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Publication Metadata only “Doing What Matters in Times of Stress” to decrease psychological distress during Covid-19: a rammed controlled pilot trial(Wolters Kluwer Medknow Publications, 2022) Uygun, Ersin; Karaoğlan Kahiloğulları, Akfer; Department of Psychology; Department of Psychology; N/A; Acartürk, Ceren; Kurt, Gülşah; İlkkurşun, Zeynep; Faculty Member; Teaching Faculty; Master Student; Department of Psychology; College of Social Sciences and Humanities; College of Social Sciences and Humanities; Graduate School of Social Sciences and Humanities; 39271; 368619; N/ADespite the increasing psychological distress during Covid-19, utilisation of face-to-face psychological interventions decreased profoundly. The aim of this study involving two parallel, two-armed pilot randomised controlled trials was to examine the effectiveness of a guided self-help intervention "Doing What Matters in Times of Stress" (DWM) in decreasing psychological distress in Turkish and Syrian participants. Seventy-four Turkish nationals and 50 Syrian refugee adults with psychological distress were randomly allocated to a DWM group or wait-list control group. The primary outcome measure was the Patient Health Questionnaire 9 postintervention. Secondary outcome measures were the Generalised Anxiety Disorder Scale, posttraumatic stress disorder (PTSD) Checklist for DSM-5, Generalized Self-Efficacy Scale and Acceptance and Action Questionnaire-II postintervention. Although this study was not powered to detect a significant effect for DWM postassessment between DWM and the control group, results showed a significant improvement in depression symptoms among Turkish participants in the DWM group (d = 0.46) and in PTSD symptoms among Syrian participants in the DWM group (d = 0.67) from pre- to postintervention assessment. These results indicate the potential of DWM to decrease mental health problems during the pandemic and importance of a fully powered, definitive controlled trial to examine its effectiveness both for the host community and refugees to reduce psychological distress during Covid-19.Publication Open Access 2D hybrid meshes for direct simulation Monte Carlo solvers(Institute of Physics (IOP) Publishing, 2013) Şengil, Nevsan; Department of Mathematics; Şengil, Uluç; Master Student; Department of Mathematics; College of SciencesThe efficiency of the direct simulation Monte Carlo (DSMC) method decreases considerably if gas is not rarefied. In order to extend the application range of the DSMC method towards non-rarefied gas regimes, the computational efficiency of the DSMC method should be increased further. One of the most time consuming parts of the DSMC method is to determine which DSMC molecules are in close proximity. If this information is calculated quickly, the efficiency of the DSMC method will be increased. Although some meshless methods are proposed, mostly structured or non-structured meshes are used to obtain this information. The simplest DSMC solvers are limited with the structured meshes. In these types of solvers, molecule indexing according to the positions can be handled very fast using simple arithmetic operations. But structured meshes are geometry dependent. Complicated geometries require the use of unstructured meshes. In this case, DSMC molecules are traced cell-by-cell. Different cell-by-cell tracing techniques exist. But, these techniques require complicated trigonometric operations or search algorithms. Both techniques are computationally expensive. In this study, a hybrid mesh structure is proposed. Hybrid meshes are both less dependent on the geometry like unstructured meshes and computationally efficient like structured meshes.Publication 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 Metadata only 3D face recognition(Institute of Electrical and Electronics Engineers (IEEE), 2006) Dutaǧaci, H.; Sankur, B.; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of Engineering; 107907In this paper, we compare face recognition performances of various features applied on registered 3D scans of faces. The features we compare are DFT or DCT- based features, ICA-based features and NNMF-based features. We apply the feature extraction techniques to three different representations of registered faces: 3D point clouds, 2D depth images and 3D voxel representations. We also consider block-based DFT or DCT-based local features on 2D depth images and their fusion schemes. Experiments using different combinations of representation types and feature vectors are conducted on the 3D-RMA dataset. / Bu bildiride, kayıtlı 3B yüz taramalarında uygulanan çeşitli özelliklerin yüz tanıma performanslarını karşılaştırıyoruz. Karşılaştırdığımız özellikler, DFT veya DCT tabanlı özellikler, ICA tabanlı özellikler ve NNMF tabanlı özelliklerdir. Öznitelik çıkarma tekniklerini kayıtlı yüzlerin üç farklı temsiline uyguluyoruz: 3B nokta bulutları, 2B derinlik görüntüleri ve 3B voksel temsilleri. Ayrıca, 2D derinlik görüntüleri ve bunların füzyon şemaları üzerindeki blok tabanlı DFT veya DCT tabanlı yerel özellikleri de dikkate alıyoruz. 3D-RMA veri seti üzerinde farklı temsil türleri ve özellik vektörleri kombinasyonları kullanılarak deneyler yapılmıştır.Publication Open Access 3D face recognition by projection based methods(Society of Photo-optical Instrumentation Engineers (SPIE), 2006) Dutaǧaci, Helin; Sankur, Bülent; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of EngineeringIn this paper, we investigate recognition performances of various projection-based features applied on registered 3D scans of faces. Some features are data driven, such as ICA-based features or NNMF-based features. Other features are obtained using DFT or DCT-based schemes. We apply the feature extraction techniques to three different representations of registered faces, namely, 3D point clouds, 2D depth images and 3D voxel. We consider both global and local features. Global features are extracted from the whole face data, whereas local features are computed over the blocks partitioned from 2D depth images. The block-based local features are fused both at feature level and at decision level. The resulting feature vectors are matched using Linear Discriminant Analysis. Experiments using different combinations of representation types and feature vectors are conducted on the 3D-RMA dataset.Publication Metadata only 3D printed biodegradable polyurethaneurea elastomer recapitulates skeletal muscle structure and function(American Chemical Society (ACS), 2021) Gokyer, Seyda; Berber, Emine; Vrana, Engin; Orhan, Kaan; Abou Monsef, Yanad; Guvener, Orcun; Zinnuroglu, Murat; Oto, Cagdas; Huri, Pinar Yilgor; Department of Chemistry; Department of Chemistry; Yılgör, Emel; Yılgör, İskender; Researcher; Faculty Member; Department of Chemistry; College of Sciences; College of Sciences; N/A; 24181Effective skeletal muscle tissue engineering relies on control over the scaffold architecture for providing muscle cells with the required directionality, together with a mechanical property match with the surrounding tissue. Although recent advances in 3D printing fulfill the first requirement, the available synthetic polymers either are too rigid or show unfavorable surface and degradation profiles for the latter. In addition, natural polymers that are generally used as hydrogels lack the required mechanical stability to withstand the forces exerted during muscle contraction. Therefore, one of the most important challenges in the 3D printing of soft and elastic tissues such as skeletal muscle is the limitation of the availability of elastic, durable, and biodegradable biomaterials. Herein, we have synthesized novel, biocompatible and biodegradable, elastomeric, segmented polyurethane and polyurethaneurea (TPU) copolymers which are amenable for 3D printing and show high elasticity, low modulus, controlled biodegradability, and improved wettability, compared to conventional polycaprolactone (PCL) and PCL-based TPUs. The degradation profile of the 3D printed TPU scaffold was in line with the potential tissue integration and scaffold replacement process. Even though TPU attracts macrophages in 2D configuration, its 3D printed form showed limited activated macrophage adhesion and induced muscle-like structure formation by C2C12 mouse myoblasts in vitro, while resulting in a significant increase in muscle regeneration in vivo in a tibialis anterior defect in a rat model. Effective muscle regeneration was confirmed with immunohistochemical assessment as well as evaluation of electrical activity produced by regenerated muscle by EMG analysis and its force generation via a custom-made force transducer. Micro-CT evaluation also revealed production of more muscle-like structures in the case of implantation of cell-laden 3D printed scaffolds. These results demonstrate that matching the tissue properties for a given application via use of tailor-made polymers can substantially contribute to the regenerative outcomes of 3D printed tissue engineering scaffolds.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 Metadata only 3D shape correspondence by isometry-driven greedy optimization(IEEE Computer Soc, 2010) N/A; Department of Computer Engineering; Sahillioğlu, Yusuf; Yemez, Yücel; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; 215195; 107907We present an automatic method that establishes 3D correspondence between isometric shapes. Our goal is to find an optimal correspondence between two given (nearly) isometric shapes, that minimizes the amount of deviation from isometry. We cast the problem as a complete surface correspondence problem. Our method first divides the given shapes to be matched into surface patches of equal area and then seeks for a mapping between the patch centers which we refer to as base vertices. Hence the correspondence is established in a fast and robust manner at a relatively coarse level as imposed by the patch radius. We optimize the isometry cost in two steps. in the first step, the base vertices are transformed into spectral domain based on geodesic affinity, where the isometry errors are minimized in polynomial time by complete bipartite graph matching. the resulting correspondence serves as a good initialization for the second step of optimization in which we explicitly minimize the isometry cost via an iterative greedy algorithm in the original 3D Euclidean space. We demonstrate the performance of our method on various isometric (or nearly isometric) pairs of shapes for some of which the ground-truth correspondence is available.Publication Metadata only 3D shape recovery and tracking from multi-camera video sequences via surface deformation(Institute of Electrical and Electronics Engineers (IEEE), 2006) Skala, V.; N/A; Department of Computer Engineering; Sahillioğlu, Yusuf; Yemez, Yücel; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; 215195; 107907This paper addresses 3D reconstruction and modeling of time-varying real objects using multicamera video. The work consists of two phases. In the first phase, the initial shape of the object is recovered from its silhouettes using a surface deformation model. The same deformation model is also employed in the second phase to track the recovered initial shape through the time-varying silhouette information by surface evolution. The surface deformation/evolution model allows us to construct a spatially and temporally smooth surface mesh representation having fixed connectivity. This eventually leads to an overall space-time representation that preserves the semantics of the underlying motion and that is much more efficient to process, to visualize, to store and to transmit. / Bu makale, çok kameralı video kullanarak zamanla değişen gerçek nesnelerin 3B yeniden yapılandırılmasını ve modellenmesini ele almaktadır. Çalışma iki aşamadan oluşmaktadır. İlk aşamada, nesnenin ilk şekli, bir yüzey deformasyon modeli kullanılarak silüetlerinden kurtarılır. Aynı deformasyon modeli, ikinci aşamada, yüzey evrimi yoluyla zamanla değişen siluet bilgisi yoluyla geri kazanılan ilk şekli izlemek için de kullanılır. Yüzey deformasyonu/evrimi modeli, sabit bağlantıya sahip uzamsal ve zamansal olarak pürüzsüz bir yüzey ağ temsili oluşturmamıza izin verir. Bu, sonunda, altta yatan hareketin anlamını koruyan ve işlemesi, görselleştirmesi, depolaması ve iletmesi çok daha verimli olan genel bir uzay-zaman temsiline yol açar.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.