Research Outputs
Permanent URI for this communityhttps://hdl.handle.net/20.500.14288/2
Browse
Publication Metadata only 1,3-bis(gamma-aminopropyl)tetramethyldisiloxane modified epoxy resins: curing and characterization(Elsevier, 1998) Department of Chemistry; Department of Chemistry; Yılgör, Emel; Yılgör, İskender; Researcher; Faculty Member; Department of Chemistry; College of Sciences; College of Sciences; 40527; 24181Incorporation of siloxane oligomers with reactive organofunctional terminal groups, such as amine, epoxy and carboxy, into the structure of epoxy networks, provides improvements in the fracture toughness, water absorption and surface properties of the resultant systems. 1,3-bis(gamma-aminopropyl) tetramethyldisiloxane (DSX) was used as a model curing agent and modifier in bis(4-aminocyclohexyl)methane (PACM-20) cured diglycidyl ether of bisphenol-A (DGEBA) based epoxy resins. Curing reactions followed by differential scanning calorimetry indicated faster reaction rates between DSX and DGEBA as compared with PACM-20 and DGEBA. Mechanical characterization of the modified products showed improvements in tensile and impact strengths as expected. Glass transition temperatures of these materials showed a decrease with an increase in DSX content.Publication Metadata only 1200 nm pumped Tm3+:Lu2O3 ceramic lasers(Optical Soc Amer, 2018) Özharar, Sarper; N/A; Department of Physics; Toker, Işınsu Baylam; Sennaroğlu, Alphan; PhD Student; Faculty Member; Department of Physics; N/A; College of Sciences; N/A; 23851We report on an experimental demonstration of a 1200-nm pumped Tm3+:Lu2O3 ceramic laser. By using a gain-switched, tunable Cr4+:forsterite laser, the excitation spectrum was measured, with optimum pumping bands centered near 1198 nm, 1204 nm, and 1211 nm. The highest slope efficiency of 21.5% was obtained at the pump wavelength of 1204 nm. Comparative energy efficiency measurements performed near 1200-nm and 800-nm pumping further showed that nearly 40% improvement was obtained in slope efficiency measured with respect to the incident pump energy for 1200-nm pumping. A transition was further observed from single-wavelength operation at 2066 nm to dual-wavelength operation near 2066 nm and 1967 nm for absorbed pump energies above 50 mu J. In this regime, two consecutive output pulses were observed in the time domain. The shortest temporal duration of the first pulse was 1.1 mu s at the incident pulse energy of 105 mu J. The duration and build-up time of the second pulse remained around 5.9 mu s and 18.5 mu s. We believe that the improved energy efficiency demonstrated for the 1.5% Tm3+:Lu2O3 ceramic with 1200-nm pumping can be used as an alternative scheme for the excitation of Tm3+:Lu2O3 ceramic lasers.Publication Metadata only 18F-FDG PET/CT mean suv and metabolic tumor volume for mean survival time in non-small cell lung cancer(Lippincott Williams and Wilkins, 2015) Kurtipek, Ercan; Çaycı, Mustafa; Düzgün, Nuri; Esme, Hıdır; Terzi, Yüksel; Bakdık, Süleyman; Ünlü, Yaşar; Burnik, Cengiz; Bekçi, Taha Tahir; N/A; Aygün, Murat Serhat; Teaching Faculty; School of Medicine; Koç University Hospital; 291692Objective: The study was designed to determine the relationship between survival time of standardized uptake value (SUVmax and SUVmean) and metabolic tumor volume (MTV) in patients with non-small cell lung cancer (NSCLC), and examine the impact of demographic, clinical, and radiological data of these patients on survival. Materials and Methods: We performed a retrospective analysis of the records of 79 patients with NSCLC who presented to our hospital between May 2010 and March 2013, received a final diagnosis, and underwent 18F-FDG PET/CT for staging. Clinical, radiological, and 18F-FDG PET/CT parameters with an impact on prognosis such as the SUVmax of the primary tumor as calculated by the volumetric region of interest in the 18F-FDG PET/CT scans during initial diagnosis, mean SUV of the tumor, and MTV obtained with a threshold of SUVmax greater than 2.5 were recorded and statistically analyzed. A statistical analysis was carried out based on the clinical, radiological, and PET/CT findings of the patients who were divided into 2 groups: survivors and nonsurvivors. Results: Seventy patients (88.6%) were men, and 9 (11.4%) were women. The mean age was 63.65 ± 11.51 years in the nonsurvivor group (n = 40) versus 62.74 ± 10.60 years in the survivor group (n = 39) (Table 1). The mean survival time from diagnosis was 7.9 ± 6.52 months in the nonsurvivor group versus 14.09 ± 7.41 months in the survivor group. The mean survival time was 12.9 ± 7.9 months for those aged 60 or younger, whereas it was 9.9 ± 7.2 years for those aged 60 or older. According to the Cox regression analysis, higher MTV [relative risk (RR), 1.006; P = 0.03] and mean SUVmax (mSUV) (RR, 1.302; P = 0.03) had a significant impact on shortening of the mean survival time. However, no statistical significance was reached for SUVmax measurements (RR, 0.970; P = 0.39). Furthermore, there was a significant relationship between increased tumor size (andlt;2 cm, 2-4 cm, and ≥4 cm) and shortened mean survival time (P = 0.03). Conclusion: The present study showed that MTV and mSUV of FDG PET/CT scans of the tumor, but not SUVmax, had a significant impact on survival time of patients with NSCLC. Based on this result, we believe that we might have more accurate information about the survival time of our patients if we also evaluate mSUV and MTV in combination with mSUV, which is frequently used for diagnosis and monitoring of patients with NSCLC during our daily practice. © 2015 Wolters Kluwer Health, Inc. All rights reserved.Publication Metadata only 18F-FDG PET/CT texture analysis of anthracotic lymph nodes detected with EBUS and comparison with cytological findings(P.Ziti and Co, 2022) N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; Çağlayan, Benan Niku; Fırat, Pınar Arıkan; Seymen, Hülya; Bulutay, Pınar; Falay, Fikri Okan; Demirtaş, Elif; Demirkol, Mehmet Onur; Meriçöz, Çisel Aydın; Faculty Member; Faculty Member; Teaching Faculty; Teaching Faculty; Teaching Faculty; Master Student; Faculty Member; Teaching Faculty; School of Medicine; School of Medicine; School of Medicine; School of Medicine; School of Medicine; Graduate School of Health Sciences; School of Medicine; School of Medicine; 230719; 207545; 350778; 133565; 246484; N/A; 196946; 162418Objective: Lymph node metastasis is the most important factor both in the selection of treatment since many alternatives have been created in recent years, and in the evaluation of prognosis in lung cancer. The most unpredictable cause of lymph node false positivity in fluorine-18-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) is anthracosis. The aim of this study is to compare 18F-FDG PET/CT texture information of anthracotic (ALN) and metastatic (MLN) lymph nodes, after re-evaluation of the cytological samples obtained from anthracotic lymph nodes by EBUS-TBNA. Subjects and Methods: Ninety nine patients, 78 of whom had primary lung cancer were included in the study. Two hundred and three lymph nodes from 99 patients sampled by EBUS-TBNA and diagnosed cytologically as ALN or MLN were evaluated retrospectively. All ALN were classified as grades 1, 2 and 3 cytologically. Volume of interest (VOI) of 203 lymph nodes was re-drawn and maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV) and total lesion glycolysis (TLG) values were recorded. Results: There was a statistically significant difference in MTV and TLG values in MLN and all ALN grades. However, only grade 1-2 ALNs could be differentiated from MLNs with SUVmax, and no statistically significant difference was found in grade 3 ALN and MLN. Metabolic tumor volume and TLG values over 4.10cm3 and 26.57 showed 60% and 59% sensitivity and 83% and 94 specificity respectively for the identification of MLN. Conclusion: The contribution of MTV and TLG values of 18F-FDG PET/CT to the differential diagnosis of ALN is much more valuable than SUVmax values, especially for grade 3 anthracosis. It was thought that cytological reporting of only grade 3 ALN could make a better contribution to the 18F-FDG PET/CT evaluation analysis.Publication Metadata only 19. yüzyıl osmanlı padişahlarının müzik politikalarından kesitler(Yakındoğu Üniversitesi, 2011) N/A; Baydar, Evren Kutlay; Teaching Faculty; College of Social Sciences and Humanities; N/AFor centuries, Turkish music has been developed in monophonic texture with its own harmonic and rhythmic rules, different than the western music system. Music took an important position in the Ottoman Court, both in education and performance practices. The Sultans were raised with a music culture. In the Ottoman Empire, music was a part of life not only in the Court but also in the Military (as in the case of janissary music); therefore a reorganization in music was encountered both in the Court and the Military. During 19th century, Ottoman Empire encountered a “Westernization process” in music (as well as in other areas). With the enterance of polyphonic western music into the Ottoman Court, beginning with Selim III, but mainly during the period of Mahmud II, a great reconstruction in the Ottoman music begins. The reformations of Mahmud II, which were the first movements of polyphony in Turkey, were a break point in the Turkish music history. In this research, the enterance and development of Western music in the Ottoman Empire is discussed based on the music politics of each Sultan in rule, chronogically. / Türk müziği, yüzyıllar boyunca, batı müziği sisteminden farklı olarak tek sesli ve kendi makam ve usulleri çerçevesinde gelişme göstermiştir. Osmanlı saraylarında müzik, gerek eğitimi gerek icrası açısından çoğunlukla büyük önem taşımış, sultanlar müzik kültürüyle iç içe büyümüşlerdir. Osmanlı’da müzik sadece sarayda değil, askeri alanda da yoğun olarak kullanılmış, dolayısıyla müziğin gelişimi saray müziğinin yanısıra bu boyutta da ağırlıklı olarak etkilenmiştir. 19. yüzyılda Osmanlı İmparatorluğu’nda müzikte (ve diğer alanlarda) batılılaşma eğilimi görülmektedir. Çok sesli batı müziğinin III. Selim zamanından başlayarak ve esas olarak II. Mahmud’la birlikte Osmanlı sarayına girmesiyle Osmanlı müziğinde büyük bir yeniden yapılanma başlar. II. Mahmud’un reformlarının Türk müziğinde bir dönüm noktası oluşturmasıyla ortaya çıkan hareket Türkiye’deki çok sesliliğin ilk adımlarıdır. Bu araştırmada, batı müziğinin Osmanlı İmparatorluğu’na girişi ve gelişimi süreci, II. Mahmud’dan itibaren 19. yüzyıl boyunca hükümdar olan her padişahın müzik politikaları bağlamında kronolojik sırasıyla ele alınmıştır.Publication Metadata only 2 July 1993 in Turkish Literature: representations of the Sivas Massacre(Routledge Journals, Taylor & Francis Ltd, 2014) Department of Comparative Literature; Ağıl, Nazmi; Faculty Member; Department of Comparative Literature; College of Social Sciences and Humanities; 50749On 2 July 1993 the fire set on Hotel Madimak in Sivas, Turkey by religious fanatics claimed the lives of 37 people. Such traumatic events need to be narrated to heal the wound they have opened in the public consciousness. Yet it is also true that they pose a serious challenge to the narrator as they lie beyond the reach of usual means of representation. This article examines the ways the massacre is represented in the two recent Turkish novels, Atesve Kugu (Fire and the Swan) by Burhan Gunel and Seytan Minareleri (Seashells) by Hidayet Karakus, with a view to examining the approaches these works offer to meet the challenge.Publication Metadata only 2.3-μm Tm3+: YLF laser passively Q-switched with a Cr2+: ZnSe saturable absorber(Optical Soc Amer, 2017) N/A; N/A; Canbaz, Ferda; Yorulmaz, İsmail; Sennaroğlu, Alphan; PhD Student; PhD Student; Faculty Member; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; 23851We report, what is to our knowledge, the first passively Q-switched operation of a 2.3-mu m Tm3+ : YLF laser by using a Cr2+ : ZnSe saturable absorber. In the experiments, a tunable Ti3+ : sapphire laser was used to end pump the Tm3+ : YLF gain medium inside an x cavity. A Cr2+ : ZnSe saturable absorber was also included in the cavity to initiate passive Q switching. At all pump power levels above lasing threshold, passively Q-switched operation of the Tm3+ : YLF laser could be obtained at 2309 nm with pulse durations and repetition frequencies in the ranges of 1.21.4 mu s and 0.3-2.1 kHz, respectively. Analysis of power dependent repetition rate data further gave an estimated value of 3.1% for the round-trip saturable loss of the Cr2+ : ZnSe saturable absorber.Publication Metadata only 21 fs Cr:LiSAF laser mode locked with a single-walled carbon nanotube saturable absorber(Optical Soc Amer, 2019) Bae, Ji Eun; Rotermund, Fabian; Demirbaş, Ümit; N/A; N/A; N/A; Department of Physics; Tanısalı, Gökhan; Toker, Işınsu Baylam; Taşçı, Mısra; Sennaroğlu, Alphan; PhD Student; PhD Student; Undergraduate Student; Faculty Member; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; School of Medicine; College of Sciences; N/A; N/A; N/A; 23851We report the shortest femtosecond pulses directly generated from a solid-state laser that is mode locked by using a single-walled carbon nanotube saturable absorber (SWCNT-SA). In the experiments, we used a 660 nm diode-pumped, low-threshold extended-cavity Cr:LiSAF laser operating around 850 nm with a repetition rate of 47.9 MHz. The SWCNT-SA mode-locked Cr:LiSAF laser produced 21 fs pulses with a time-bandwidth product of 0.56 by using only 210 mW of pump power. Pump-probe spectroscopy measurements showed that the SWCNT-SA exhibited saturable absorption with slow and fast decay times of 2.7 ps and 0.4 ps. The single-pass modulation depth and saturation fluence of the SWCNT-SA were further determined as 0.3% and 45 mu J/cm(2) at the pump wavelength of 850 nm.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 Metadata only 2d -> 3d polycatenated and 3d -> 3d interpenetrated metal-organic frameworks constructed from thiophene-2,5-dicarboxylate and rigid bis(imidazole) ligands(Elsevier, 2014) Erer, Hakan; Yesilel, Okan Zafer; Arici, Mursel; Buyukgungor, Orhan; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548Hydrothermal reactions of rigid 1,4-bis(imidazol-1-yl)benzene (dib) and 1,4-bis(imidazol-1-yl)-2, 5-dimethylbenzene (dimb) with deprotonated thiophene-2,5-dicarboxylic acid (H(2)tdc) in the presence of Zn(II) and Cd(II) salts in H2O produced three new metal-organic frameworks, namely, [Zn(mu-tdc)(H2O) (mu-dib)](n) (1), [Cd(mu-tdc)(H2O)(mu-dib)(n) (2), and {[Cd-2(mu(3)-tdc)(2)(mu-dimb)(2)] center dot (H2O)}(n) (3). These MOFs were characterized by FT-IR spectroscopy, elemental, thermal (TG, DTA, DTG and DSC), and single-crystal X-ray diffraction analyses. Isomorphous complexes 1 and 2 reveal polycatenated 2D+2D -> 3D framework based on an undulated (4,4)-sql layer. Complex 3 exhibits a new 4-fold interpenetrating 3D framework with the point symbol of 6(6). Molecular simulations were used to assess the potentials of the complexes for H-2 storage application. Moreover, these coordination polymers exhibit blue fluorescent emission bands in the solid state at room temperature.Publication Metadata only 3D coffee stains(Royal Soc Chemistry, 2017) N/A; N/A; Department of Electrical and Electronics Engineering; N/A; N/A; N/A; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Chemistry; Department of Electrical and Electronics Engineering; Doğru-Yüksel, Itır Bakış; Söz, Çağla Koşak; Press, Daniel Aaron; Melikov, Rustamzhon; Begar, Efe; Çonkar, Deniz; Karalar, Elif Nur Fırat; Yılgör, Emel; Yılgör, İskender; Nizamoğlu, Sedat; PhD Student; PhD Student; Researcher; PhD Student; PhD Student; PhD Student; PhD Student; Faculty Member; Researcher; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Electrical and Electronics Engineering; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; N/A; N/A; N/A; N/A; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 206349; N/A; 24181; 130295When a liquid droplet (e.g., coffee, wine, etc.) is splattered on a surface, the droplet dries in a ring-shaped stain. This widely observed pattern in everyday life occurs due to the phenomenon known as a coffee stain (or coffee ring) effect. While the droplet dries, the capillary flow moves and deposits the particles toward the pinned edges, which shows a 2D ring-like structure. Here we demonstrate the transition from a 2D to a 3D coffee stain that has a well-defined and hollow sphere-like structure, when the substrate surface is switched from hydrophilic to superhydrophobic. The 3D stain formation starts with the evaporation of the pinned aqueous colloidal droplet placed on a superhydrophobic surface that facilitates the particle flow towards the liquid-air interface. This leads to spherical skin formation and a cavity in the droplet. Afterwards the water loss in the cavity due to pervaporation leads to bubble nucleation and growth, until complete evaporation of the solvent. In addition to the superhydrophobicity of the surface, the concentration of the solution also has a significant effect on 3D coffee stain formation. Advantageously, 3D coffee stain formation in a pendant droplet configuration enables the construction of all-protein lasers by integrating silk fibroin with fluorescent proteins. No tools, components and/or human intervention are needed after the construction process is initiated; therefore, 3D coffee-stains hold promise for building self-assembled and functional 3D constructs and devices from colloidal solutions.Publication Metadata only 3D convective Cahn-Hilliard equation(Amer Inst Mathematical Sciences-Aims, 2007) Eden, Alp; Department of Mathematics; Kalantarov, Varga; Faculty Member; Department of Mathematics; College of Sciences; 117655We consider the initial boundary value problem for the 3D convective Cahn - Hilliard equation with periodic boundary conditions. This gives rise to a continuous dynamical system on L-2(ohm). Absorbing balls in L-2(ohm), H-per(1)(ohm) and H-per(2)(ohm) are shown to exist. Combining with the compactness property of the solution semigroup we conclude the existence of the global attractor. Restricting the dynamical system on the absorbing ball in H-per(2)(ohm) and using the general framework in Eden et. all. [] the existence of an exponential attractor is guaranteed. This approach also gives an explicit upper estimate of the dimension of the exponential attractor, albeit of the global attractor.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 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 Metadata only 3D model retrieval using probability density-based shape descriptors(IEEE Computer Society, 2009) Akgul, Ceyhun Burak; Sankur, Buelent; Schmitt, Francis; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of Engineering; 107907We address content-based retrieval of complete 3D object models by a probabilistic generative description of local shape properties. The proposed shape description framework characterizes a 3D object with sampled multivariate probability density functions of its local surface features. This density-based descriptor can be efficiently computed via kernel density estimation (KDE) coupled with fast Gauss transform. The nonparametric KDE technique allows reliable characterization of a diverse set of shapes and yields descriptors which remain relatively insensitive to small shape perturbations and mesh resolution. Density-based characterization also induces a permutation property which can be used to guarantee invariance at the shape matching stage. As proven by extensive retrieval experiments on several 3D databases, our framework provides state-of-the-art discrimination over a broad and heterogeneous set of shape categories.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 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.Publication Metadata only 3D printed poly(lactic acid) scaffolds modified with chitosan and hydroxyapatite for bone repair applications(Elsevier, 2020) N/A; N/A; N/A; N/A; Department of Chemistry; Department of Chemical and Biological Engineering; Department of Chemistry; Nazeer, Muhammad Anwaar; Önder, Özgün Can; Sevgili, İlkem; Yılgör, Emel; Kavaklı, İbrahim Halil; Yılgör, İskender; PhD Student; PhD Student; PhD Student; Researcher; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Sciences; N/A; N/A; N/A; N/A; 40319; 241813D printed poly(lactic acid) (PLA) scaffolds surface modified with chitosan (CS) and hydroxyapatite (HA) to produce a novel bioactive composite scaffold is reported. Excellent mechanical properties of PLA, the bioactivity of CS, and osteogenic characteristics of HA are combined to fabricate composite scaffolds using a simple desktop 3D printer. Scaffolds were characterized through attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, X-ray diffraction (XRD) and water contact angle measurements before and after modification. Formic acid was used as a solvent to prepare stable CS/HA dispersions and was found to be a suitable solvent for producing PLA/CS/HA composites. Surface properties of modified scaffolds were superior in terms of hydrophilicity and bioactivity, which resulted in enhanced attachment and proliferation of human osteosarcoma cells in vitro compared to the unmodified PLA scaffolds.Publication Metadata only 3D printing of cytocompatible gelatin-cellulose-alginate blend hydrogels(Wiley-V C H Verlag Gmbh, 2020) Erkoc, Pelin; Uvak, Ileyna; Odeh, Yazan Nitham; Akdogan, Ozan; Odeh, Yazan Nitham; Akdogan, Ozan; N/A; Department of Chemistry; Department of Chemical and Biological Engineering; Nazeer, Muhammad Anwaar; Batool, Syeda Rubab; Kızılel, Seda; PhD Student; Researcher; Faculty Member; Department of Chemistry; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; 283763D bioprinting of hydrogels has gained great attention due to its potential to manufacture intricate and customized scaffolds that provide favored conditions for cell proliferation. Nevertheless, plain natural hydrogels can be easily disintegrated, and their mechanical strengths are usually insufficient for printing process. Hence, composite hydrogels are developed for 3D printing. This study aims to develop a hydrogel ink for extrusion-based 3D printing which is entirely composed of natural polymers, gelatin, alginate, and cellulose. Physicochemical interactions between the components of the intertwined gelatin-cellulose-alginate network are studied via altering copolymer ratios. The structure of the materials and porosity are assessed using infrared spectroscopy, swelling, and degradation experiments. The utility of this approach is examined with two different crosslinking strategies using glutaraldehyde or CaCl2. Multilayer cylindrical structures are successfully 3D printed, and their porous structure is confirmed by scanning electron microscopy and Brunauer-Emmett-Teller surface area analyses. Moreover, cytocompatibility of the hydrogel scaffolds is confirmed on fibroblast cells. The developed material is completely natural, biocompatible, economical, and the method is facile. Thus, this study is important for the development of advanced functional 3D hydrogels that have considerable potential for biomedical devices and artificial tissues.