Fen Edebiyat Fakültesi / Faculty of Letters and Sciences
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Browsing Fen Edebiyat Fakültesi / Faculty of Letters and Sciences by Type "Book chapter"
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Publication Aging-related diseases and autophagy(2016) Çoker Gürkan , Ajda; Palavan Unsal, Narcin; ARISAN, ELİF DAMLA; YERLİKAYA, PINAR OBAKANAutophagy is fundamental, evolutionary conserved physiological process at molecular level which targets long-lived cytosolic proteins and organelles to be recycled through lysosomal degradation. Diminished autophagic activity caused cellular stress in many organisms following aging, and inhibition of autophagy in model organisms causes degenerative changes and pathologic diseases observed with high incidence ratio generally in older ages. Consequently the delayed senescence or increased longevity in model organisms often stimulate autophagy, and autophagy inhibition compromises anti-aging effects. The cytoprotective function of autophagy is presented in various human diseases such as lung, liver, cardiovascular diseases, neurodegeneration, myopathies, cancer, stroke, infections and metabolic diseases which are found associated with autophagic targets. These pathologies are defined with their age-dependent characteristics, is not fully understood that how autophagy network regulates metabolism and may cause diseases in age-related manner. In this book chapter, we are going to discuss the autophagy and aging relationship in three different parts. In the first section autophagy and aging relationship is going to be presented through explaining responsible signalling network. The autophagy and age-related neurological disorders, genetic basis of age-dependent diseases and the functional role of autophagy is going to be discussed in the second and third part of the chapter.Publication Biotic Stress-Tolerant Plants Through Small Rna Technology(Elsevier, 2020) ÇELİK, ÖZGE; MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMENWith an increasing population around the world, the rapid loss of agricultural fields shows us the urgent importance of finding solutions to develop agricultural productivity. Besides industrialization, several effectors such as abiotic and biotic factors cause losses in crop productivity. Biotic factors threaten production and transportation of products worldwide. Bacteria, fungi, viruses, and oomycetes cause losses both pre- and postharvest. It is crucial to improve biotic stress-tolerant plants to overcome reduction in plant productivity. For many years, researchers focused on understanding plant defense mechanisms. Anatomical, physiological, and molecular adaptive mechanisms were investigated for several plant species. Besides the innate immunity mechanisms, including cross-talk, among the phytohormones to manage appropriate defense mechanisms against pathogens, new generation strategies in crop improvements are widely used in plant biotechnology. Although conventional breeding has importance in breeding new varieties, new technologies increase the possibility of success. Recently, new combinations of technologies have been proven effective to develop new cultivars. Small RNA technology is one of the developing crop improvement technologies relying on regulating specific genes together with their sequence identity. In this chapter, we focus on the small RNA technologies used in improvement of biotic stress-tolerant plants.Publication Blockchain based secure communication for Iot devices in smart sities(2019-04) Yetiş, R.; ŞAHİNGÖZ, ÖZGÜR KORAYIn smart city technologies we have witnessed advanced technological improvements in small computing devices, which can be connected to the Internet and named as Internet of Thing (IoT) devices, and cooperatively working complex systems. With this increased use of new technologies, the security problem is becoming more and more important because complex systems lead to unpredictable security vulnerabilities, which result in financial and private information losses. As a recently emerged technology, Blockchain was emerged as an alternative solution to security breaches of a different application environment. In contrast to the central structure used by most systems, it is preferred especially in the area of security by its distributed structure and the cryptographic hash algorithm it uses. Today, structures such as Smart Home, Smart City, Smart Environment and Smart Agriculture, which are created by using IoT are seen as active research areas with more security shortages. The reason for the security weakness in these areas arises from the hardware restriction on the IoT devices used. In the proposed system, an authorization system for IoT devices has been tried to be set up by using the distributed node structure of Blockchain system and blocks kept in these nodes. UDP (User Datagram Protocol), which uses a simple communication model without establishing a connection to the minimum protocol mechanism for communication of nodes in the system, was preferred. The communication between the nodes has been encrypted using encryption methods, thus creating a secure environment.Publication Blood Serum-Infrared Spectra-Based Chemometric Models for Auxiliary Diagnosis of Autism Spectrum Disorder(Elsevier, 2021) ILDIZ, GÜLCE ÖĞRÜÇ; Bayarı, Sevgi; Yorguner, Neşe; Fausto, RuiThis chapter focuses on the use of chemometric models developed from infrared (IR) spectroscopic data of blood serum as an auxiliary tool for autism spectrum disorder (ASD) diagnosis. In the introductory sections the fundamentals of IR spectroscopy are shortly reviewed and brief descriptions of the different chemometric methods used in the case study described in the last section of the chapter are presented. The last section deals with the application of the described strategy to the diagnosis of ASD in children and adolescents. © 2021 Elsevier Inc. All rights reserved.Publication Deep learning based classification of malaria from slide images(2019) Kalkan, Soner Can; ŞAHİNGÖZ, ÖZGÜR KORAYAs one of the most life-threatening disease in the tropical and warmer-climate countries, Malaria affects not only animals but also humans who can be infected by only a single bite from a mosquito. Although this disease is wiped out in high-income countries, as a result of traveling people, it can even emerge in all part of the world. World Health Organization announced that more than 400,000 people are expected to die due to this illness. However, it is a curable and preventable disease, if early detection is possible. Traditionally, Pathologists diagnosed this disease manually by using microscope which is a time-consuming process in our computerized world, and this model depends on the experience of the Pathologists, which is a critical problem in rural areas. Therefore, in recent years detection of Malaria using computerized image analysis which is trained using some dynamic learning mechanism has gained increasing importance. In this paper, we proposed an image processing-based Malaria detection system which is trained by deep learning. We used relatively big data for increasing the accuracy of the system, and the reached accuracy showed that the proposed system has an outstanding classification rate that can be used in real-world detection.Publication Diffused label popagation based transductive classification algorithm for Wwrd sense disambiguation(2019-07) Kocaman, G.; Gerek, A.; Altınel, B.; Ganiz, M.C.; ŞİPAL, BİLGEA major natural language processing problem, word sense disambiguation is the task of identifying the correct sense of a polysemous word based on its context. In terms of machine learning, this can be considered as a supervised classification problem. A better alternative can be the use of semi-supervised classifiers since labeled data is usually scarce yet we can access large quantities of unlabeled textual data. We propose an improvement to Label Propagation which is a well-known transductive classification algorithm for word sense disambiguation. Our approach make use of a semantic diffusion kernel. We name this new algorithm as diffused label propagation algorithm (DILP). We evaluate our proposed algorithm with experiments utilizing various sizes of training sets of disambiguated corpora. With these experiments we try to answer the following questions: 1. Does our algorithm with semantic kernel formulation yield higher classification performance than the popular kernels? 2. Under which conditions does a kernel design perform better than others? 3. What kind of regularization methods result with better performance? Our experiments demonstrate that our approach can outperform baseline in terms of accuracy in several conditions.Publication Glimmmerring Light of Transcendence(2011) Sezgin, ErkutPhenomenology differs from the traditional epistemological ontological theories in that theorizing with words are given up for elucidating the signifying phenomena in the weave of which intentionality are structured to operate with words used as means to describe ends, in which means are described as "words and descriptions", "language" as such; and ends are described as "the reality", "objects", "things", "events", "world" as such. Such way of using language in theories of subject object epistemologies is a form of expression of an intentionality the modalities of which are operationally structured with learning and operating with the rules of pictures held fast as standards, rules of criteria of the truth beliefs in identifying what is "true" and "real" in language. Failure of awareness of manifest internal connections of signifying phenomena expressive of intentionality and truth beliefs in connection with the use of pictures and rules of language manifests with its own doxa in the form of attributing or denying essential qualities as to subject object descriptions and as to their interactions, in contrast to an awareness that is capable of tracing back and forth the historical structuring of intentionality operational with pictures and rules of historical languages. The latter only clarifies manifest phenomena expressive of intentionality in internal connections operating and using signs as means and ends without presupposing or introducing entities by means of projecting pictures of language. That clarification works by elucidating the identities and differences attributed to entities in terms of the uses of pictures or signs in internal connection with the uses of other signs the rules of which are kept fast and change by the changing paradigms of cultural-conventional-historical language-games. Here transcendence amounts to the trans-historical dimension of awareness which unknots the knots of operational thinking habits with rules and pictures of historical languages; which are habits that otherwise so chain thinking with the historical intentionality of a historical epoch and systems of beliefs as not to respond and communicate anymore with the self-illuminating light of awareness as characterized by Plato's cave metaphor.Publication GMO analysis methods for food: From today to tomorrow(2017) Çakır, Özgür; Arı, Şule; MERİÇ, SİNANIn the last decades, the dynamic face of biotechnology increased the number of M plants and abled the production of more precise genetically modified organisms. Since the introduction of recently developed new breeding techniques, there has been on-going debate on food safely and on the regulation concern of new biotech crops. The presently used one-by-one approach for CMOs which has been commercialized and developed by mainly transforming the usage of a transgenic insert so far, is reorganized for legislation needs of these new organisms. Furthermore, the growing number of complexities of G MOs in the commercialization pipeline and the possibility of the presence of unauthorized CMOs in the food chain has led to a demand for new technologies and stratagies to detect CMOs. In order to provide readers with current viewpoints on this topic, this chapter focuses on the key points at present. These are developing biotech plants, analysis methods for food and feed in the light of new breeding technologies, and the unintended effects of genetic transformation. It will summarize the DNA-based polymerase chain reaction (PCR) technique, the most widely accepted GMO detection method, which is classified into screening, gene-specific, construct specific, and transgenic event-specific methods according to the level of specificity. 'ubsequently, this chapter will elaborate the envisaged evolution of the GMO crops and the challenge for the detection methods of new biotech crops.Publication Heavy Metal Stress-Responsive Phyto-miRNAs(Springer Science and Business Media B.V., 2020) ÇELİK, ÖZGE; AYAN, ALP; MERİÇ, SİNAN; ATAK, ÇİMENHeavy metal stress is a leading abiotic stress factor in the twenty-first century as a reflection of industrial developments and extensive urbanization. Plants adopt several adaptation mechanisms to cope with deleterious effects of heavy metal stress. Biosynthesis of amino acids/organic acids, phytochelatins (PCs), metallothioneins (MTs), heat-shock proteins (HSPs), metal chelators, chaperons, ABC-type transporters, and CDF family metal transporters are among the heavy metal binding or transporting mechanisms in plants. This chapter emphasizes phyto-miRNAs related to these tolerance mechanism pathways. Moreover, transcription factors which are targeted by heavy metal-related phyto-miRNAs are also summarized under the effect of various heavy metals due to their intertwined regulatory mechanisms.Publication Hydantoins and mercaptoimidazoles: Vibrational spectroscopy as a probe of structure and reactivity in different environments, from the isolated molecule to polymorphs(2019) Fausto, Rui; Brás, E.M.; Nogueira, Bernardo A.; ILDIZ, GÜLCE ÖĞRÜÇIn this chapter, we highlight the power of vibrational spectroscopy as central technique to investigate the structure and reactivity of two relevant families of nitrogen-containing heterocyclic molecules: hydantoins and mercaptoimidazoles. Infrared spectroscopy is used in connection with the matrix isolation technique to investigate the structures of the isolated molecules and their photochemistry, while both infrared and Raman spectroscopies, supplemented by thermodynamics, microscopy, and diffraction techniques, are used to investigate neat condensed phases of the compounds and transitions between these phases. The experimental studies are supported by extensive computational studies, which include several approaches for detailed analysis of the electron density.Publication The Importance of Polymers in Medicine and their FTIR and Raman Spectroscopic Investigations(IGI Global, 2023) Çelik, Sefa; AKYÜZ, SEVİM; Özel, Ayşen E.Polymers are macromolecules with a very high molecular weight that are formed as a result of one or more small molecules bonding to each other, typically by covalent bonds. The concept of macromolecules consisting of many repeating units are published in the article titled "Uber Polymerization," which was first published in 1920 by Hermann Staudinger. The idea of polymers, which have been in our lives for a long time, has thus become an important field of study. Polymers are commonly used in tissue engineering because of their properties such as biocompatibility and biodegradability. In addition, polymers have a wide range of applications in tissue regeneration, drug delivery, and wound healing. Polymers have varying structural properties based on their backbone structure, molecular weight, and crystallinity. For this cause, a great deal of study in the medicine has been based on this category of materials. This workfocuses on the importance of polymers in the medicine, 3D printed polymer composites and Fourier transform infrared, and Raman spectroscopic investigations of polymeric structures.Publication Smart home hecurity with the use of WSNs on future intelligent cities(2019-04) Dine, G.; ŞAHİNGÖZ, ÖZGÜR KORAYIn recent years, smart cities use some advanced technologies such as Cyber-Physical Systems and Internet of Things for improving the quality of human life by enabling extra security and communication abilities. In a recent survey of ICMA which is the world's leading association of professional city and county managers, ICMA emphasizes the importance of the safety and security benefits of smart cities by categorizing it as one of the five important motivating factors. Therefore, in this paper, we proposed a new security model for smart buildings and smart homes by using a hot topic research area of Cyber-Physical Systems: WSNs. With the use of this system, it is aimed to construct a smart security system by using a minimum number of sensor nodes with the increased coverage rate for smart buildings and homes.Publication The Effects Of Teachers' Attitudes On Students' Personality And Performance(Elsevier Science Bv, Po Box 211, 1000 Ae Amsterdam, Netherlands, 2011) Uluğ, Mücella; Eryılmaz, Ahu; YILDIRIM, MELİS SERAY ÖZDEN; TR142331; TR107268The emphasize of student centered educational topics is usually on the effect of teachers' attitudes on students' academical success with a lack of lifespan developmental perspective. A teacher with his teaching methods and furthermore with his attitudes and behaviours, provides his students to gain a mentally healthy personality and to have a new clear world view by leaving unforgettable traces on them. This is a prepatory study to uncover how attitudes of teachers affect the personalities and performances of students. In this sense this study will provide an emic understanding of education and the dynamics of relationship between teachers and students beyond the limited areas of classes and courses. Sample group of research consists of totally 353 students from different departments of Istanbul Kultur University and Maltepe University. By giving a questionaire the students were asked to give samples of their primary school, secondary school, high school and university teachers' positive and negative attitudes and behaviours as well as to tell how it effects their personality development and performances by giving samples. The most important findings of the research evidenced that teachers' positive attitudes have positively influence students' personality as well as their life performances. Based on these findings teachers' role in lifespan education as beyond a simple knowledge transformation is discussed. (C) 2011 Published by Elsevier Ltd. Selection and/or peer-review under responsibility of the 2nd World Conference on Psychology, Counselling and Guidance.