WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Editorial Editors' Introduction: Fall 2025(Cambridge Univ Press, 2025-10-28) Dincer, Evren M.; Yukseker, Deniz; Kolluoglu, BirayArticle Citation - WoS: 1When the Railway Reached Istanbul: The Making of Sirkeci Terminus, 1870-1888(Routledge Journals, Taylor & Francis Ltd, 2017-07-16) Tozoglu, AhmetSince its establishment as a capital city, the historical topography of Istanbul has witnessed significant changes, created not only by devastating earthquakes and fires, but also by the implementation of large-scale imperial projects. In the existing literature, the transformation of Istanbul's urban area in the nineteenth century has largely explored the topics of new urban regulations, institutions and their implication after the Tanzimat (reform) decree of 1839. This article aims to explore a lesser-known dimension of nineteenth-century developments of the city: the extension of the railway into the heart of Istanbul's historical peninsula, and the spatial change around the Sirkeci district due to the physical expansion of the terminus area. The construction of a larger terminus (inaugurated in 1890) is relatively well documented in architectural history, yet developments prior to this monumental construction have been less explored so far. Thus, this article also aims to investigate the project's development and implementation phases in the second half of the nineteenth century, when the city witnessed continuous urban reformation processes by focusing on the intertwined relations of different agents in the urban space.Review The Crusade of 1456 Texts and Documentation in Translation(Routledge Journals, Taylor & Francis Ltd, 2023-10-18) Duzgun, Hulya Tafli; Akcadag, HaydarArticle Citation - Scopus: 1Textual Manifestations of Ottoman Architectural Revival and the Search for a National Idiom in the Late Ottoman Period(Cambridge Univ Press, 2022-09-06) Tozoglu, Ahmet ErdemThis article applies a critical approach to rethinking the relationship between nationalism and Ottoman architectural historiography by examining the intellectual medium during the late Ottoman period. More precisely, it examines how the history and theory of Ottoman architecture were initially established by Tanzimat (Reform) intelligentsia with the publication of Usul-i Mimari-i Osmani (Fundamentals of Ottoman Architecture) (1873). It addresses how the text was later comprehended and criticized by their successors, who utilized it to constitute their own vision of Turkish national architecture. By detailing the rise of the Turkish nationalist movement and the transition from Ottomanism to Turkism as the dominant identity, this article highlights the demand for the materialization of a national architecture as a component of the cultural construction of a national architectural style and the role of new public buildings as the site of nationalizing endeavors at the beginning of the twentieth century. Finally, this article problematizes the extent to which these new constructions can be deemed "national" by investigating the works of a pioneer figure of architecture, Kemaleddin Bey's writings and the design and construction of his dormitory building, the Fifth Vakif Han, in Istanbul.Article Citation - WoS: 1Citation - Scopus: 2Settling Down the Crisis: Planning and Implementation of the Immigrant Settlements in the Balkans During the Late Ottoman Period(Routledge Journals, Taylor & Francis Ltd, 2019-04-18) Tozoglu, Ahmet Erdem; Akgun, Seda Nehir GumuslueSince the Crimean War (1853-56), the Ottomans encountered with the problem of settling the Muslim immigrants and it was initially resolved by establishing new towns and villages on vast arable plains in the Balkans and Anatolia. However, it became a necessity to let the immigrants settle in the cities after the massive influx of refugees in 1877-78, when available agricultural lands to assign remained limited in the empire. With the consent of the Sultan, a new urban typology emerged at the outskirts of the cities, which were called immigrant (muhajir) neighbourhoods. This article aims to explore the spatial development of these settlements by the close examination of two cases based on archival materials. Mecidiye, which was established after the Crimean War, stands as an archetypal example and acted as an experimental laboratory. The success of Mecidiye case encouraged the Ottoman bureaucrats for further in post-1878 period. Hence, immigrant neighbourhood in uskub demonstrates us how the experience of Mecidiye was disseminated in the empire to establish a new planned settlement at the edges of an existing city. The close examination of uskub case provides us with the necessary tools to understand how the resettlement of refugees had cross-geographical spatial patterns.Article Citation - WoS: 7Citation - Scopus: 11Protein Β-Sheet Prediction Using an Efficient Dynamic Programming Algorithm(Elsevier Sci Ltd, 2017-10) Sabzekar, Mostafa; Naghibzadeh, Mahmoud; Eghdami, Mandie; Aydin, ZaferPredicting the beta-sheet structure of a protein is one of the most important intermediate steps towards the identification of its tertiary structure. However, it is regarded as the primary bottleneck due to the presence of non-local interactions between several discontinuous regions in beta-sheets. To achieve reliable long-range interactions, a promising approach is to enumerate and rank all beta-sheet conformations for a given protein and find the one with the highest score. The problem with this solution is that the search space of the problem grows exponentially with respect to the number of beta-strands. Additionally, brute force calculation in this conformational space leads to dealing with a combinatorial explosion problem with intractable computational complexity. The main contribution of this paper is to generate and search the space of the problem efficiently to reduce the time complexity of the problem. To achieve this, two tree structures, called sheet-tree and grouping-tree, are proposed. They model the search space by breaking it into sub-problems. Then, an advanced dynamic programming is proposed that stores the intermediate results, avoids repetitive calculation by repeatedly uses them efficiently in successive steps and reduces the space of the problem by removing those intermediate results that will no longer be required in later steps. As a consequence, the following contributions have been made. Firstly, more accurate beta-sheet structures are found by searching all possible conformations, and secondly, the time complexity of the problem is reduced by searching the space of the problem efficiently which makes the proposed method applicable to predict beta-sheet structures with high number of beta-strands. Experimental results on the BetaSheet916 dataset showed significant improvements of the proposed method in both execution time and the prediction accuracy in comparison with the state-of-the-art beta-sheet structure prediction methods Moreover, we investigate the effect of different contact map predictors on the performance of the proposed method using BetaSheet1452 dataset. The source code is available at http://www.conceptsgate.com/BetaTop.rar. (C) 2017 Elsevier Ltd. All rights reserved.Article Citation - WoS: 27Citation - Scopus: 31Proteomic Fertility Markers in Ram Sperm(Elsevier, 2021-12) Hitit, Mustafa; Ozbek, Mehmet; Ayaz-Guner, Serife; Guner, Huseyin; Oztug, Merve; Bodu, Mustafa; Kaya, AbdullahPrecise estimation of ram fertility is important for sheep farming to sustain reproduction efficiency and profitability of production. There, however, is no conventional method to accurately predict ram fertility. The objective of this study, therefore, was to ascertain proteomic profiles of ram sperm having contrasting fertility phenotypes. Mature rams (n = 66) having greater pregnancy rates than average (89.4 +/- 7.2%) were assigned into relatively-greater fertility (GF; n = 31; 94.5 +/- 2.8%) whereas those with less-than-average pregnancy rates were assigned into a lesserfertility (LF; n = 25; 83.1 +/- 5.73%; P = 0.028) group. Sperm samples from the outlier greatestand least-fertility rams (n = 6, pregnancy rate; 98.4 +/- 1.8% and 76.1 +/- 3.9%) were used for proteomics assessments utilizing Label-free LC-MS/MS. A total of 997 proteins were identified, and among these, 840 were shared by both groups, and 57 and 93 were unique to GF and LF, respectively. Furthermore, 190 differentially abundant proteins were identified; the abundance of 124 was larger in GF while 66 was larger in LF rams. The GF ram sperm had 79 GO/pathway terms in ten major biological networks while there were 47 GO/pathway terms in six biological networks in sperm of LF rams. Accordingly, differential abundances of sperm proteins between sperm of GF and LF rams were indicative of functional implications of sperm proteome on male fertility. The results of this study emphasize there are potential protein markers for evaluation of semen quality and estimation of ram sperm fertilizing capacity.Article Citation - WoS: 2Citation - Scopus: 3Power, Conflict and Negotiation Between the Agents: An Alternative Vision for Contestation on the Public Space in the Late Ottoman Empire(Routledge Journals, Taylor & Francis Ltd, 2019-12-04) Tozoglu, Ahmet ErdemThis article posits the territorial claim and control of the Ottoman government in the city centre by analyzing confrontations and conflicts of the state with the other agents via critical examination of a provincial case in the late nineteenth century. I examine the critical moments in making of public space to understand how the state authority claimed and enlarged its territorial influence during foundation and development of Dedeagac (Alexandroupolis) port in Edirne province through many agency confrontations. The conflicts between the state and other agents extend from the choice of location for a new port and taxation of the new port neighbourhood to the provision of public works and constitution of an administrative centre. In this context, foundation and growth of Dedeagac case demonstrate presence of many civic agents in clash with the state and they had to agree on an interim resolution for spatial construction of the town centre. This article aims to provide an alternative ground to examine the agency of the state in the late nineteenth century urban setting. It aims to be more inclusive by revealing the dynamic and substantial role of the other underrepresented agents in making of the cityscape in the late Ottoman Empire.Article Citation - WoS: 5Citation - Scopus: 7New Perspectives on Turkey Roundtable on the COVID-19 Pandemic : Prospects for the International Political Economic Order in the Post-Pandemic World(Cambridge Univ Press, 2020-09-21) Bugra, Ayse; Gurkaynak, Refet; Keyder, Caglar; Palat, Ravi Arvind; Pamuk, Sevket; Dincer, Evren M.Article Citation - WoS: 14Citation - Scopus: 15Image-Analysis Based Readout Method for Biochip: Automated Quantification of Immunomagnetic Beads, Micropads and Patient Leukemia Cell(Pergamon-Elsevier Science Ltd, 2020-06) Uslu, Fatma; Icoz, Kutay; Tasdemir, Kasim; Dogan, Refika S.; Yilmaz, BulentFor diagnosing and monitoring the progress of cancer, detection and quantification of tumor cells is utmost important. Beside standard bench top instruments, several biochip-based methods have been developed for this purpose. Our biochip design incorporates micron size immunomagnetic beads together with micropad arrays, thus requires automated detection and quantification of not only cells but also the micropads and the immunomagnetic beads. The main purpose of the biochip is to capture target cells having different antigens simultaneously. In this proposed study, a digital image processing-based method to quantify the leukemia cells, immunomagnetic beads and micropads was developed as a readout method for the biochip. Color, size-based object detection and object segmentation methods were implemented to detect structures in the images acquired from the biochip by a bright field optical microscope. It has been shown that manual counting and flow cytometry results are in good agreement with the developed automated counting. Average precision is 85 % and average error rate is 13 % for all images of patient samples, average precision is 99 % and average error rate is 1% for cell culture images. With the optimized micropad size, proposed method can reach up to 95 % precision rate for patient samples with an execution time of 90 s per image.