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Publication Metadata only A comprehensive model of simultaneous denitrification and methanogenic fermentation processes(2010) Tugtas, Adile Evren; Tezel, Ulaş; Pavlostathis, Spyros G.; Tugtas, Adile Evren, Department of Environmental Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Tezel, Ulaş, College of Engineering, Atlanta, United States; Pavlostathis, Spyros G., College of Engineering, Atlanta, United StatesThe denitrification process was incorporated into the IWA Anaerobic Digestion Model No. 1 (ADM1) in order to account for the effect of denitrification on the methanogenic fermentation process. The model was calibrated and optimized using previously published experimental data and kinetic parameter values obtained with a mixed, mesophilic (358C) methanogenic culture. Model simulations were used to predict the effect of nitrate reduction on the methanogenic fermentation process in batch, semi-continuous, and continuous flow reactors experiencing operational changes and/or system disturbances. The extended model clearly revealed the importance of substrate competition between denitrifiers and non-denitrifiers as well as the impact of N-oxide inhibition on process interactions between fermentation, methanogenesis, and denitrification. © 2009 Wiley Periodicals, Inc. © 2010 Elsevier B.V., All rights reserved., MEDLINE® is the source for the MeSH terms of this document.Publication Metadata only Information system design for a hospital emergency department: A usability analysis of software prototypes(2010) Karahoca, Adem; Bayraktar, Erkan; Tatoglu, Ekrem; Karahoca, Dilek Yiğit; Karahoca, Adem, Faculty of Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Bayraktar, Erkan, Faculty of Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Tatoglu, Ekrem, Faculty of Economics and Administrative Sciences, Bahçeşehir Üniversitesi, Istanbul, Turkey; Karahoca, Dilek Yiğit, Faculty of Engineering, Bahçeşehir Üniversitesi, Istanbul, TurkeyStudy objective: The purpose of this study is to evaluate the usability of emergency department (ED) software prototypes developed for Tablet personal computers (Tablet PCs) in order to keep electronic health records (EHRs) of patients errorless and accessible through mobile technologies. In order to serve this purpose, two alternative prototypes were developed for Tablet PCs: Mobile Emergency Department Software (MEDS) and Mobile Emergency Department Software Iconic (MEDSI) among which the user might choose the more appropriate one for ED operations based on a usability analysis involving the target users. Methods: The study is based on a case study of 32 potential users of our prototypes at the ED of Kadikoy-AHG in Istanbul, Turkey. We examined usability of the prototypes for medical information systems by means of Nielsen's heuristic evaluation and cognitive walkthrough methods relying on 7-point scales, and scenario completion success rate and average scenario completion time, respectively. Results: The implementation of MEDSI in our case study confirmed the view that the usability evaluation results of iconic GUIs were better than those of non-iconic GUIs in terms of Nielsen's heuristic evaluation, effectiveness and user satisfaction. For the whole sample, paired t-test scores indicated that there was a significant difference (p < 0.01) between mean values of Nielsen's usability scores toward MEDS and MEDSI indicating that MEDSI was evaluated more favorably than MEDS. As for effectiveness of the prototypes, significant differences (p < 0.01) were noted between MEDS and MEDSI in terms of both overall scenario completion success rate and average scenario completion time. Similarly, for the full sample of users independent sample t-test scores indicated that MEDSI was perceived significantly more favorable (p < 0.01) than MEDS in terms of overall user satisfaction. Conclusion: The study provides two important contributions to the extant literature. First, it addresses a topic and methodology that serves potentially interesting to the biomedical informatics community. Drawing on good background information and appropriate context, it involves various aspects of usability testing. Another contribution of the study lies in its examination of two different prototypes during the design phase involving the target users. © 2009 Elsevier Inc. All rights reserved. © 2010 Elsevier B.V., All rights reserved., MEDLINE® is the source for the MeSH terms of this document.Publication Metadata only Classification of the colonic polyps in CT-colonography using region covariance as descriptor features of suspicious regions(2010) Kılıç, Niyazi; Kursun, Olcay; Uçan, Osman Nuri; Kılıç, Niyazi, Department of Electrical and Electronics Engineering, Istanbul Üniversitesi, Istanbul, Turkey; Kursun, Olcay, Department of Electrical and Electronics Engineering, Istanbul Üniversitesi, Istanbul, Turkey; Uçan, Osman Nuri, Department of Computer Engineering, Bahçeşehir Üniversitesi, Istanbul, TurkeyWe present an algorithm to classify polyps in CT colonography images utilizing covariance matrices as object descriptors. Since these descriptors do not lie on a vector space, they cannot simply be fed to traditional machine learning tools such as support vector machines (SVMs) or artificial neural networks (ANNs). To benefit from the simple yet one of the most powerful nonparametric machine learning approach k-nearest neighbor classifier, it suffices to compute the pairwise distances among the covariance descriptors using a distance metric involving their generalized eigenvalues, which also follows from the Lie group structure of positive definite matrices. This approach is fast and discriminates polyps from non-polyps with high accuracy using only a small size descriptor, which consists of 36 unique features per image region extracted from the suspicious regions that we have obtained by combined cellular neural network (CNN) and template matching detection method. These suspicious regions are, in average, 15 × 17 = 255 pixels in our experiments. © Springer Science + Business Media, LLC 2008. © 2010 Elsevier B.V., All rights reserved., MEDLINE® is the source for the MeSH terms of this document.Publication Metadata only Telediagnosis of parkinson's disease using measurements of dysphonia(2010) Sakar, C. Okan; Kursun, Olcay; Sakar, C. Okan, Department of Computer Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Kursun, Olcay, Department of Computer Engineering, Bahçeşehir Üniversitesi, Istanbul, TurkeyParkinson's disease (PD) is a neurological illness which impairs motor skills, speech, and other functions such as mood, behavior, thinking, and sensation. It causes vocal impairment for approximately 90% of the patients. As the symptoms of PD occur gradually and mostly targeting the elderly people for whom physical visits to the clinic are inconvenient and costly, telemonitoring of the disease using measurements of dysphonia (vocal features) has a vital role in its early diagnosis. Such dysphonia features extracted from the voice come in variety and most of them are interrelated. The purpose of this study is twofold: (1) to select a minimal subset of features with maximal joint relevance to the PD-score, a binary score indicating whether or not the sample belongs to a person with PD, and (2) to build a predictive model with minimal bias (i.e. to maximize the generalization of the predictions so as to perform well with unseen test examples). For these tasks, we apply the mutual information measure with the permutation test for assessing the relevance and the statistical significance of the relations between the features and the PD-score, rank the features according to the maximum-relevance-minimum-redundancy (mRMR) criterion, use a Support Vector Machine (SVM) for building a classification model and test it with a more suitable cross-validation scheme that we called leave-one-individual-out that fits with the dataset in hand better than the conventional bootstrapping or leave-one-out validation methods. © 2009 Springer Science+Business Media, LLC. © 2010 Elsevier B.V., All rights reserved., MEDLINE® is the source for the MeSH terms of this document.Publication Metadata only Coupled nonparametric shape and moment-based intershape pose priors for multiple basal ganglia structure segmentation(2010) Uzunbaş, Mustafa Gökhan; Soldea, Octavian; Ünay, Devrim; Çetin, Müjdat; Unal, Gozde Bozkurt; Erçil, Aytül; Ekin, Ahmet; Uzunbaş, Mustafa Gökhan, Faculty of Engineering and Natural Sciences, Sabancı Üniversitesi, Tuzla, Turkey, Department of Computer Science, Piscataway, United States; Soldea, Octavian, Faculty of Engineering and Natural Sciences, Sabancı Üniversitesi, Tuzla, Turkey; Ünay, Devrim, Department of Electrical and Electronic Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Çetin, Müjdat, Faculty of Engineering and Natural Sciences, Sabancı Üniversitesi, Tuzla, Turkey; Unal, Gozde Bozkurt, Faculty of Engineering and Natural Sciences, Sabancı Üniversitesi, Tuzla, Turkey; Erçil, Aytül, Faculty of Engineering and Natural Sciences, Sabancı Üniversitesi, Tuzla, Turkey; Ekin, Ahmet, Video Processing and Analysis Group, Philips Research, Eindhoven, NetherlandsThis paper presents a new active contour-based, statistical method for simultaneous volumetric segmentation of multiple subcortical structures in the brain. In biological tissues, such as the human brain, neighboring structures exhibit co-dependencies which can aid in segmentation, if properly analyzed and modeled. Motivated by this observation, we formulate the segmentation problem as a maximum a posteriori estimation problem, in which we incorporate statistical prior models on the shapes and intershape (relative) poses of the structures of interest. This provides a principled mechanism to bring high level information about the shapes and the relationships of anatomical structures into the segmentation problem. For learning the prior densities we use a nonparametric multivariate kernel density estimation framework. We combine these priors with data in a variational framework and develop an active contour-based iterative segmentation algorithm. We test our method on the problem of volumetric segmentation of basal ganglia structures in magnetic resonance images. We present a set of 2-D and 3-D experiments as well as a quantitative performance analysis. In addition, we perform a comparison to several existent segmentation methods and demonstrate the improvements provided by our approach in terms of segmentation accuracy. © 2010 IEEE. © 2010 Elsevier B.V., All rights reserved.Publication Metadata only Denoising embolic Doppler ultrasound signals using Dual Tree Complex Discrete Wavelet Transform(2010) Serbes, Görkem; Aydın, Nizamettin; Serbes, Görkem, Department of Electrical Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Aydın, Nizamettin, Department of Computer Engineering, Yıldız Teknik Üniversitesi, Istanbul, TurkeyEarly and accurate detection of asymptomatic emboli is important for monitoring of preventive therapy in stroke-prone patients. One of the problems in detection of emboli is the identification of an embolic signal caused by very small emboli. The amplitude of the embolic signal may be so small that advanced processing methods are required to distinguish these signals from Doppler signals arising from red blood cells. In this study instead of conventional discrete wavelet transform, the Dual Tree Complex Discrete Wavelet Transform was used for denoising embolic signals. Performances of both approaches were compared. Unlike the conventional discrete wavelet transform discrete complex wavelet transform is a shift invariant transform with limited redundancy. Results demonstrate that the Dual Tree Complex Discrete Wavelet Transform based denoising outperforms conventional discrete wavelet denoising. Approximately 8 dB improvement is obtained by using the Dual Tree Complex Discrete Wavelet Transform compared to the improvement provided by the conventional Discrete Wavelet Transform (less than 5 dB). © 2010 IEEE. © 2011 Elsevier B.V., All rights reserved.Publication Metadata only Investigations of zero-field splitting (ZFS) and local distortion parameters of ZnAl2S4:Mn2+ by theoretical analysis(2011) Aikgöz, Muhammed; Aikgöz, Muhammed, Faculty of Arts and Sciences, Bahçeşehir Üniversitesi, Istanbul, TurkeyFourth-order perturbation formula on the basis of the dominant spin-orbit coupling mechanism is employed to investigate the local environment around Mn2+ centers in ZnAl2S4 single crystals. The zero-field splitting (ZFS) parameter D is calculated for the Mn2+ ions at the Al3+ site with local symmetry D3d using the different orbital reduction factors. Both the contributions of the lattice distortions to the crystal-field (CF) parameters and the D are examined by means of different cases. The comparison between the calculated results in this study and the previous experimental and theoretical values reveals a good agreement and reasonable distortion parameters for Mn2+ ions at Al3+ sites. © 2010 Elsevier B.V. All rights reserved. © 2011 Elsevier B.V., All rights reserved., MEDLINE® is the source for the MeSH terms of this document.Publication Metadata only A wavelet packet adaptive filtering algorithm for enhancing manatee vocalizations(2011) Gür, M. Berke; Niezrecki, Christopher; Gür, M. Berke, Department of Mechanical Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Niezrecki, Christopher, Francis College of Engineering, Lowell, United StatesApproximately a quarter of all West Indian manatee (Trichechus manatus latirostris) mortalities are attributed to collisions with watercraft. A boater warning system based on the passive acoustic detection of manatee vocalizations is one possible solution to reduce manatee-watercraft collisions. The success of such a warning system depends on effective enhancement of the vocalization signals in the presence of high levels of background noise, in particular, noise emitted from watercraft. Recent research has indicated that wavelet domain pre-processing of the noisy vocalizations is capable of significantly improving the detection ranges of passive acoustic vocalization detectors. In this paper, an adaptive denoising procedure, implemented on the wavelet packet transform coefficients obtained from the noisy vocalization signals, is investigated. The proposed denoising algorithm is shown to improve the manatee detection ranges by a factor ranging from two (minimum) to sixteen (maximum) compared to high-pass filtering alone, when evaluated using real manatee vocalization and background noise signals of varying signal-to-noise ratios (SNR). Furthermore, the proposed method is also shown to outperform a previously suggested feedback adaptive line enhancer (FALE) filter on average 3.4 dB in terms of noise suppression and 0.6 dB in terms of waveform preservation. © 2011 Acoustical Society of America. © 2011 Elsevier B.V., All rights reserved., MEDLINE® is the source for the MeSH terms of this document.Publication Metadata only Optimizing the driving scheme of a self-actuated atomic force microscope probe for high-speed applications(2011) Balantekin, Müjdat; Deǧertekin, Fahrettin Levent; Balantekin, Müjdat, Department of Electrical and Electronic Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Deǧertekin, Fahrettin Levent, The George W. Woodruff School of Mechanical Engineering, Atlanta, United StatesWe investigate the optimum driving scheme of a dynamic atomic force microscope with a self-actuated probe for high-speed applications by performing numerical simulations. We compare the recently developed methods such as Q-control, dynamic PID control, and modified Q-control methods to the standard tapping mode by considering scan speed and peak transient forces. In addition, the effects of driving frequency and set-point amplitude on the maximum achievable scan speed for the same probe-sample system are discussed. We find that the scan speed can be increased significantly at the expense of increased peak transient forces. © 2011 Elsevier B.V. © 2012 Elsevier B.V., All rights reserved.Publication Metadata only Investigations of zero-field splitting (ZFS) and local distortion parameters of Fe3+ ions doped into three oxi-spinels (ZnAl 2O4, MgAl2O4, and ZnGa 2O4) by theoretical analysis(2011) Aikgöz, Muhammed; Aikgöz, Muhammed, Faculty of Arts and Sciences, Bahçeşehir Üniversitesi, Istanbul, TurkeyThe local environment around the paramagnetic centers formed by the Fe 3+ ions doped into three oxi-spinel crystals (ZnAl2O 4, MgAl2O4, and ZnGa2O4) is investigated utilizing the fourth-order perturbation formula of the axial zero-field splitting parameter D on the basis of the dominant spin-orbit coupling mechanism. In order to fix a plausible cubic space group for B-sites located by Al3+/Ga3+ cations, several modeling approaches are used and the results are discussed in detail. © 2011 Elsevier B.V. All rights reserved. © 2011 Elsevier B.V., All rights reserved., MEDLINE® is the source for the MeSH terms of this document.