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Publication Open Access Evaluating current Turkish politics in light of democratization and europeanization theories: The case of education reforms(Bogazici Universitesi bjournal@boun.edu.tr, 2011) Özalay-Şanlı, Eren; Özalay-Şanli, Eren, Department of Political Science and International Relations, Boğaziçi Üniversitesi, Bebek, Turkey, Department of EU Studies, Bahçeşehir Üniversitesi, Istanbul, TurkeyThis article traces the achievements of democratization and Europeanization in Turkey through debates about reforming education. After a discussion on Europeanization and democratization theories and on how well these theories explain the reform process in Turkey, the article delves into the question of how education norms that were developed during the European integration have affected domestic policy in Turkey. Education is a policy area left to the discretion of national governments within the European Union, therefore supranational legislation governing education does not exist. Education is not a problematic issue in the Turkish accession negotiations. Nevertheless, the pressing need for reform is stated in the annual progress reports when the practice of education in Turkey contradicts the norms of human rights as well as cultural and democratic rights. Recent education reforms and debates about future developments in education suggest important trajectories for understanding the current state of Turkey-EU relations and how far the mechanisms offered by the EU and other European institutions have worked for the further democratization of Turkey. The fact that some norms are accepted while others are rejected proves the instrumental impact of Europeanization in Turkey. The article finds the norm diffusion model accords with the rational institutionalist model of Europeanization in explaining education reforms in Turkey. © 2017 Elsevier B.V., All rights reserved.Publication Open Access Statistical inference and reverse engineering of gene regulatory networks from observational expression data(2012) Emmert Streib, Frank; Glazko, Galina V.; Altay, Gökmen; de Matos Simoes, Ricardo; Emmert–Streib, Frank, Computational Biology and Machine Learning Laboratory, Queen's University Belfast, Belfast, United Kingdom, Statistics and Computational Biology Laboratory, University of Cambridge, Cambridge, United Kingdom; Glazko, Galina V., UAMS College of Medicine, Little Rock, United States; Altay, Gökmen, Computational Biology and Machine Learning Laboratory, Queen's University Belfast, Belfast, United Kingdom, Department of Oncology, University of Cambridge, Cambridge, United Kingdom, Department of Electrical and Electronic Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; de Matos Simoes, Ricardo, Computational Biology and Machine Learning Laboratory, Queen's University Belfast, Belfast, United KingdomIn this paper, we present a systematic and conceptual overview of methods for inferring gene regulatory networks from observational gene expression data. Further, we discuss two classic approaches to infer causal structures and compare them with contemporary methods by providing a conceptual categorization thereof. We complement the above by surveying global and local evaluation measures for assessing the performance of inference algorithms. © 2012 Emmert-Streib, Glazko, Altay and de Matos Simoes. © 2013 Elsevier B.V., All rights reserved.Publication Open Access The history of urinary stones: In parallel with civilization(Hindawi Publishing Corporation 410 Park Avenue, 15th Floor, 287 pmb New York NY 10022, 2013) Tefekli, Ahmet Hamdi; Cezayirli, Fatin; Tefekli, Ahmet Hamdi, Bahçeşehir Üniversitesi, Istanbul, Turkey; Cezayirli, Fatin, VKV Amerikan Hastanesi, Istanbul, TurkeyThe roots of modern science and history of urinary stone disease go back to the Ancient Egyptians and Mesopotamia. Hippocrates defined the symptoms of bladder stones. The first recorded details of perineal lithotomy were those of Cornelius Celsus. Ancient Arabic medicine was based mainly on classical Greco-Roman works. Interestingly, the Fourth Lateran Council in 1215 forbade physicians from performing surgical procedures, as contact with blood or body fluids was viewed as contaminating to men. With Renaissance new procedures could be tried on criminals. The first recorded suprapubic lithotomy was carried out by Pierre Franco in 1561. In 1874, Bigelow developed a lithotrite, which was introduced into the bladder under anaesthesia (called as litholopaxy). Young was the first to report ureteroscopy (1929). With advances in intracorporeal lithotripsy techniques, ureteroscopy became the treatment of choice for ureteric stones. In 1976, Fernstrom and Johannson established percutaneous access to remove a renal stone. However, with the introduction of the first extracorporeal shock wave machine in 1980, a dramatic change in stone management was observed. Civilization in parallel with scientific developments has brought us to a point where we try not to cut our patients for stone disease, as Hippocrates admonishes, but rather manage them with minimal invasive alternatives. © 2013 Ahmet Tefekli and Fatin Cezayirli. © 2014 Elsevier B.V., All rights reserved.Publication Open Access Hematopoetic stem cell transplantation in children, Çocuklarda hematopoetik kök hücre nakli(Kare Publishing, 2014) Yeşilipek, Mehmet Akif; Yeşilipek, Mehmet Akif, Bahçeşehir Üniversitesi, Istanbul, TurkeyBone marrow transplantation is called hematopoetic stem cell transplantation (HSCT), since peripheral blood and umbilical cord blood can also be used as sources of stem cell currently. In children, bone marrow transplantation is used as a definite treatment method in many diseases including hemoglobinopaties, immune deficiencies, bone marrow failure and congenital metabolic diseases in addition to hematological malignancies. In addition to the underlying disease, the most important factors which have an impact on prognosis include infections which develop during the process of transplantation and graft-versus-host disease. In this article, it was aimed to give brief information on stem cell sources, preparation therapies, HSCT indications and post-transplantation complications in children. © 2014 by Turkish Pediatric Association. © 2019 Elsevier B.V., All rights reserved.Publication Open Access Cervical premalignant lesions and their management(AVES Ibrahim Kara info@avesyayincilik.com 105/9 Buyukdere Cad Mecidiyekoy,Sisli, Istanbul 34394, 2014) Köse, Mehmet Faruk; Naki, Mehmet Murat; Köse, Mehmet Faruk, Department of Obstetrics and Gynecology, Bahçeşehir Üniversitesi, Istanbul, Turkey; Naki, Mehmet Murat, Department of Obstetrics and Gynecology, Bahçeşehir Üniversitesi, Istanbul, TurkeyCervical cancer is the tenth most common cancer in women in developed countries that have national screening programs, while it is in the second line in underdeveloped countries. According to Ministry of Health registry data, cervical cancer is the eighth most common cancer among female cancers in Turkey. Today, the most effective screening for cervical cancer is to obtain smears from the cervix. Therefore, periodic screening programs are of great importance in identifying preinvasive lesions to prevent their progression to invasive cancer. Today, with the use of human papilloma virus (HPV) vaccine, screening programs have brought new insights into the prevention of cervical cancer. Management of preinvasive lesions has to be known by each obstetrics and gynecology specialist. Redundant procedures and treatments can be avoided by directing patients correctly at this step. Cancer phobia should not be created. Ablative or destructive treatments should not be done without histological diagnosis, hysterectomy, which has an equal risk of recurrence, should not be recommended. © 2014 by the Turkish-German Gynecological Education and Research Foundation. © 2014 Elsevier B.V., All rights reserved.Publication Open Access Biological approaches to treating intervertebral disk degeneration: Devising stem cell therapies(Cognizant Communication Corporation inquiries@cognizantcommunication.com 3 Hartsdale Road Elmsford NY 10523-3701, 2015) Han, Inbo; Ropper, Alexander Eli; Konya, Deniz; Kabataş, Serdar; Toktaş, Zafer Orkun; Aljuboori, Zaid S.; Zeng, Xiang; Chi, John H.; Zafonte, Ross D.; Teng, Yang D.; Han, Inbo, Department of Neurosurgery, Brigham and Women's Hospital, Boston, United States, Department of Neurosurgery, College of Medicine, Pochon CHA University, Pocheon, South Korea; Ropper, Alexander Eli, Department of Neurosurgery, Brigham and Women's Hospital, Boston, United States, Department of Neurosurgery, Barrow Neurological Institute, Phoenix, United States; Konya, Deniz, Department of Neurosurgery, Bahçeşehir Üniversitesi, Istanbul, Turkey; Kabatas, Serdar, Department of Neurosurgery, Reyap Hospital, Tekirdag, Turkey; Toktaş, Zafer Orkun, Department of Neurosurgery, Bahçeşehir Üniversitesi, Istanbul, Turkey; Aljuboori, Zaid S., Department of Neurosurgery, Brigham and Women's Hospital, Boston, United States, University of Louisville School of Medicine, Louisville, United States; Zeng, Xiang, Department of Neurosurgery, Brigham and Women's Hospital, Boston, United States, Department of Neurosurgery, College of Medicine, Pochon CHA University, Pocheon, South Korea; Chi, John H., Department of Neurosurgery, Brigham and Women's Hospital, Boston, United States; Zafonte, Ross D., Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital Network, Boston, United States; Teng, Yang D., Department of Neurosurgery, Brigham and Women's Hospital, Boston, United States, Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital Network, Boston, United States, Division of SCI Research, VA Medical Center, United StatesIntervertebral disk (IVD) degeneration is a common, chronic, and complex degeneration process that frequently leads to back pain and disability, resulting in a major public health issue. In this review we describe biological therapies under preclinical or clinical development with an emphasis on stem cell-based multimodal approaches that target prevention and treatment of IVD degeneration. Systematical review of the basic science and clinical literature was performed to summarize the current status of devising biological approaches to treating IVD degeneration. Since the exact mechanisms underlying IVD degeneration have not yet been fully elucidated and conservative managements appear to be mostly ineffective, current surgical treatment focuses on removal of the pathological disk tissues combined with spinal fusion. The treatment options, however, often produce insufficient efficacy and even serious complications. Therefore, there have been growing demands and endeavors for developing novel regenerative biology-guided strategies for repairing the IVD via delivery of exogenous growth factors, introduction of therapeutic genes, and transplantation of stem cells, or combinatorial therapies. Overall, the data suggest that when applied under a recovery neurobiology principle, multimodal regimens comprising ex vivo engineered stem cell-based disks hold a high potential promise for efficacious clinical translations. © 2017 Elsevier B.V., All rights reserved.Publication Open Access Shock wave treatment, practice changing from past to the future, Şok dalga tedavisi, geçmişten geleceğe değişen uygulama alanları(Logos Medical Publishing, 2015) Ural, İbrahim Halil; Alptekin, Hasan Kerem; Ural, Ibrahim Halil, Fiziksel Tıp ve Rehabilitasyon Bölümü, Bahçeşehir Üniversitesi, Istanbul, Turkey; Alptekin, Hasan Kerem, Fizyoterapi ve Rehabilitasyon Bölümü, Bahçeşehir Üniversitesi, Istanbul, TurkeyUse of shock wave therapy in urological field dates back to 1970-1980. Experimental studies for ureteral stones in the 1970s showed osteoblastic activity changes in ilium, and revived ability of shock waves in the treatment of musculoskeletal system. Treatment with shock waves has become popular in recent decades. It has been used as first- choice or as a supportive treatment for plantar fasciitis, calcaneal spur, lateral epicondylitis and calcific tendonitis of the shoulder. Shock wave applications recently have begun to be tested in the treatment of various diseases, and favourable result have been reported. The purpose of this review is to summarize the use of shock wave therapy in terms of dose and duration of application in the treatment of dental diseases, myocardial ischemia, spasticity, and tendonitis. © 2021 Elsevier B.V., All rights reserved.Publication Open Access Interferometric reflectance imaging sensor (IRIS)—a platform technology for multiplexed diagnostics and digital detection(MDPI AG Postfach Basel CH-4005, 2015) Avcı, Oğuzhan; Lortlar Ünlü, Neşe; Yalçın Ozkumur, Ayça; Ünlü, M. Selim; Avci, Oğuzhan, Boston University College of Engineering, Boston, United States; Lortlar Ünlü, Nese, Boston University College of Engineering, Boston, United States, Department of Electrical and Electronic Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Yalcin Ozkumur, Ayca, Department of Electrical and Electronic Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Ünlü, M. Selim Selim, Boston University College of Engineering, Boston, United States, Boston University College of Engineering, Boston, United StatesOver the last decade, the growing need in disease diagnostics has stimulated rapid development of new technologies with unprecedented capabilities. Recent emerging infectious diseases and epidemics have revealed the shortcomings of existing diagnostics tools, and the necessity for further improvements. Optical biosensors can lay the foundations for future generation diagnostics by providing means to detect biomarkers in a highly sensitive, specific, quantitative and multiplexed fashion. Here, we review an optical sensing technology, Interferometric Reflectance Imaging Sensor (IRIS), and the relevant features of this multifunctional platform for quantitative, label-free and dynamic detection. We discuss two distinct modalities for IRIS: (i) low-magnification (ensemble biomolecular mass measurements) and (ii) high-magnification (digital detection of individual nanoparticles) along with their applications, including label-free detection of multiplexed protein chips, measurement of single nucleotide polymorphism, quantification of transcription factor DNA binding, and high sensitivity digital sensing and characterization of nanoparticles and viruses. © 2018 Elsevier B.V., All rights reserved.Publication Open Access Best method for analysis of brain oscillations in healthy subjects and neuropsychiatric diseases(Elsevier B.V., 2016) BaÅŸar, Erol; Gölbaşı, Bilge Turp; Tülay, Elif Elif; Aydın, Serap; Başar-Eroǧlu, Canan; BaÅŸar, Erol, Cognition and Complex Systems Research Center, T.C. Istanbul Kültür Üniversitesi, Istanbul, Turkey; Gölbaşı, Bilge Turp, Cognition and Complex Systems Research Center, T.C. Istanbul Kültür Üniversitesi, Istanbul, Turkey; Tülay, Elif Elif, Cognition and Complex Systems Research Center, T.C. Istanbul Kültür Üniversitesi, Istanbul, Turkey; Aydın, Serap, Department of Biomedical Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Başar-Eroǧlu, Canan, Universität Bremen, Bremen, GermanyThe research related to brain oscillations and their connectivity is in a new take-off trend including the applications in neuropsychiatric diseases. What is the best strategy to learn about functional correlation of oscillations? In this report, we emphasize combined application of several analytical methods as power spectra, adaptive filtering of Event Related Potentials, inter-trial coherence and spatial coherence. These combined analysis procedure gives the most profound approach to understanding of EEG responses. Examples from healthy subjects, Alzheimer's Diseases, schizophrenia, and Bipolar Disorder are described. © 2017 Elsevier B.V., All rights reserved.Publication Open Access Comprehensive review of association estimators for the inference of gene networks(Turkiye Klinikleri Journal of Medical Sciences Talapapa Bulvary no. 102 Hamammonu 1 06230, 2016) Kurt, Zeyneb; Aydın, Nizamettin; Altay, Gökmen; Kurt, Zeyneb, Department of Computer Engineering, Yıldız Teknik Üniversitesi, Istanbul, Turkey; Aydın, Nizamettin, Department of Computer Engineering, Yıldız Teknik Üniversitesi, Istanbul, Turkey; Altay, Gökmen, Department of Biomedical Engineering, Bahçeşehir Üniversitesi, Istanbul, TurkeyGene network inference (GNI) algorithms allow us to explore the vast amount of interactions among the molecules in cells. In almost all GNI algorithms the main process is to estimate association scores among the variables of the dataset. However, there is no commonly accepted estimator to compute association scores for the current GNI algorithms. In this paper the association estimators that might be used in GNI applications are reviewed. The aim is to prepare a comprehensive and comparative review of all the important association estimators available in the literature. We performed this main aim by presenting, classifying, comparing, and discussing them to reveal which association estimator is more suitable for use in GNI applications by considering only the information available in the literature. Twenty-seven different estimators from various areas are investigated. The estimators were compared according to the GNI performances in the literature. The most promising association estimators for the GNI applications are suggested. As a result of the study, we identified eight promising methods for effective use in GNI. We expect this study to assist many researchers before using those estimators in their own GNI studies. © 2017 Elsevier B.V., All rights reserved.