Research Outputs
Permanent URI for this communityhttps://hdl.handle.net/20.500.14288/2
Browse
785 results
Filters
Advanced Search
Filter by
Settings
Search Results
Publication Metadata only 3D articulated shape segmentation using motion information(Institute of Electrical and Electronics Engineers (IEEE), 2010) Department of Computer Engineering; N/A; Yemez, Yücel; Kalafatlar, Emre; Faculty Member; Master Student; Department of Computer Engineering; College of Engineering; Graduate School of Sciences and Engineering; 107907; N/AWe present a method for segmentation of articulated 3D shapes by incorporating the motion information obtained from time-varying models. We assume that the articulated shape is given in the form of a mesh sequence with fixed connectivity so that the inter-frame vertex correspondences, hence the vertex movements, are known a priori. We use different postures of an articulated shape in multiple frames to constitute an affinity matrix which encodes both temporal and spatial similarities between surface points. The shape is then decomposed into segments in spectral domain based on the affinity matrix using a standard K-means clustering algorithm. The performance of the proposed segmentation method is demonstrated on the mesh sequence of a human actor.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 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 spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients(Public Library of Science, 2019) Dinçer, Cansu; Kaya, Tuğba; Tunçbağ, Nurcan; Department of Chemical and Biological Engineering; Department of Computer Engineering; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; 26605; 8745Glioblastoma multiforme (GBM) is the most aggressive type of brain tumor. Molecular heterogeneity is a hallmark of GBM tumors that is a barrier in developing treatment strategies. In this study, we used the nonsynonymous mutations of GBM tumors deposited in The Cancer Genome Atlas (TCGA) and applied a systems level approach based on biophysical characteristics of mutations and their organization in patient-specific subnetworks to reduce inter-patient heterogeneity and to gain potential clinically relevant insights. Approximately 10% of the mutations are located in "patches" which are defined as the set of residues spatially in close proximity that are mutated across multiple patients. Grouping mutations as 3D patches reduces the heterogeneity across patients. There are multiple patches that are relatively small in oncogenes, whereas there are a small number of very large patches in tumor suppressors. Additionally, different patches in the same protein are often located at different domains that can mediate different functions. We stratified the patients into five groups based on their potentially affected pathways, revealed from the patient-specific subnetworks. These subnetworks were constructed by integrating mutation profiles of the patients with the interactome data. Network-guided clustering showed significant association between each group and patient survival (P-value = 0.0408). Also, each group carries a set of signature 3D mutation patches that affect predominant pathways. We integrated drug sensitivity data of GBM cell lines with the mutation patches and the patient groups to analyze the therapeutic outcome of these patches. We found that Pazopanib might be effective in Group 3 by targeting CSF1R. Additionally, inhibiting ATM that is a mediator of PTEN phosphorylation may be ineffective in Group 2. We believe that from mutations to networks and eventually to clinical and therapeutic data, this study provides a novel perspective in the network-guided precision medicine.Publication Metadata only [BMIM] [PF6] incorporation doubles CO2 selectivity of ZIF-8: elucidation of interactions and their consequences on performance(Amer Chemical Soc, 2016) N/A; N/A; N/A; N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Kınık, Fatma Pelin; Altıntaş, Çiğdem; Balcı, Volkan; Koyutürk, Burak; Uzun, Alper; Keskin, Seda; Master Student; Researcher; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; 59917; 40548Experiments were combined with atomically detailed simulations and density functional theory (DFT) calculations to understand the effect of incorporation of an ionic liquid (IL), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]), into a metal organic framework (MOF with a zeolitic imidazolate framework), ZIF-8, on the CO2 separation performance. The interactions between [BMIM] [PF6] and ZIF-8 were examined in deep detail, and their consequences on CO2/CH4, CO2/N-2, and CH4/N-2 separation have been elucidated by using experimental measurements complemented by DFT calculations and atomically detailed simulations. Results suggest that IL-MOF interactions strongly affect the gas affinity of materials at low pressure, whereas available pore volume plays a key role for gas adsorption at high pressures. Direct interactions between IL and MOF lead to at least a doubling of CO2/CH4 and CO2/N-2 selectivities of ZIF-8. These results provide opportunities for rational design and development of IL-incorporated MOFs with exceptional selectivity for target gas separation applications.Publication Metadata only A bi-criteria optimization model to analyze the impacts of electric vehicles on costs and emissions(Elsevier, 2017) N/A; N/A; Department of Industrial Engineering; Kabatepe, Bora; Türkay, Metin; Master Student; Faculty Member; Department of Industrial Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 24956Electric vehicles (EV) are emerging as a mobility solution to reduce emissions in the transportation sector. The studies environmental impact analysis of EVs in the literature are based on the average energy mix or pre-defined generation scenarios and construct policy recommendations with a cost minimization objective. However, the environmental performance of EVs depends on the source of the marginal electricity provided to the grid and single objective models do not provide a thorough analysis on the economic and environmental impacts of EVs. In this paper, these gaps are addressed by a four step methodology that analyzes the effects of EVs under different charging and market penetration scenarios. The methodology includes a bi-criteria optimization model representing the electricity market operations. The results from a real-life case analysis show that EVs decrease costs and emissions significantly compared to conventional vehicles.Publication Metadata only A blind fractionally spaced equalization algorithm with global convergence(IEEE, 2007) Department of Electrical and Electronics Engineering; Erdoğan, Alper Tunga; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 41624In this article we present a fractionally spaced extension of the SubGradient based Blind equalization Algorithm (SGBA). The basic features of the proposed algorithm are the non-linear constraint on the search vector and the selection of the weighting and step size applied to the search vector. It is proven that the algorithm is globally convergent to a perfect equalization point under the well known equalizability conditions for the fractionally spaced setting. The simulation results provided at the end of the article illustrates the relative merit of the proposed algorithm in comparison to the state of the art algorithms.Publication Metadata only A CAM-based path generation method for rapid prototyping applications(Springer London Ltd, 2011) N/A; Department of Mechanical Engineering; Lazoğlu, İsmail; N/A; Faculty Member; Department of Mechanical Engineering; Manufacturing and Automation Research Center (MARC); N/A; College of Engineering; N/A; 179391A wide range of rapid prototyping (RP) methods are available commercially. Even though the hardware and production materials of these RP methods differ, their production techniques are built on the same idea: layer-by-layer material additive manufacturing. Whatever the material is used, it is deposited, vulcanized, or melted by following a pre-determined path, and each layer is stowed on the previous one to create the 3D model which is designed by using a computer-aided design program. The path which is followed while creating the model is very crucial. In this paper, a novel idea for path generation for RP processes is introduced. This new method is based on computer numerical controlled milling operation. Although the RP process and the milling process are completely opposite of each other since one of them is an additive and the other one is a subtractive method, the paths which are followed for these operations are very similar and based on the same idea: The progress goes on layer by layer. In this novel method, cutter location source files are used to create paths for RP processes. Examples of the prototypes produced by using this new method are also presented in the paper.Publication Open Access A cartridge based sensor array platform for multiple coagulation measurements from plasma(Royal Society of Chemistry (RSC), 2015) Bulut, Serpil; Yaralioglu, G. G.; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Çakmak, Onur; Ermek, Erhan; Kılınç, Necmettin; Barış, İbrahim; Kavaklı, İbrahim Halil; Ürey, Hakan; PhD Student; Other; Researcher; Teaching Faculty; Faculty Member; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; 109991; N/A; 111629; 40319; 8579This paper proposes a MEMS-based sensor array enabling multiple clot-time tests for plasma in one disposable microfluidic cartridge. The versatile LoC (Lab-on-Chip) platform technology is demonstrated here for real-time coagulation tests (activated Partial Thromboplastin Time (aPTT) and Prothrombin Time (PT)). The system has a reader unit and a disposable cartridge. The reader has no electrical connections to the cartridge. This enables simple and low-cost cartridge designs and avoids reliability problems associated with electrical connections. The cartridge consists of microfluidic channels and MEMS microcantilevers placed in each channel. The microcantilevers are made of electroplated nickel. They are actuated remotely using an external electro-coil and the read-out is also conducted remotely using a laser. The phase difference between the cantilever oscillation and the coil drive is monitored in real time. During coagulation, the viscosity of the blood plasma increases resulting in a change in the phase read-out. The proposed assay was tested on human and control plasma samples for PT and aPTT measurements. PT and aPTT measurements from control plasma samples are comparable with the manufacturer's datasheet and the commercial reference device. The measurement system has an overall 7.28% and 6.33% CV for PT and aPTT, respectively. For further implementation, the microfluidic channels of the cartridge were functionalized for PT and aPTT tests by drying specific reagents in each channel. Since simultaneous PT and aPTT measurements are needed in order to properly evaluate the coagulation system, one of the most prominent features of the proposed assay is enabling parallel measurement of different coagulation parameters. Additionally, the design of the cartridge and the read-out system as well as the obtained reproducible results with 10 mu l of the plasma samples suggest an opportunity for a possible point-of-care application.Publication Open Access A characterization of the extended serial correspondence(Elsevier, 2015) Heo, Eun Jeong; Department of Economics; Yılmaz, Özgür; Faculty Member; Department of Economics; College of Administrative Sciences and Economics; 108638We study the problem of assigning objects to a group of agents. We focus on probabilistic methods that take agents' ordinal preferences over the objects. Importantly, we allow for indifferences among objects. Katta and Sethuraman (2006) propose the extended serial correspondence to solve this problem. Our main result is a characterization of the extended serial correspondence in welfare terms by means of stochastic dominance efficiency, stochastic dominance no-envy and "limited invariance," a requirement we adapt from Heo (2014a). We also prove that an assignment matrix is selected by the extended serial correspondence if and only if it satisfies "non-wastefulness" and "ordinal fairness," which we adapt from Kesten et al.