WoS İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394

Browse

Now showing 1 - 20 of 41

Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data
(MDPIST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND, 2021) Yousef, Malik; Kumar, Abhishek; Bakir-Gungor, Burcu; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Bakir-Gungor, Burcu
In the last two decades, there have been massive advancements in high throughput technologies, which resulted in the exponential growth of public repositories of gene expression datasets for various phenotypes. It is possible to unravel biomarkers by comparing the gene expression levels under different conditions, such as disease vs. control, treated vs. not treated, drug A vs. drug B, etc. This problem refers to a well-studied problem in the machine learning domain, i.e., the feature selection problem. In biological data analysis, most of the computational feature selection methodologies were taken from other fields, without considering the nature of the biological data. Thus, integrative approaches that utilize the biological knowledge while performing feature selection are necessary for this kind of data. The main idea behind the integrative gene selection process is to generate a ranked list of genes considering both the statistical metrics that are applied to the gene expression data, and the biological background information which is provided as external datasets. One of the main goals of this review is to explore the existing methods that integrate different types of information in order to improve the identification of the biomolecular signatures of diseases and the discovery of new potential targets for treatment. These integrative approaches are expected to aid the prediction, diagnosis, and treatment of diseases, as well as to enlighten us on disease state dynamics, mechanisms of their onset and progression. The integration of various types of biological information will necessitate the development of novel techniques for integration and data analysis. Another aim of this review is to boost the bioinformatics community to develop new approaches for searching and determining significant groups/clusters of features based on one or more biological grouping functions.
Association Rules on Traffic Accident: Case Of Ankara
(EGE UNIV, FAC ECONOMICS & ADMIN SCIENCESDEPT BUSINESS ADMIN, BORNOVA, 35100, TURKEY, 2016) Soylemez, Ismet; Dogan, Ahmet; Ozcan, Ugur; AGÜ, Mühendislik Fakültesi, Endüstri Mühendisliği Bölümü; Soylemez, Ismet
In this study, association rules analysis of the data mining techniques are used for data of traffic accidents in 2010 and some rules are obtained. With this rules, what is the possibility of accident which resulted anybody injured for "different weather conditions (snowy, rainy etc.)", "where the accidents occurred (street, road etc.)" and "way situations (separated road or not)". Different algorithms are used to analyze the association rules. Apriori algorithm is selected for this study and SPSS Clementine 12.0 is used for this algorithm. Firstly, frequency of items are found. Then, items are grouped. In this study, data preprocessing is done and missing values are filled or rejected. In the second phase, outliers are rejected and data type is converted type of 1-0 (binary). In the third phase, Apriori algorithm is applied and results are evaluated.
Blockchain for genomics and healthcare: a literature review, current status, classification and open issues
(PEERJ INC341-345 OLD ST, THIRD FLR, LONDON EC1V 9LL, ENGLAND, 2021) Dedeturk, Beyhan Adanur; Soran, Ahmet; Bakir Gungor, Burcu; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Dedeturk, Beyhan Adanur; Soran, Ahmet; Bakir Gungor, Burcu
The tremendous boost in the next generation sequencing technologies and in the "omics"technologies resulted in the generation of hundreds of gigabytes of data per day. Nowadays, via integrating -omics data with other data types, such as imaging and electronic health record (EHR) data, panomics studies attempt to identify novel and potentially actionable biomarkers for personalized medicine applications. In this respect, for the accurate analysis of -omics data and EHR, there is a need to establish secure and robust pipelines that take the ethical aspects into consideration, regulate privacy and ownership issues, and data sharing. These days, blockchain technology has picked up significant attention in diverse fields, including genomics, since it offers a new solution for these problems from a different perspective. Blockchain is an immutable transaction ledger, which offers secure and distributed system without a central authority. Within the system, each transaction can be expressed with cryptographically signed blocks, and the verification of transactions is performed by the users of the network. In this review, firstly, we aim to highlight the challenges of EHR and genomic data sharing. Secondly, we attempt to answer "Why"or "Why not"the blockchain technology is suitable for genomics and healthcare applications in detail. Thirdly, we elucidate the general blockchain structure based on the Ethereum, which is a more suitable technology for the genomic data sharing platforms. Fourthly, we review current blockchain-based EHR and genomic data sharing platforms, evaluate the advantages and disadvantages of these applications, and classify these applications using different metrics. Finally, we conclude by discussing the open issues and introducing our suggestion on the topic. In summary, to facilitate the diagnosis, monitoring and therapy of diseases with the effective analysis of -omics data with other available data types, through this review, we put forward the possible implications of the blockchain technology to life sciences and healthcare.
Cascade Control of Magnetic Levitation with Sliding Modes
(E D P SCIENCES, 17 AVE DU HOGGAR PARC D ACTIVITES COUTABOEUF BP 112, F-91944 CEDEX A, FRANCE, 2016) Eroglu, Yakup; Ablay, Gunyaz; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü;
The effectiveness and applicability of magnetic levitation systems need precise feedback control designs. A cascade control approach consisting of sliding mode control plus sliding mode control (SMC plus SMC) is designed to solve position control problem and to provide a high control performance and robustness to the magnetic levitation plant. It is shown that the SMC plus SMC cascade controller is able to eliminate the effects of the inductance related uncertainties of the electromagnetic coil of the plant and achieve a robust and precise position control. Experimental and numerical results are provided to validate the effectiveness and feasibility of the method.
CC2D1A AS A NOVEL CILIOPATHY GENE
(SPRINGERNATURE, CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND, 2020) Sakin, I.; Tuncel, G.; Sag, S. Ozemri; Kaplan, O. I.; Khokha, M. K.; Ergoren, M. C.; Deniz, E.; Temel, S. G.; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü
Özet bulunamamıştır
Cell Proliferation and Cytotoxicity Assays
(BENTHAM SCIENCE PUBL LTDEXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES, 2016) Adan, Aysun; Kiraz, Yagmur; Baran, Yusuf; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü; Adan, Aysun; Kiraz, Yagmur; Baran, Yusuf
Cell viability is defined as the number of healthy cells in a sample and proliferation of cells is a vital indicator for understanding the mechanisms in action of certain genes, proteins and pathways involved cell survival or death after exposing to toxic agents. Generally, methods used to determine viability are also common for the detection of cell proliferation. Cell cytotoxicity and proliferation assays are generally used for drug screening to detect whether the test molecules have effects on cell proliferation or display direct cytotoxic effects. Regardless of the type of cell-based assay being used, it is important to know how many viable cells are remaining at the end of the experiment. There are a variety of assay methods based on various cell functions such as enzyme activity, cell membrane permeability, cell adherence, ATP production, co-enzyme production, and nucleotide uptake activity. These methods could be basically classified into different categories: (I) dye exclusion methods such as trypan blue dye exclusion assay, (II) methods based on metabolic activity, (III) ATP assay, (IV) sulforhodamine B assay, (V) protease viability marker assay, (VI) clonogenic cell survival assay, (VII) DNA synthesis cell proliferation assays and (V) raman micro-spectroscopy. In order to choose the optimal viability assay, the cell type, applied culture conditions, and the specific questions being asked should be considered in detail. This particular review aims to provide an overview of common cell proliferation and cytotoxicity assays together with their own advantages and disadvantages, their methodologies, comparisons and intended purposes.
Comparison of 3D texture features and metabolic parameters obtained from 18-F FDG-PET/CT images for evaluating tumor stage and subtype in non-small cell lung cancer
(SPRINGER, 2015) Karacavus, S.; Yılmaz, Bülent; Ayyildiz, Oğuzhan; Kayaalti, O.; Tasdemir, A.; Kaya, E.; İçer, Semra; Eset, K.; Vardareli, E.; Asyali, M. H.; 0000-0002-8473-9720; 0000-0003-2954-1217; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Yılmaz, Bülent; Ayyildiz, Oğuzhan
....
Değişen Yükseköğretim Sistemini Sosyokültürel ve Mekânsal Bağlamlarda Yeniden Düşünmek
(DEOMED PUBL, ISTANBUL, GUR SOK 7-B, FIKIRTEPE 34720 KADIKOY, ISTANBUL, 00000, TURKEY, 2020) Ayten, Asim Mustafa; Gover, Ibrahim Hakan; 0000-0002-4464-6204; 0000-0002-1258-0124; AGÜ, Mimarlık Fakültesi, Mimarlık Bölümü
Education and research are vital for social development and progress. The changing sociocultural structures and new needs have resulted in some important functional changes in higher education systems with a deep impact on universities serving these needs at the highest level. Besides experiencing these functional changes, the universities today have become spaces of socialization with their social, cultural and sports facilities, replacing their traditional spatial role of offering education only. The local dynamics changing with globalization have now reshaped the global and local roles of universities, highlighting the added value they provide to the society. Sociocultural changes trigger all these functional and structural changes in universities. Therefore, sociocultural factors and their importance should not be ignored in a changing higher education system. In this study, the impact of sociocultural factors with their related spatial structures on world higher education system will be analyzed within their historical contexts, and some suggestions for future universities will be offered considering the current changes. In the first part of the study, the changes in societies and universities will be presented within the historical context. In the second part, the spatial forms and structures of universities will be discussed. In the third part, the catalytic effects of the specific sociocultural factors will be highlighted and elaborated on. Finally, some suggestions will be made for the universities of the future in the light of the current situation and the data available.
Designing and Modelling Selective Replication for Fault-tolerant HPC Applications
(IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2017) Subasi, Omer; Yalcin, Gulay; Zyulkyarov, Ferad; Unsal, Osman; Labarta, Jesus; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü;
Fail-stop errors and Silent Data Corruptions (SDCs) are the most common failure modes for High Performance Computing (HPC) applications. There are studies that address fail-stop errors and studies that address SDCs. However few studies address both types of errors together. In this paper we propose a software-based selective replication technique for HPC applications for both fail-stop errors and SDCs. Since complete replication of applications can be costly in terms of resources, we develop a runtime-based technique for selective replication. Selective replication provides an opportunity to meet HPC reliability targets while decreasing resource costs. Our technique is low-overhead, automatic and completely transparent to the user.
EEG informational code dependence on the functional state: General trends and characteristic period
(ELSEVIER, 2014) Mekler, Alexey A.; Borisenok, Sergey V.; 0000-0002-1992-628X; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Borisenok, Sergey V.
EEG signal is an important source to study the brain signalization in all its variety. The consideration of this signal as an informational process leads to the exploration of the properties of these processes, which are described in the terms of the information theory. Particularly, we can study the specifics of the information coding in EEG, such as: ‘vocabulary’ diversity (the information code), its evolution and characteristic time-scales of the latter. In order to study characteristics mentioned above, the Lempel–Ziv complexity (LZC) values were applied in our research. The EEGs we used were recorded for two states (relaxed arousal with open and closed eyes). The international electrode position system 10-20 was used. We used EEGs recorded in band range from 0.16 to 50 Hz and 50 Hz notch filter as well. For the processing, we selected artefacts-free EEG fragments.
Enhancing smart grid with microgrids: Challenges and opportunities
(PERGAMON-ELSEVIER SCIENCE LTDTHE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND, 2017) Yoldas, Yeliz; Onen, Ahmet; Muyeen, S. M.; Vasilakos, Athanasios V.; Alan, Irfan; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Yoldas, Yeliz; Onen, Ahmet; Alan, Irfan
The modern electric power systems are going through a revolutionary change because of increasing demand of electric power worldwide, developing political pressure and public awareness of reducing carbon emission, incorporating large scale renewable power penetration, and blending information and communication technologies with power system operation. These issues initiated in establishing microgrid concept which has gone through major development and changes in last decade, and recently got a boost in its growth after being blessed by smart grid technologies. The objective of this paper is to presents a detailed technical overview of microgrid and smart grid in light of present development and future trend. First, it discusses microgrid architecture and functions. Then, smart features are added to the microgrid to demonstrate the recent architecture of smart grid. Finally, existing technical challenges, communication features, policies and regulation, etc. are discussed from where the future smart grid architecture can be visualized.
Exploring CsPbX3 (X = Cl, Br, I) Perovskite Nanocrystals in Amorphous Oxide Glasses: Innovations in Fabrication and Applications
(WILEY Online Library, 2024) Samiei, Sadaf; Soheyli, Ehsan; Vighnesh, Kunnathodi; Nabiyouni, Gholamreza; Rogach, Andrey L.; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Soheyli, Ehsan
Metal halide perovskites with excellent optical and electronic properties have become a trending material in the current research. However, their limited stability under ambient conditions degrades quality and threatens their potential commercialization as optoelectronic devices. Various approaches are adopted to improve the stability of perovskite nanocrystals (PeNC) while maintaining their advantageous optical properties, particularly strong luminescence. Among different possible improvement strategies, encapsulation of PeNCs within the amorphous glass matrices of inorganic oxides has drawn widespread attention because it ensures high resistance against chemical corrosion and high temperature, thus enhancing their chemical, thermal, and mechanical stability with improved light-emission characteristics. In this article, two types of materials, namely all-inorganic metal halide PeNCs and amorphous oxide glasses are briefly introduced, and then the methods are reviewed to fabricate and improve the quality of PeNC@glass composites. These methods are classified into three universal categories: compositional modification, structural modification, and dual encapsulation. In the final part of this review paper, examples of applications of PeNCs@glass composites in light-emitting devices and displays, data storage and anti-counterfeiting, lasing, photodetectors and X-ray detectors, photocatalysis, optical filters, solar concentrators, and batteries are provided.
Exploring the relationship among CO2 emissions, real GDP, energy consumption and tourism in the EU and candidate countries: Evidence from panel models robust to heterogeneity and cross-sectional dependence
(PERGAMON-ELSEVIER SCIENCE LTDTHE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND, 2017) Dogan, Eyup; Aslan, Alper; 0000-0003-1408-0921; 0000-0003-0476-5177; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü
A major criticism to the existing energy-growth-environment literature, we notice, is the selection of methodology. Panel estimation techniques that fail to consider both heterogeneity and cross-sectional dependence across countries may cause forecasting errors. The other concern related to the literature is that only a small number of studies analyze the influence of tourism on CO2 emissions even though tourism sector has potential for affecting the environment. To fulfill the mentioned gaps in the literature, this study analyzes the relationship among carbon emissions, real income, energy consumption and tourism for a panel of the EU and candidate countries over the period 1995-2011 by using heterogeneous panel estimation techniques with cross-sectional dependence. Results from the CADF and the CIPS panel unit root tests show that the analyzed variables become stationary at their first-differences. The LM bootstrap panel cointegration test indicates the presence of a long run relationship among the analyzed variables. Results from the OLS with fixed effects, the FMOLS, the DOLS and the group-mean estimator reveal that energy consumption contributes to the level of emissions while real income and tourism mitigate CO2 emissions. The Emirmahmutoglu-Kose panel Granger causality test suggests that there is one-way causality running from tourism to carbon emissions, and two-way causality between CO2 emissions and energy consumption, and between real income and CO2 emissions. Policy implications are further discussed.
Flow cytometry: basic principles and applications
(TAYLOR & FRANCIS LTD2-4 PARK SQUARE, MILTON PARK, ABINGDON OR14 4RN, OXON, ENGLAND, 2017) Adan, Aysun; Alizada, Gunel; Kiraz, Yagmur; Baran, Yusuf; Nalbant, Ayten; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü
Flow cytometry is a sophisticated instrument measuring multiple physical characteristics of a single cell such as size and granularity simultaneously as the cell flows in suspension through a measuring device. Its working depends on the light scattering features of the cells under investigation, which may be derived from dyes or monoclonal antibodies targeting either extracellular molecules located on the surface or intracellular molecules inside the cell. This approach makes flow cytometry a powerful tool for detailed analysis of complex populations in a short period of time. This review covers the general principles and selected applications of flow cytometry such as immunophenotyping of peripheral blood cells, analysis of apoptosis and detection of cytokines. Additionally, this report provides a basic understanding of flow cytometry technology essential for all users as well as the methods used to analyze and interpret the data. Moreover, recent progresses in flow cytometry have been discussed in order to give an opinion about the future importance of this technology.
Human-oriented approaches for assistive and rehabilitation robotics - Engineering methods, technical implementation, and treatment
(ELSEVIERRADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS, 2017) Beckerle, P.; Salvietti, G.; Unal, R.; Mastrogiovanni, F.; AGÜ, Mühendislik Fakültesi, Makine Mühendisliği Bölümü; Unal, Ramazan
Human-oriented approaches for assistive and rehabilitation robotics - Engineering methods, technical implementation, and treatment
The influence of real output, renewable and non-renewable energy, trade and financial development on carbon emissions in the top renewable energy countries
(PERGAMON-ELSEVIER SCIENCE LTDTHE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND, 2016) Dogan, Eyup; Seker, Fahri; 0000-0003-0476-5177; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü; Dogan, Eyup
Due to tremendous increase in the level of carbon dioxide (CO2) emissions in the last several decades, a number of studies in the energy-growth-environment literature have attempted to identify the determinants of CO2 emissions. A major criticism related to the existing studies, we realize, is the selection of panel estimation techniques. Almost all studies use panel methods that ignore the issue of cross-sectional dependence even though countries in the panel are most likely heterogeneous and cross-sectionally dependent In addition, the majority of existing studies use aggregate energy consumption, and thus fail to identify the impacts of energy consumption by sources on the environment In order to fulfill the mentioned gaps in the literature, this empirical study analyzes the influence of the real income, renewable energy consumption, non-renewable energy consumption, trade openness and financial development on CO2 emissions in the EKC model for the top countries listed in the Renewable Energy Country Attractiveness Index by employing heterogeneous panel estimation techniques with cross-section dependence. We find that the analyzed variables become stationary at their first-differences by using the CADF and the CIPS unit root tests, and the analyzed variables are cointegrated by employing the LM bootstrap cointegration test By using the FMOLS and the DOLS, we also find that increases in renewable energy consumption, trade openness and financial development decrease carbon emissions while increases in non-renewable energy consumption contribute to the level of emissions, and the EKC hypothesis is supported for the top renewable energy countries. (C) 2016 Elsevier Ltd. All rights reserved.
Major apoptotic mechanisms and genes involved in apoptosis
(SAGE PUBLICATIONS LTD1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND, 2016) Kiraz, Yagmur; Adan, Aysun; Yandim, Melis Kartal; Baran, Yusuf; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü; Baran, Yusuf; Kiraz, Yagmur
As much as the cellular viability is important for the living organisms, the elimination of unnecessary or damaged cells has the opposite necessity for the maintenance of homeostasis in tissues, organs and the whole organism. Apoptosis, a type of cell death mechanism, is controlled by the interactions between several molecules and responsible for the elimination of unwanted cells from the body. Apoptosis can be triggered by intrinsically or extrinsically through death signals from the outside of the cell. Any abnormality in apoptosis process can cause various types of diseases from cancer to auto-immune diseases. Different gene families such as caspases, inhibitor of apoptosis proteins, B cell lymphoma (Bcl)-2 family of genes, tumor necrosis factor (TNF) receptor gene superfamily, or p53 gene are involved and/or collaborate in the process of apoptosis. In this review, we discuss the basic features of apoptosis and have focused on the gene families playing critical roles, activation/inactivation mechanisms, upstream/downstream effectors, and signaling pathways in apoptosis on the basis of cancer studies. In addition, novel apoptotic players such as miRNAs and sphingolipid family members in various kind of cancer are discussed.
Measuring temperature change on photothermal Au nanorod and nanocage upon laser irradiation
(AMER CHEMICAL SOC, 2015) Cavusoglu, Halit; Sakalak, Huseyin; Buyukbekar, Burak Zafer; Demirel, Gokhan; Citir, Murat; Yavuz, Mustafa Selman; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü; Citir, Murat
....
Mixture of Learners for Cancer Stem Cell Detection Using CD13 and H&E Stained Images
(SPIE-INT SOC OPTICAL ENGINEERING, 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA, 2016) Oguz, Oguzhan; Akbas, Cem Emre; Mallah, Maen; Tasdemir, Kasim; Guzelcan, Ece Akhan; Muenzenmayer, Christian; Wittenberg, Thomas; Uner, Aysegul; Cetin, A. Enis; Atalay, Rengul Cetin; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü;
In this article, algorithms for cancer stem cell (CSC) detection in liver cancer tissue images are developed. Conventionally, a pathologist examines of cancer cell morphologies under microscope. Computer aided diagnosis systems (CAD) aims to help pathologists in this tedious and repetitive work. The first algorithm locates CSCs in CD13 stained liver tissue images. The method has also an online learning algorithm to improve the accuracy of detection. The second family of algorithms classify the cancer tissues stained with H&E which is clinically routine and cost effective than immunohistochemistry (IHC) procedure. The algorithms utilize 1D-SIFT and eigen-analysis based feature sets as descriptors. Normal and cancerous tissues can be classified with 92.1% accuracy in H&E stained images. Classification accuracy of low and high-grade cancerous tissue images is 70.4%. Therefore, this study paves the way for diagnosing the cancerous tissue and grading the level of it using HSLE stained microscopic tissue images.
Mobile Sensor Networks: Theory, Control, Communication, and Computation Issues
(HINDAWI PUBLISHING CORPORATION, 410 PARK AVENUE, 15TH FLOOR, #287 PMB, NEW YORK, NY 10022 USA, 2013) Gungor, V. Cagri; Gulez, Kayhan; Kawabata, Kuniaki; Tas, Nazif Cihan; Tuna, Gurkan; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü;
[Özet Yok]

Browse

Browsing WoS İndeksli Yayınlar Koleksiyonu by Publication Category "Diğer"