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Publication Metadata only Retrospective review of epidemic viral pneumonia cases in Turkey: A multicenter study(SPANDIDOS PUBL LTD, 2017) Cortuk, Mustafa; Acat, Murat; Yazici, Onur; Yasar, Zehra; Kiraz, Kemal; Ataman, Sena Yapicioglu; Tanriverdi, Elif; Zitouni, Burcak; Kirakli, Cenk; Ediboglu, Ozlem; Tuksavul, Fevziye; Dirican, Adem; Celik, Hale Kefeli; Ozkaya, Sevket; Cetinkaya, Erdogan; Karabuk University; Adnan Menderes University; Abant Izzet Baysal University; Antalya Ataturk State Hospital; Izmir Dr Suat Seren Chest Diseases & Thoracic Surgery Training & Research Hospital; Istanbul Yedikule Chest Diseases & Thoracic Surgery Training & Research Hospital; Medical Park Hospitals Group; Samsun Training & Research Hospital; Samsun Training & Research Hospital; Bahcesehir UniversityInfluenza A (H1N1) caused its first pandemic in 2009 in USA and Mexico. Since then, clinicians have exercised great care in order to make an early diagnosis of viral pneumonias. This is due in part to pandemic influenza A infection having greater impact on populations <65 years old than other viral strains, including seasonal influenza. Chest radiographies of those affected displayed a rapid progression of patchy infiltrates, and a large proportion of individuals required admission to intensive care units (ICU). Despite efforts, patients infected with the virus had a high mortality rate. The present multicenter study aimed to retrospectively evaluate the clinical, demographic and prognostic characteristics of patients diagnosed with epidemic viral pneumonia in Turkey. A total of 92 patients were included in the study. The Student's t-test and Chi-square tests were performed to analyze quantitative data, assuming a normal distribution, and to analyze qualitative data, respectively. Stepwise logistic regression was used to evaluate the effects of demographic variables and laboratory values on the virus mortality rate. The male/female ratio was 42/50 and the mean age was 48.74 +/- 16.65 years. A total of 69 (75%) patients were unvaccinated against influenza. The most common symptoms were cough (87%) and fever (63%). Chest computed tomography showed peripheral patchy areas of the lungs of ground glass density in 38 patients (41.3%). A total of 22 (59.4%) patients had H1N1, 5 (12.5%) patients had influenza B, and 38 (41.3%) patients met the criteria for admission to the ICU. Of these patients, 20 (52.63%) were monitored with a mechanical ventilator, with a noninvasive ventilator being adequate for 10 (26.32%) of patients. The length of stay in the ICU was 6.45 +/- 5.97 days and the duration of mechanical ventilation was 5.06 +/- 4.69 days. A total of 12 (13.04%) patients in the ICU succumbed. Logistic regression analysis revealed that among the parameters possibly associated with mortality, being an active smoker increased the risk of mortality 7.08-fold compared to other groups (P=0.005). In conclusion, viral pneumonia remains a significant health problem during the winter period. Considering the high number of ICU admissions and high rate of mortality for patients in the present study, earlier initiation of antiviral therapy is necessary. Active smoking increased mortality in viral pneumonia.Publication Metadata only The effect of depression and side effects of antiepileptic drugs on injuries in patients with epilepsy(WILEY, 2017) Gur-Ozmen, S.; Mula, M.; Agrawal, N.; Cock, H. R.; Lozsadi, D.; von Oertzen, T. J.; City St Georges, University of London; City St Georges, University of London; Bahcesehir UniversityBackground and purposePeople with epilepsy are at increased risk of accidents and injuries but, despite several studies on this subject, data regarding preventable causes are still contradictory. The aim of this study was to investigate the relationship between injuries, side effects of antiepileptic drugs (AEDs) and depression. MethodsData from a consecutive sample of adult patients with epilepsy attending the outpatient clinics at St George's University Hospital in London were included. All patients were asked if they had had any injury since the last clinic appointment and completed the Liverpool Adverse Event Profile (LAEP) and Neurological Disorders Depression Inventory for Epilepsy. ResultsAmong 407 patients (243 females, mean age 43.1years), 71 (17.4%) reported injuries since the last appointment. A two-step cluster analysis revealed two clusters with the major cluster (53.5% of the injured group) showing a total score for LAEP 45, a positive Neurological Disorders Depression Inventory for Epilepsy screening and presence of AED polytherapy. A total score for LAEP 45 was the most important predictor. ConclusionsAntiepileptic drug treatment should be reviewed in patients reporting injuries in order to evaluate the potential contribution and burden of AED side effects.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 Open Access Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations(2010) Bilgüvar, Kaya; Öztürk, Ali Kemal; Louvi, Angeliki; Kwan, Kenneth Y.; Choi, Murim; Tatlí, Burak; Yalnizoǧlu, Dilek; Tüysüz, Beyhan; Caglayan, Ahmet Okay; Gökben, Sarenur; Bilgüvar, Kaya, Department of Neurosurgery, Yale School of Medicine, New Haven, United States, Department of Neurobiology, Yale School of Medicine, New Haven, United States, Department of Genetics, Yale School of Medicine, New Haven, United States; Öztürk, Ali Kemal, Department of Neurosurgery, Yale School of Medicine, New Haven, United States, Department of Neurobiology, Yale School of Medicine, New Haven, United States, Department of Genetics, Yale School of Medicine, New Haven, United States; Louvi, Angeliki, Department of Neurosurgery, Yale School of Medicine, New Haven, United States, Department of Neurobiology, Yale School of Medicine, New Haven, United States, Department of Genetics, Yale School of Medicine, New Haven, United States; Kwan, Kenneth Y., Department of Neurobiology, Yale School of Medicine, New Haven, United States, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, United States; Choi, Murim, Department of Genetics, Yale School of Medicine, New Haven, United States; Tatlí, Burak, Department of Pediatrics, İstanbul Tıp Fakültesi, Istanbul, Turkey; Yalnizoǧlu, Dilek, Department of Pediatrics, Hacettepe Üniversitesi, Ankara, Turkey; Tüysüz, Beyhan, Department of Pediatrics, İstanbul University-Cerrahpaşa Cerrahpaşa Faculty of Medicine, Istanbul, Turkey; Caglayan, Ahmet Okay,; Gökben, Sarenur, Department of Pediatrics, Ege University Medical School, Izmir, TurkeyThe development of the human cerebral cortex is an orchestrated process involving the generation of neural progenitors in the periventricular germinal zones, cell proliferation characterized by symmetric and asymmetric mitoses, followed by migration of post-mitotic neurons to their final destinations in six highly ordered, functionally specialized layers1,2. An understanding of the molecular mechanisms guiding these intricate processes is in its infancy, substantially driven by the discovery of rare mutations that cause malformations of cortical development3-6. Mapping of disease loci in putative Mendelian forms of malformations of cortical development has been hindered by marked locus heterogeneity, small kindred sizes and diagnostic classifications that may not reflect molecular pathogenesis. Here we demonstrate the use of whole-exome sequencing to overcome these obstacles by identifying recessive mutations in WD repeat domain 62 (WDR62) as the cause of a wide spectrum of severe cerebral cortical malformations including microcephaly, pachygyria with cortical thickening as well as hypoplasia of the corpus callosum. Some patients with mutations in WDR62 had evidence of additional abnormalities including lissencephaly, schizencephaly, polymicrogyria and, in one instance, cerebellar hypoplasia, all traits traditionally regarded as distinct entities. In mice and humans, WDR62 transcripts and protein are enriched in neural progenitors within the ventricular and subventricular zones. Expression of WDR62 in the neocortex is transient, spanning the period of embryonic neurogenesis. Unlike other known microcephaly genes, WDR62 does not apparently associate with centrosomes and is predominantly nuclear in localization. These findings unify previously disparate aspects of cerebral cortical development and highlight the use of whole-exome sequencing to identify disease loci in settings in which traditional methods have proved challenging. © 2010 Macmillan Publishers Limited. All rights reserved. © 2012 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 The 2010 Eurobarometer on the life sciences(2011) Gaskell, George D.; Allansdottir, Agnes; Allum, Nick; Castro, Paula; Esmer, Yilmaz; Fischler, Claude; Jackson, Jonathan; Kronberger, Nicole; Hampel, Jürgen; Mejlgaard, Niels; Gaskell, George D., London School of Economics and Political Science, London, United Kingdom; Allansdottir, Agnes, Università degli Studi di Siena, Siena, Italy; Allum, Nick, University of Essex, Colchester, United Kingdom; Castro, Paula, Iscte – Instituto Universitário de Lisboa, Lisbon, Portugal; Esmer, Yilmaz, Bahçeşehir Üniversitesi, Istanbul, Turkey; Fischler, Claude, École des Hautes Études en Sciences Sociales, Paris, France; Jackson, Jonathan, London School of Economics and Political Science, London, United Kingdom; Kronberger, Nicole, Johannes Kepler University Linz, Linz, Austria; Hampel, Jürgen, Universität Stuttgart, Stuttgart, Germany; Mejlgaard, Niels, Aarhus Universitet, Aarhus, Denmark[No abstract available]Publication Open Access Recessive LAMC3 mutations cause malformations of occipital cortical development(2011) Barak, Tanyeri; Kwan, Kenneth Y.; Louvi, Angeliki; Demirbilek, Veysi; Sütçü Saygı, Serap; Tüysüz, Beyhan; Choi, Murim; Boyacı, Hüseyin; Doerschner, Katja; Zhu, Ying; Barak, Tanyeri, Department of Neurosurgery, Yale School of Medicine, New Haven, United States, Department of Neurobiology, Yale School of Medicine, New Haven, United States, Department of Genetics, Yale School of Medicine, New Haven, United States; Kwan, Kenneth Y., Department of Neurobiology, Yale School of Medicine, New Haven, United States, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, United States; Louvi, Angeliki, Department of Neurosurgery, Yale School of Medicine, New Haven, United States, Department of Neurobiology, Yale School of Medicine, New Haven, United States; Demirbilek, Veysi, Department of Neurology, Istanbul University-Cerrahpasa, Istanbul, Turkey; Saygı, Serap Sütçü, Department of Neurology, Hacettepe Üniversitesi, Ankara, Turkey; Tüysüz, Beyhan, Department of Pediatrics, Istanbul University-Cerrahpasa, Istanbul, Turkey; Choi, Murim, Department of Genetics, Yale School of Medicine, New Haven, United States; Boyaci, Huseyin, Department of Psychology, Bilkent Üniversitesi, Ankara, Turkey, National Magnetic Resonance Research Center, Bilkent Üniversitesi, Ankara, Turkey; Doerschner, Katja, Department of Psychology, Bilkent Üniversitesi, Ankara, Turkey, National Magnetic Resonance Research Center, Bilkent Üniversitesi, Ankara, Turkey; Zhu, Ying, Department of Neurobiology, Yale School of Medicine, New Haven, United States, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, United StatesThe biological basis for regional and inter-species differences in cerebral cortical morphology is poorly understood. We focused on consanguineous Turkish families with a single affected member with complex bilateral occipital cortical gyration abnormalities. By using whole-exome sequencing, we initially identified a homozygous 2-bp deletion in LAMC3, the laminin 33 gene, leading to an immediate premature termination codon. In two other affected individuals with nearly identical phenotypes, we identified a homozygous nonsense mutation and a compound heterozygous mutation. In human but not mouse fetal brain, LAMC3 is enriched in postmitotic cortical plate neurons, localizing primarily to the somatodendritic compartment. LAMC3 expression peaks between late gestation and late infancy, paralleling the expression of molecules that are important in dendritogenesis and synapse formation. The discovery of the molecular basis of this unusual occipital malformation furthers our understanding of the complex biology underlying the formation of cortical gyrations. © 2011 Nature America, Inc. All rights reserved. © 2011 Elsevier B.V., All rights reserved., MEDLINE® is the source for the MeSH terms of this document.