propose a cross-layer design to meet the QoS requirements for smart grids employing the cognitive radio sensor networks for their control and monitoring operations. Existing routing protocols pertaining to QoS support are not able to simultaneously handle traffic of different characteristics present in smart grids. Therefore, considering the traffic heterogeneity of smart grid applications exhibiting diverse QoS requirements, a set of priority classes is defined in order to differentiate the traffic for the respective service. Specifically, the problem is formulated as a weighted network utility maximization (WNUM) whose objective is to maximize the weighted sum of flows service. A cross-layer heuristic solution is provided to solve the utility optimization problem by performing joint routing, dynamic spectrum allocation and medium access. Performance of the proposed protocol is evaluated using ns-2, which shows that the number of flows belonging to each class are served according to their weight fraction with their respective data rate, latency and reliability requirement.Publication Open Access A novel Fontan Y-graft for interrupted inferior vena cava and azygos continuation(Oxford University Press (OUP), 2022) Çicek, Murat; Köse, Banu; Yılmaz, Emine Hekim; Aydemir, Numan Ali; Özkök, Serçin; Yurtseven, Nurgül; Erdem, Hasan; Sasmazel, Ahmet; Department of Mechanical Engineering; Lashkarinia, Seyedeh Samaneh; Pekkan, Kerem; Rezaeimoghaddam, Mohammad; Rasooli, Reza; Faculty Member; Researcher; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 161845; N/A; N/AObjectives: to evaluate the hemodynamicdynamic advantage of a new Fontan surgical template that is intended for complex single-ventricle patients with interrupted inferior vena cava-azygos and hemi-azygos continuation. The new technique has emerged from a comprehensive pre-surgical simulation campaign conducted to facilitate a balanced hepatic flow and somatic Fontan pathway growth after Kawashima procedure. Methods: for 9 patients, aged 2 to 18 years, majority having poor preoperative oxygen saturation, a pre-surgical computational fluid dynamics customization is conducted. Both the traditional Fontan pathways and the proposed novel Y-graft templates are considered. Numerical model was validated against in vivo phase-contrast magnetic resonance imaging data and in vitro experiments. Results: the proposed template is selected and executed for 6 out of the 9 patients based on its predicted superior hemodynamic performance. Pre-surgical simulations performed for this cohort indicated that flow from the hepatic veins (HEP) do not reach to the desired lung. The novel Y-graft template, customized via a right- or left-sided displacement of the total cavopulmonary connection anastomosis location resulted a drastic increase in HEP flow to the desired lung. Orientation of HEP to azygos direct shunt is found to be important as it can alter the flow pattern from 38% in the caudally located direct shunt to 3% in the cranial configuration with significantly reversed flow. The postoperative measurements prove that oxygen saturation increased significantly (P-value = 0.00009) to normal levels in 1 year follow-up. Conclusions: the new Y-graft template, if customized for the individual patient, is a viable alternative to the traditional surgical pathways. This template addresses the competing hemodynamic design factors of low physiological venous pressure, high postoperative oxygen saturation, low energy loss and balanced hepatic growth factor distribution possibly assuring adequate lung development.Publication Open Access A preliminary attempt to construct a geospatial, multimodal Ottoman transport network for 1899(Koç University Press (KUP) / Koç Üniversitesi Yayınları (KÜY), 2021) Gerrits, Piet; Department of History; Kabadayı, Mustafa Erdem; Özkan, Osman; Koçak, Turgay; Faculty Member; Teaching Faculty; Department of History; College of Social Sciences and Humanities; 33267; N/A; N/APublication Open Access A proximity mapping journey into the biology of the mammalian centrosome/cilium complex(Multidisciplinary Digital Publishing Institute (MDPI), 2020) Department of Molecular Biology and Genetics; Arslanhan, Melis Dilara; Gülensoy, Dila; Karalar, Elif Nur Fırat; Faculty Member; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; 206349The mammalian centrosome/cilium complex is composed of the centrosome, the primary cilium and the centriolar satellites, which together regulate cell polarity, signaling, proliferation and motility in cells and thereby development and homeostasis in organisms. Accordingly, deregulation of its structure and functions is implicated in various human diseases including cancer, developmental disorders and neurodegenerative diseases. To better understand these disease connections, the molecular underpinnings of the assembly, maintenance and dynamic adaptations of the centrosome/cilium complex need to be uncovered with exquisite detail. Application of proximity-based labeling methods to the centrosome/cilium complex generated spatial and temporal interaction maps for its components and provided key insights into these questions. In this review, we first describe the structure and cell cycle-linked regulation of the centrosome/cilium complex. Next, we explain the inherent biochemical and temporal limitations in probing the structure and function of the centrosome/cilium complex and describe how proximity-based labeling approaches have addressed them. Finally, we explore current insights into the knowledge we gained from the proximity mapping studies as it pertains to centrosome and cilium biogenesis and systematic characterization of the centrosome, cilium and centriolar satellite interactomes.