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Publication Open Access "Whole" vs "fragmented" approach to EAACI pollen season definitions: a multicenter study in six Southern European cities(Wiley, 2020) Hoffmann, Tara Maria; Şahin, Aydan Acar; Aggelidis, Xenophon; Arasi, Stefania; Barbalace, Andrea; Bourgoin, Anne; Bregu, Blerina; Brighetti, Maria Antonia; Caeiro, Elsa; Sozmen, Sule Caglayan; Caminiti, Lucia; Charpin, Denis; Couto, Mariana; Delgado, Luis; Businco, Andrea Di Rienzo; Dimier, Claire; Dimou, Maria, V; Fonseca, Joao A.; Göksel, Özlem; Güvensen, Aykut; Hernandez, Dolores; Jang, Dah Tay; Kalpaklıoğlu, Füsun; Lame, Blerta; Llusar, Ruth; Makris, Michael P.; Mazon, Angel; Mesonjesi, Eris; Nieto, Antonio; Pahus, Laurie; Pajno, Giovanni Battista; Panasiti, Ilenia; Panetta, Valentina; Papadopoulos, Nikolaos G.; Pellegrini, Elisabetta; Pelosi, Simone; Pereira, Ana Margarida; Pereira, Mariana; Pinar, Munevver; Pfaar, Oliver; Potapova, Ekaterina; Priftanji, Alfred; Psarros, Fotis; Sfika, Ifigenia; Suarez, Javier; Thibaudon, Michel; Travaglini, Alessandro; Tripodi, Salvatore; Verdier, Valentine; Villella, Valeria; Xepapadaki, Paraskevi; Matricardi, Paolo M.; Dramburg, Stephanie; Öztürk, Ayşe Bilge; Saçkesen, Cansın; Yazıcı, Duygu; Faculty Member; Faculty Member; PhD Student; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; Graduate School of Health Sciences; Koç University Hospital; 147629; 182537; N/ABackground: the adequate definition of pollen seasons is essential to facilitate a correct diagnosis, treatment choice, and outcome assessment in patients with seasonal allergic rhinitis. A position paper by the European Academy of Allergy and Clinical Immunology (EAACI) proposed season definitions for Northern and Middle Europe. Objective To test the pollen season definitions proposed by EAACI in six Mediterranean cities for seven pollen taxa. Methods: as part of the @IT.2020 multi-center study, pollen counts for Poaceae, Oleaceae, Fagales, Cupressaceae, Urticaceae (Parietaria spp.), and Compositae (Ambrosia spp., Artemisia spp.) were collected from January 1 to December 31, 2018. Based on these data, pollen seasons were identified according to EAACI criteria. A unified monitoring period for patients in AIT trials was created and assessed for feasibility. Results: the analysis revealed a great heterogeneity between the different locations in terms of pattern and length of the examined pollen seasons. Further, we found a fragmentation of pollen seasons in several segments (max. 8) separated by periods of low pollen counts (intercurrent periods). Potential monitoring periods included often many recording days with low pollen exposure (max. 341 days). Conclusion: the Mediterranean climate leads to challenging pollen exposure times. Monitoring periods for AIT trials based on existing definitions may include many intermittent days with low pollen concentrations. Therefore, it is necessary to find an adapted pollen season definition as individual solution for each pollen and geographical area.Publication Open Access #COVID19 and #Breastcancer: a qualitative analysis of tweets(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Naganathan, G.; Cleland, J.; Reel, E.; Cil, T.; Bilgen, İdil; School of MedicineRapid and efficient communication regarding quickly evolving medical information was paramount for healthcare providers and patients throughout the COVID-19 pandemic. Over the last several years, social media platforms such as Twitter have emerged as important tools for health promotion, virtual learning among healthcare providers, and patient support. We conducted a qualitative thematic content analysis on tweets using the hashtags #BreastSurgery, #BreastCancer, #BreastOncology, #Pandemic, and #COVID19. Advocacy organizations were the most frequent authors of tweets captured in this dataset, and most tweets came from the United States of America (64%). Seventy-three codes were generated from the data, and, through iterative, inductive analysis, three major themes were developed: patient hesitancy and vulnerability, increased efforts in knowledge sharing, and evolving best practices. We found that Twitter was an effective way to share evolving best practices, education, and collective experiences among key stakeholders. As Twitter is increasingly used as a tool for health promotion and knowledge translation, a better understanding of how key stakeholders engage with healthcare-related topics on the platform can help optimize the use of this powerful tool.Publication Open Access 25-hydroxyvitamin D levels are low but not associated with disease activity in chronic spontaneous urticaria and depression(AEPress, 2020) Vurgun, Eren; Güntaş, Gürkan; Kocatürk Göncü, Özgür Emek; Memet, Bachar; Doctor; School of Medicine; Koç University Hospital; 217219; N/AAim: to evaluate vitamin D levels in patients with chronic spontaneous urticaria (CSU), depression and both of them, thus to fi nd out whether vitamin D may be a common causative factor of CSU and depression. Methods: thirty patients with CSU, 30 patients with depression, 30 patients with both CSU and depression and 30 healthy volunteers as control group were involved in the study. Serum 25-hydroxyvitamin D (25(OH) D) levels of these groups were measured and compared. Correlations between 25(OH)D levels and the activity of CSU and depression were analyzed. Results: healthy controls' 25(OH)D levels (17.2±8.8 ng/mL) were higher than patients with CSU (9.1±5.1 ng/mL), depression (8.9±6.1 ng/mL) and CSU with depression (7.7±4.7 ng/mL) (p<0.001, p<0.001 and p<0.001, respectively). There were no differences in 25(OH)D levels between CSU patients with and without depression, between depression patients and CSU patients with and without depression (p=0.43, p=0.82 and p=0.92, respectively). There were no correlations between 25(OH)D levels and the activity of CSU or depression (p=0.99 and p=0.76, respectively). Conclusion: Lower 25(OH)D levels in CSU and/or depression may appear as a secondary phenomenon, which means being result of these diseases rather than the cause (Tab. 1, Fig. 2, Ref. 41).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 Open Access 3D engineered neural co-culture model and neurovascular effects of marine fungi-derived citreohybridonol(American Institute of Physics (AIP) Publishing, 2022) Polat, İrem; Özkaya, Ferhat Can; El-Neketi, Mona; Ebrahim, Weaam; Şengül, Gülgün; Department of Mechanical Engineering; Sokullu, Emel; Sarabi, Misagh Rezapour; Taşoğlu, Savaş; Faculty Member; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); School of Medicine; Graduate School of Sciences and Engineering; College of Engineering; 163024; N/A; 291971Marine-based biomolecules are emerging metabolites that have gained attention for developing novel biomaterials, drugs, and pharmaceutical in vitro platforms. Here, we developed a 3D engineered neural co-culture model via a 3D prototyped sliding frame-platform for multi-step UV lithography and investigated the neurovascular potential of citreohybridonol in neuroblastoma treatment. Citreohybridonol was isolated from a sponge-derived fungus Penicillium atrovenetum. The model was characterized by Fourier-transform infrared spectroscopy and scanning electron microscopy analysis. Human umbilical cord vein endothelial cells (HUVECs) and neuroblastoma (SH-SY5Y) cell lines were encapsulated in gelatin methacrylate (GelMA) with and without citreohybridonol. The effect of citreohybridonol on the proliferation capacity of cells was assessed via cell viability and immunostaining assays. GelMA and 3D culture characterization indicated that the cells were successfully encapsulated as axenic and mixed with/without citreohybridonol. The cytotoxic test confirmed that the 3D microenvironment was non-toxic for cultural experiments, and it showed the inhibitory effects of citreohybridonol on SH-SY5Y cells and induced the proliferation of HUVECs. Finally, immunohistochemical staining demonstrated that citreohybridonol suppressed SH-SY5Y cells and induced vascularization of HUVECs in mixed 3D cell culture.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 Open Access 3D microprinting of iron platinum nanoparticle-based magnetic mobile microrobots(Wiley, 2021) Giltinan, Joshua; Sridhar, Varun; Bozüyük, Uğur; Sheehan, Devin; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; School of Medicine; College of Engineering; 297104Wireless magnetic microrobots are envisioned to revolutionize minimally invasive medicine. While many promising medical magnetic microrobots are proposed, the ones using hard magnetic materials are not mostly biocompatible, and the ones using biocompatible soft magnetic nanoparticles are magnetically very weak and, therefore, difficult to actuate. Thus, biocompatible hard magnetic micro/nanomaterials are essential toward easy-to-actuate and clinically viable 3D medical microrobots. To fill such crucial gap, this study proposes ferromagnetic and biocompatible iron platinum (FePt) nanoparticle-based 3D microprinting of microrobots using the two-photon polymerization technique. A modified one-pot synthesis method is presented for producing FePt nanoparticles in large volumes and 3D printing of helical microswimmers made from biocompatible trimethylolpropane ethoxylate triacrylate (PETA) polymer with embedded FePt nanoparticles. The 30 mu m long helical magnetic microswimmers are able to swim at speeds of over five body lengths per second at 200Hz, making them the fastest helical swimmer in the tens of micrometer length scale at the corresponding low-magnitude actuation fields of 5-10mT. It is also experimentally in vitro verified that the synthesized FePt nanoparticles are biocompatible. Thus, such 3D-printed microrobots are biocompatible and easy to actuate toward creating clinically viable future medical microrobots.Publication Open Access 3D printed microneedles for point of care biosensing applications(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Department of Mechanical Engineering; Sarabi, Misagh Rezapour; Nakhjavani, Sattar Akbar; Taşoğlu, Savaş; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); 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); Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 291971Microneedles (MNs) are an emerging technology for user-friendly and minimally invasive injection, offering less pain and lower tissue damage in comparison to conventional needles. With their ability to extract body fluids, MNs are among the convenient candidates for developing biosensing setups, where target molecules/biomarkers are detected by the biosensor using the sample collected with the MNs. Herein, we discuss the 3D printing of microneedle arrays (MNAs) toward enabling point-of-care (POC) biosensing applications.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.