Research Outputs

Permanent URI for this communityhttps://hdl.handle.net/20.500.14288/2

Browse

Now showing 1 - 20 of 36

Metadata only
A chemically inducible organelle rerouting assay to probe primary cilium assembly, maintenance, and disassembly in cultured cells
(Humana Press Inc., 2024) Department of Molecular Biology and Genetics; İşsezer, Fatma Başak Turan; Ercan, Muhammed Erdem; Karalar, Elif Nur Fırat; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Sciences
The primary cilium is a conserved, microtubule-based organelle that protrudes from the surface of most vertebrate cells as well as sensory cells of many organisms. It transduces extracellular chemical and mechanical cues to regulate diverse cellular processes during development and physiology. Loss-of-function studies via RNA interference and CRISPR/Cas9-mediated gene knockouts have been the main tool for elucidating the functions of proteins, protein complexes, and organelles implicated in cilium biology. However, these methods are limited in studying acute spatiotemporal functions of proteins as well as the connection between their cellular positioning and functions. A powerful approach based on inducible recruitment of plus or minus end-directed molecular motors to the protein of interest enables fast and precise control of protein activity in time and in space. In this chapter, we present a chemically inducible heterodimerization method for functional perturbation of centriolar satellites, an emerging membrane-less organelle involved in cilium biogenesis and function. The method we present is based on rerouting of centriolar satellites to the cell center or the periphery in mammalian epithelial cells. We also describe how this method can be applied to study the temporal functions of centriolar satellites during primary cilium assembly, maintenance, and disassembly.
Metadata only
An overview of security issues in cognitive radio ad hoc networks
(IGI Global, 2023) Islam, Noman; Syed, Darakhshan; Zia, Muhammad Furqan; ; Graduate School of Sciences and Engineering;
Cognitive radio ad hoc network (CRAHN) is an emerging discipline of network computing. It combines the advantages of cognitive radio networks and mobile ad hoc networks. This chapter starts with an overview of various research issues of CRAHN along with representative solutions for these research issues. Among the various research issues presented, security is discussed in detail due to its prime importance. A review of existing literature reveals that not much work on security has been reported for cognitive radio networks. Specifically, an overview of security issues in CRAHN, presented in this article, is a novel work of this kind. A major part of this article highlights the importance of security in CRAHN and presents an overview of major security issues and the solutions proposed to address these issues in CRAHN. © 2023, IGI Global. All rights reserved.
Metadata only
Application of aerogels in optical devices
(Springer Science and Business Media Deutschland Gmbh, 2023) Özbakır, Yaprak; Jonáš, Alexandr; Department of Electrical and Electronics Engineering;Department of Chemical and Biological Engineering;Department of Physics; Kiraz, Alper; Erkey, Can; College of Engineering; College of Sciences
Integrated optical devices can provide sophisticated, innovative solutions for handling light in a number of scientific and technological applications ranging from detection and chemical and biological analysis, through imaging to activation of photochemical reactions. Aerogels – with their unusually low refractive index, spectrally tunable optical transparency, possibility of doping the bulk material with chemically active atoms, molecules, and nanoparticles, and relatively low production cost – represent an attractive platform for fabricating integrated photonic circuits. This chapter provides a comprehensive review of the literature on the use of aerogels for a wide range of optical applications. First, we present an overview of the material properties of aerogels that are essential for their optical applications, concentrating, in particular, on the use of aerogels for controlled light guiding. Subsequently, we discuss possible techniques for fabricating channel waveguides in aerogel monoliths and describe in detail methods for making the channel surfaces hydrophobic. We summarize the studies in the literature on the characterization of light propagation in liquid-filled channels formed within aerogel monoliths, as well as on the quantification of light-guiding characteristics of aerogel-based waveguides. We then describe the current and possible future applications of aerogel-based optofluidic waveguides and briefly address the subject of using aerogels for fabricating lightweight optical reflectors. We conclude by a perspective on the emerging directions in the development of aerogel-based optical and photonic components and devices. © Springer Nature Switzerland AG 2023.
Metadata only
Applicative problems regarding the Turkish certificate of succession
(Springer Nature, 2023) Tarman, Zeynep Derya; Law School
Considering the intensifying transnational migrations, multicultural families and the Turkish population living abroad, requesting a Certificate of Succession (the legal document which names a deceased person’s heirs) from Turkish authorities, or the recognition of a foreign Certificate of Succession in Turkey, is gaining increasing practical importance. However, determining the international jurisdiction of Turkish courts for the issuance of a Certificate of Succession containing a foreign element brings up certain debates under Turkish law. The competence of the notary publics in the issuance of a Certificate of Succession is also contentious. In addition, where a Certificate of Succession is requested from a competent Turkish court, the law applicable to succession appears as another issue, especially with regards to the right of inheritance of the surviving spouse in same-sex marriages. Further, the recognition of a foreign Certificate of Succession involves debates and presents obstacles relating to the preconditions and the requirements for recognition. This paper examines the following issues: the doctrinal debates and the problems in practice, with particular attention given to the competent authority to issue a Certificate of Succession in a case with a foreign element, the applicable law in succession cases, and the recognition of foreign Certificates of Succession in Turkey. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.
Metadata only
Artificial intelligence and medical decision-making: Wind of change for medical malpractice liability and insurance?
(Edward Elgar Publishing Ltd., 2023) N/A; Çelebi, Özgün; Buğra, Ayşegül; Law School
In the field of health care, computing systems' extensive capabilities and ongoing improvements as to their autonomy raise the question of whether the patient's expectations from healthcare professionals and the corresponding rules regarding assessment of medical liability will and shall remain the same. This chapter attempts to analyse the impact of cognitive computing systems - regarded neither as a human-dependent medical device nor as an autonomous and trustworthy agent - upon medical malpractice and the development of an adequate insurance system. In particular, the chapter deals with the difficulties relating to the detection of the root cause of the misdiagnosis, the impact of the use of cognitive computer systems upon the standard of care expected from health practitioners, the interactions of the systems with the requirements regarding the patient's informed consent and the role of medical liability insurance upon patient safety and compensation. © Edward Elgar Publishing 2023.
Metadata only
Biodegradable sensor platforms
(Elsevier, 2023) Department of Mechanical Engineering; Bathaei, Mohammad Javad; Singh, Rahul; İstif, Emin; Beker, Levent; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering
Recent advances in materials chemistry and fabrication methods have led to the advent of an eco-friendly class of sensors utilizing biodegradable and sustainable materials to minimize electronic waste and hazardous by-products. Biodegradable sensors can be disintegrated and dissolved in the surrounding environment, remaining minimal trace after a prescribed functional lifetime due to their transient nature. This feature enables them to be widely used in numerous fields, ranging from medical diagnostics and point-of-care to environmental monitoring and food/agricultural analysis. The application of biodegradable materials has been extensively investigated in various sensor components, resulting in several unique features. In the first part, the overview of the recent developments in biodegradable sensor platforms will be introduced, followed by widely used biodegradable materials for building sensors. The recent progress and challenges in fabricating biodegradable sensors are reviewed in the second part. Finally, a range of applications enabled by the biodegradable sensors are represented. © 2023 Elsevier Ltd. All rights reserved.
Metadata only
Challenges with atomically dispersed supported metal catalysts: controlling performance, improving stability, and enhancing metal loading
(Elsevier, 2023) Kurtoğlu-Öztulum, Samira Fatma; Uzun, Alper; Department of Chemical and Biological Engineering; Öztulum, Samira Fatma Kurtoğlu; Uzun, Alper; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Engineering
Atomically dispersed supported metal catalysts offer opportunities of maximum utilization of expensive noble metals and provide unprecedented catalytic properties. Thus, these novel materials have received tremendous attention, especially in the last decade. Notwithstanding their advantages and such rapidly growing interest, these novel materials face various challenges, which need to be overcome to make them industrially viable. One of these challenges is the limited ability to control their catalytic properties. Changing the ligand environment, which also includes the support, varying the metal nuclearity, and the use of promoters (also including ionic liquid sheets) have shown to offer broad opportunities for tuning the catalytic performance. The other challenges are mostly related with the limited stability of the active species under reaction conditions, which also limits the metal loadings on the support surfaces. Control of electronic structure on the metal sites and the use of functional groups on support surfaces have been shown to be effective in this direction. In this chapter, some of the recent approaches aiming at overcoming these challenges related with the atomically dispersed supported metal catalysts are presented.
Metadata only
Codesign of technology-enriched place-based SSI lesson plans
(Springer Science and Business Media B.V., 2024) Tosunoğlu, Çiğdem Han; Özer, Ferah; Koç University Office of Learning and Teaching (KOLT)
One of the major challenges for teachers is the lack of experience with incorporating technology into socioscientific issues (SSI). In-service and preservice teachers may not have the required expertise and resources to make the most of these digital tools and technology. Thus, they may require assistance and additional support to effectively utilize these technologies and tools within their teaching practices, specifically with SSI. In light of these, this study aims to provide support in the form of a professional development program to preservice biology teachers and examine their experiences in developing co-designed, technology-enriched, place-based SSI lesson plans. The participants were 17 (16 female;1 male) senior preservice teachers studying in the undergraduate biology teaching program at a university located in Istanbul, Türkiye. An 11-week professional development program was designed and delivered with the content of the theoretical background of SSI and opportunities provided to experience practical implementations into classroom practices through the development of lesson plans. The preservice teachers chose two SSI contexts, namely biodiversity and water pollution, to be integrated into the lesson plans, drawing inspiration from local issues. Lesson plans and interviews were the two main data sources of the study. Results showed that preservice teachers embedded numerous digital tools in their lesson plans for various purposes, and their repertoire diversified, especially when co-designing with their peers. It was found that the co-design aspect of the study allowed them to learn from each other and increased their level of expertise in terms of incorporating digital tools. In sum, the study created a rich learning environment where they could build collaborative relationships with their peers, improve the quality of their tangible work, and increase their level of expertise with digital tools.
Metadata only
Diseases of the gallbladder
(Elsevier, 2023) Basturk, Olca; Adsay, Nazmi Volkan; School of Medicine
Gallbladder is a relatively common specimen, but a significant proportion of cases present as clinically and grossly inapparent lesions, and grossing protocols are not well established. Also, pathologists are less familiar with specific diagnostic characteristics. As a result, it may become problematic when encountered in daily practice. In the following section, clinical and pathological characteristics of its non-neoplastic and neoplastic lesions will be discussed.
Metadata only
Dual transcriptomics data and detection of host-pathogen interactions
(Elsevier, 2024) Eldem, Vahap; Çınar, Yusuf Ulaş; Çay, Selahattin Barış; Kuralay, Selim Can; Zararsız, Gökmen; Bakır, Yakup; Dikmen, Fatih; N/A; Kayalar, Özgecan; Koç University Research Center for Translational Medicine (KUTTAM); N/A; Koç University Hospital
Recent developments in high-throughput sequencing-based transcriptomics have expanded our understanding of host-pathogen interactions over the course of infection. Taking advantage of high-resolution spatiotemporal transcriptomics, we can measure simultaneously the expression profile of coding and noncoding genes in both pathogen and host without the need to physically separate their cells or RNA. Through this approach, known as “dual transcriptomics” or “RNA-Seq,” a range of immunological, metabolic, and physiological changes can be identified in both pathogen and host by in-depth analysis of interspecies gene regulatory networks. For these reasons, dual RNA-Seq has emerged as the high-throughput method of choice for elucidating the molecular mechanisms underlying host-pathogen interactions, examining the genetic characteristics of key virulence genes, assessing whole-body pathogen load, and identifying potential pathways for therapeutic targets. In this chapter, we review the most recent theoretical and experimental progress in dual RNA-Seq studies, best practices in analyzing dual RNA-Seq data, emerging applications, and ongoing challenges. This chapter provides a good starting point for researchers interested in harnessing the potential of dual RNA-Seq. © 2024 Elsevier Inc. All rights reserved.
Metadata only
Duality of language as a tool for integration versus mobility at work: utility of a polyphonic perspective
(Edward Elgar Publishing Ltd, 2023) Erbil, Cihat; Baglama, Sercan Hamza; Department of Business Administration; Özbilgin, Mustafa; Department of Business Administration; College of Administrative Sciences and Economics
N/A
Metadata only
Fundamentals of biological recognition elements
(Elsevier, 2023) Uygun, Zihni Onur; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM)
This chapter provides a general outline of biorecognition receptors and their use and development. In introduction, brief information is given about biosensors and their methods. In the second part, details are offered about biorecognition receptors used in biosensor systems as well as immobilization methods and measurement principles. In this chapter, biorecognition receptors are divided according to their structural activity: protein-based biorecognition, peptide-based biorecognition, nucleic acid–based biorecognition and whole cell–based biorecognition. Biorecognition receptors are divided based on structural activity because these molecules may be used according to their catalytic and affinity properties. The advantages and disadvantages of artificial and natural biorecognition receptors are discussed. The overall principles, types of bonding, and pros and cons of these types are reviewed in the conclusion. © 2023 Elsevier Ltd. All rights reserved.
Metadata only
Histology and genetics of cancer of the papilla, distal common bile duct, and duodenum
(Wiley, 2023) Xue, Yue; Reid, Michelle D.; N/A; Adsay, Nazmi Volkan; School of Medicine; Koç University Hospital
N/A
Metadata only
Hydrogels for 3D frameworks
(CRC Press, 2023) Department of Chemical and Biological Engineering; Karaoğlu, İsmail Can; Yalçın, Esra; Gülzar, Ayesha; Göktan, Işılay; Kızılel, Seda; Department of Chemical and Biological Engineering; ; Graduate School of Sciences and Engineering; College of Engineering;
Hydrogels are 3D polymer networks that can absorb large amounts of water, making them a promising construct for tissue engineering applications. This chapter focuses on the use of hydrogels in vascularization, ophthalmology-related diseases, and pancreatic islet transplantation. Hydrogels can support blood vessel growth, known as vascularization. This is an important aspect of tissue engineering, as the formation of new blood vessels is necessary for supplying nutrients and oxygen to the engineered tissue. In the field of ophthalmological tissue engineering, hydrogels can be used as a scaffold to support the growth of limbal stem cells to repair or replace damaged corneal tissue. They can help regenerate the cornea. In addition, hydrogels can be used in islet transplantation, which is a promising approach for treating diabetes. In this context, hydrogels can create a protective environment for the transplanted islets, helping them to survive and function properly in the body. By limiting the immune response, hydrogels can help to prevent the body from rejecting the engineered tissue, improving the chances of success for transplantation. In conclusion, hydrogels are promising materials for tissue engineering, particularly in ophthalmological diseases, islet transplantation, and vascularization. By providing a supportive environment for the growth of cells and tissues, hydrogels can help improve the success of these therapies, offering new hope for patients with various conditions. © 2024 selection and editorial matter, Ram K. Gupta and Anuj Kumar;individual chapters, the contributors.
Metadata only
In the name of order: (im)mobilising wage labour for the ottoman naval industry in the nineteenth century
(Univ Coll London Press - UCL Press, 2024) Sefer, Akın; Graduate School of Social Sciences and Humanities
Metadata only
Index modulation: from waveform design to reconfigurable intelligent surfaces
(Springer Science and Business Media Deutschland Gmbh, 2024) Wen, Miaowen; Department of Electrical and Electronics Engineering; Doğukan, Ali Tuğberk; Başar, Ertuğrul; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering
While the first 5G-Advanced standard is being developed step by step with certain advancements, wireless researchers have already begun exploring radical communication paradigms toward 6G wireless networks of 2030 and beyond. Within this context, index modulation (IM) technologies might provide spectrum- and energy-efficient solutions by utilizing the promising concept of indexing transmit entities. © 2024, The Author(s), under exclusive license to Springer Nature Switzerland AG.
Metadata only
Ka’b ibn Zuhayr weeps for Sultan Murad IV: Baghdad, heritage, and the Ottoman Empire in Ma’rūf al- Ruṣāfī‘s poetry
(Taylor and Francis, 2023) Department of Comparative Literature; Arslan, Ceylan Ceyhun; Department of Comparative Literature; College of Social Sciences and Humanities
This chapter situates Ma’rūf al-Ruṣāfī‘s (1875-1945) poetry within the transcultural context of the Ottoman Empire. The work first provides a brief biography of al-Ruṣāfī, with particular focus on his time in Istanbul. I also pay attention to shifting socioeconomic conditions in the Ottoman Iraq that facilitated al-Ruṣāfī‘s engagement with Ottoman Turkish writings. The chapter then gives a close reading of Süleyman Nazif’s (1870-1927) Firak-ı Irak (The Separation from Iraq, 1918) and al-Ruṣāfī‘s “Nuwāḥ Dijla” (The Lamentation of the Tigris). Both works express a strong grief about the Ottoman defeat in Baghdad during World War I; however, they capture different receptions of the Arabic poetic heritage. In Firak-ı Irak, Ka’b ibn Zuhayr (d. ca. 646/7), Ḥassān ibn Thābit (d. 674), and al-Mutanabbī (d. 965) turn into “Ottoman poets” as they weep for Sultan Murad IV (r. 1623-1640) and ultimately serve an Ottoman imperialistic discourse. Ka’b ibn Zuhayr and Ḥassān ibn Thābit even live in the same world with the Ottoman poet Nef’i (d. 1635) and speak to him in Turkish. While “Nuwāḥ Dijla” also expresses a deep sorrow for the Ottoman defeat, al-Ruṣāfī did not posit the Ottoman defeat in Baghdad as a tragic defeat for Ka’b ibn Zuhayr or al-Mutanabbī. As the chapter’s final section pays attention to representations of heritage and homeland in al-Ruṣāfī‘s works, it examines how different receptions of the Arabic poetic heritage could have contributed to the construction of diverse communal identities. Al-Ruṣāfī situated poets such as al-Mutanabbī within the Arabic heritage (al-turāth); in contrast, Süleyman Nazif saw the same poets as part of an Ottoman canon that members of the Ottoman literati upheld. Finally, I emphasize the need to flesh out the Ottoman literary heritage’s multilingual character to reassesses some key categories that critics take for granted, such as “classical Arabic literature” and “Ottoman literature.”. © 2024 selection and editorial matter, Huda J. Fakhreddine and Suzanne Pinckney Stetkevych; individual chapters, the contributors.
Metadata only
Leadership, creativity, and emotions
(Cambridge University Press, 2023) Connelly, Shane; Burak, Elif Gizem Demirağ; Graduate School of Social Sciences and Humanities
Metadata only
Mechanisms of action of radiotherapy and immunotherapy in lung cancer: implications for clinical practice
(Springer Science and Business Media Deutschland Gmbh, 2023) He, Kewen; Barsoumian, Hampartsoum B.; Sezen, Duygu; Ning, Matthew S.; Puebla-Osorio, Nahum; Schoenhals, Jonathan E.; Chen, Dawei; Leuschner, Carola; Cortez, Maria Angelica; Welsh, James W.; Selek, Uğur; School of Medicine
Radiotherapy (RT) remains an essential component of treatment for localized or advanced lung cancer that is not amenable to surgery. Immunotherapies such as checkpoint inhibitors have attracted much attention in recent years and offer promise for the treatment of several types of cancer; however, response rates and overall survival in patients with lung cancer remain low. Combining RT with immunotherapy is actively being explored as a way of boosting the effectiveness of both types of therapy. Here, we discuss various aspects and types of RT and their activity in combination with immunotherapy, including radiation dose and fractionation, modality (photons versus protons), and ultrahigh dose rate (FLASH) radiation. We then review the basic mechanisms of how RT interacts with immunotherapy in lung cancer in terms of the type of immune cell, e.g., CD8/CD4 T cells, Tregs, macrophages, natural killer (NK) cells, B cells, and dendritic cells. We also introduce promising new RT methods that involve “pulsed” dosing or high-dose plus low-dose RT, and their role in treating multiple isocenters of disease. We hope to provide some implications for better clinical practice.
Metadata only
Metal-organic frameworks in biosensors
(American Chemical Society, 2024) Uygun, Hilmiye Deniz Ertuğrul; Uygun, Zihni Onur; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM)
Biosensors have emerged as powerful analytical tools with applications wide range from healthcare diagnosis to environment detection. Metal-organic frameworks (MOFs) with biosensing platforms has garnered significant attention for their superior specialties, such as increased surface area, adaptable porosity, and excellent chemical and thermal stability. This book chapter provides an overview of the recent advances in the synthesis, characterization, and applications of MOFs for biosensors. The chapter also discusses the challenges associated with MOF integration, such as biocompatibility and compatibility with biological matrices, and presents strategies to overcome these hurdles. It delves into the importance of structural and morphological analysis, surface functionalization, and stability assessment to optimize the performance and longevity of MOF-based biosensors. Moreover, it discusses advanced techniques, spectroscopy, microscopy, and electrochemical monitoring, used for interaction of biomolecules and analyte detection. It highlights the utilization of MOF-based biosensors for the analysis and quantification of biomarkers, toxins, heavy metals, pathogens, and other analytes of interest. Overall, this book chapter serves as a comprehensive resource for researchers, engineers, and practitioners study/work on biosensors who seek to explore the potential of MOFs for advancing the sensitivity, selectivity, and versatility of biosensing platforms. It provides valuable insights into the design principles, fabrication techniques, characterization methods, and applications of MOF-based biosensors, paving the way for the development of next-generation analytical tools with enhanced performance and broad societal impact. © 2024 American Chemical Society.