Izmir Institute of Technology

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Citation - Scopus: 6
The 1st workshop on model-based verification & validation: Directed acyclic graph modeling of security policies for firewall testing
(2009) Tuglular, T.; Kaya, Ö.; Müftüoǧlu, C.A.; Belli, F.; Tuğlular, Tuğkan; Bilgisayar Mühendisliği Bölümü
Currently network security of institutions highly depend on firewalls, which are used to separate untrusted network from trusted one by enforcing security policies. Security policies used in firewalls are ordered set of rules where each rule is represented as a predicate and an action. This paper proposes modeling of firewall rules via directed acyclic graphs (DAG), from which test cases can be automatically generated for firewall testing. The approach proposed follows test case generation algorithm developed for event sequence graphs. Under a local area network setup with the aid of a specifically developed software for this purpose, generated test cases are converted to network test packets, test packets are sent to the firewall under test (FUT), and sent packets are compared with passed packets to determine test result. © 2009 IEEE.
Citation - WoS: 15
Citation - Scopus: 17
Achieving query performance in the cloud via a cost-effective data replication strategy
(Springer, 2021) Tos, Uras; Mokadem, Riad; Hameurlain, Abdelkader; Ayav, Tolga; Ayav, Tolga; Bilgisayar Mühendisliği Bölümü
Meeting performance expectations of tenants without sacrificing economic benefit is a tough challenge for cloud providers. We propose a data replication strategy to simultaneously satisfy both the performance and provider profit. Response time of database queries is estimated with the consideration of parallel execution. If the estimated response time is not acceptable, bottlenecks are identified in the query plan. Data replication is realized to resolve the bottlenecks. Data placement is heuristically performed in a way to satisfy query response times at a minimal cost for the provider. We demonstrate the validity of our strategy in a performance evaluation study.
Citation - Scopus: 19
Advanced Sensor and Detection Materials
(Wiley Blackwell, 2014) Tiwari A.; Demir, M.M.
Presents a comprehensive and interdisciplinary review of the major cutting-edge technology research areas-especially those on new materials and methods as well as advanced structures and properties-for various sensor and detection devices. The development of sensors and detectors at macroscopic or nanometric scale is the driving force stimulating research in sensing materials and technology for accurate detection in solid, liquid, or gas phases; contact or non-contact configurations; or multiple sensing. The emphasis on reduced-scale detection techniques requires the use of new materials and methods. These techniques offer appealing perspectives given by spin crossover organic, inorganic, and composite materials that could be unique for sensor fabrication. The influence of the length, composition, and conformation structure of materials on their properties, and the possibility of adjusting sensing properties by doping or adding the side-groups, are indicative of the starting point of multifarious sensing. The role of intermolecular interactions, polymer and ordered phase formation, as well as behavior under pressure and magnetic and electric fields are also important facts for processing ultra-sensing materials. The 15 chapters written by senior researchers in Advanced Sensor and Detection Materials cover all these subjects and key features under three foci: 1) principals and perspectives, 2) new materials and methods, and 3) advanced structures and properties for various sensor devices. © 2014 Scrivener Publishing LLC. All rights reserved.
Citation - WoS: 41
Citation - Scopus: 45
Advances in Electrospun Fiber-Based Flexible Nanogenerators for Wearable Applications
(Wiley-v C H verlag Gmbh, 2021) Arica, Tugce A.; Isik, Tugba; Guner, Tugrul; Horzum, Nesrin; Demir, Mustafa M.; Demir, Mustafa
In today's digital age, the need and interest in personal and portable electronics shows a dramatic growth trend in daily life parallel to the developments in sensors technologies and the internet. Wearable electronics that can be attached to clothing, accessories, and the human body are one of the most promising subfields. The energy requirement for the devices considering the reduction in device sizes and the necessity of being flexible and light, the existing batteries are insufficient and nanogenerators have been recognized a suitable energy source in the last decade. The mechanical energy created by the daily activities of the human body is an accessible and natural energy source for nanogenerators. Fiber-structured functional materials contribute to the increase in energy efficiency due to their effective surface to volume ratio while providing the necessary compatibility and comfort for the movements in daily life with its flexibility and lightness. Among the potential solutions, electrospinning stands out as a promising technique that can meet these requirements, allowing for simple, versatile, and continuous fabrication. Herein, wearable electronics and their future potential, electrospinning, and its place in energy applications are overviewed. Moreover, piezoelectric, triboelectric, and hybrid nanogenerators fabricated or associated with electrospun fibrous materials are presented.
Citation - Scopus: 11
The amphibian and reptile species of Bozdaǧ (Ödemiş)
(2004) Kumlutaş,Y.; Özdemir,A.; Ilgaz,Ç.; Tosunoǧlu,M.
The herpetofauna of Bozdaǧ in western Anatolia was investigated. In the study area, 152 samples belonging to 22 species from 14 amphibian and reptile families were described. One of these species is an urodelan, 5 are anurans, 1 is a tortoise, 10 are lizards and 5 are snakes. A specimen of Eumeces schneideri was found at Bozdaǧ for the first time. © TÜBİTAK.
Citation - WoS: 5
Analysis of adhesively bonded joints of laser surface treated composite primary components of aircraft structures
(Elsevier Sci Ltd, 2023) Nuhoglu, Kaan; Aktas, Engin; Tanoglu, Metin; Martin, Seckin; Iplikci, Hande; Barisik, Murat; Iris, Mehmet Erdem; Tanoğlu, Metin
The performance of the adhesively bonded aerospace structures highly depends on the adhesion strength between the adhesive and adherents, which is affected by, in particular, the condition of the bonding surface. Among the various surface treatment methods, as state of the art, laser surface treatment is a suitable option for the CFRP composite structures to enhance the adhesion performance, adjusting the roughness and surface free energy with relatively minimizing the damage to the fibers. The aim of this study is the validation and evaluation of the adhesive bonding behavior of the laser surface-treated CFRP composite structures, using the finite element technique to perform a conservative prediction of the failure load and damage growth. Such objectives were achieved by executing both experimental and numerical analyses of the secondary bonded CFRP parts using a structural adhesive. In this regard, to complement physical experiments by means of numerical simulation, macro-scale 3D FEA of adhesively bonded Single Lap Joint and Skin-Spar Joint specimens has been developed employing the Cohesive Zone Model (CZM) technique in order to simulate bonding behavior in composite structures especially skin-spar relation in the aircraft wing-box.
Citation - WoS: 8
An answer to colon cancer treatment by mesenchymal stem cell originated from adipose tissue
(Mashhad Univ Med Sciences, 2018) Iplik, Elif Sinem; Ertugrul, Baris; Kozanoglu, Ilknur; Baran, Yusuf; Cakmakoglu, Bedia; Baran, Yusuf
Objective(s): Colon cancer is risen up with its complex mechanism that directly impacts on its treatment as well as its common prevalence. Mesenchymal stem cells (MSCs) have been considered as a therapeutic candidate for conventional disease including cancer. In this research, we have focused on apoptotic effects of adipose tissue-derived MSCs in colon cancer. Materials and Methods: MSCs were obtained from adipose tissue and characterized by Flowcytometer using suitable antibodies. MSCs, HT-29, HCT-116, RKO and healthy cell line MRC5 were cultured by different seeding procedure. After cell viability assay, changes in caspase 3 enzyme activity and the level of phosphatidylserine were measured. Results: For cell viability assay, a 48 hr incubation period was chosen to seed all cells together. There was a 1.36-fold decrease in caspase 3 enzyme activity by co-treatment of RKO and MSCs in addition to 2.02-fold decrease in HT-29 and MSCs co-treatment, and 1.103-fold increase in HCT-116 and MSCs. The results demonstrated that HCT-116 led to the highest rate of apoptotic cell death (7.5%) compared with other cells. Conclusion: We suggest that MSCs might remain a new treatment option for cancer by its differentiation and repair capacity.
Citation - WoS: 18
Apoptotic Effects of Resveratrol, a Grape Polyphenol, on Imatinib-Sensitive and Resistant K562 Chronic Myeloid Leukemia Cells
(int inst Anticancer Research, 2012) Can, Geylani; Cakir, Zeynep; Kartal, Melts; Gunduz, Ufuk; Baran, Yusuf; Baran, Yusuf
Aim: To examine the antiproliferative and apoptotic effects of resveratrol on imatinib-sensitive and imatinib-resistant K562 chronic myeloid leukemia cells. Materials and Methods: Antiproliferative effects of resveratrol were determined by the 3-Bis[2-methoxy-4-nitro-5-sulphophenyl]-2H-tetrazolium-5-carboxanilide inner salt (XTT) cell proliferation assay. Apoptotic effects of resveratrol on sensitive K562 and resistant K562/IMA-3 cells were determined through changes in caspase-3 activity, loss of mitochondrial membrane potential (MMP), and apoptosis by annexin V-(FITC). Results: The concentrations of resveratrol that inhibited cell growth by 50% (IC50) were calculated as 85 and 122 mu M for K562 and K562/IMA-3 cells, respectively. There were 1.91-, 7.42- and 14.73-fold increases in loss of MMP in K562 cells treated with 10, 50, and 100 mu M resveratrol, respectively. The same concentrations of resveratrol resulted in 2.21-, 3.30- and 7.65-fold increases in loss of MMP in K562/IMA3 cells. Caspase-3 activity increased 1.04-, 2.77- and 4.8-fold in K562 and 1.02-, 1.41- and 3.46-fold in K562/IMA3 cells in response to the same concentrations of resveratrol, respectively. Apoptosis was induced in 58.7%- and 43.3% of K562 and K562/IMA-3 cells, respectively, in response to 100 mu M resveratrol. Conclusion: Taken together these results may suggest potential use of resveratrol in CML, as well as in patients with primary and/or acquired resistance to imatinib.
Citation - WoS: 0
An Architecture for Verification of Access Control Policies with Multi Agent System Ontologies
(Ieee, 2009) Tekbacak, Fatih; Tuglular, Tugkan; Dikenelli, Oguz; Tuğlular, Tuğkan; Bilgisayar Mühendisliği Bölümü
Multi-agent systems (MAS) which communicate with intra-domain and inter-domain agent platforms have access control requirements. Instead of a central mechanism, a fine-graned access control mechanism could have been applied to MAS platforms. This paper emphasizes MAS-based domain and security ontologies with XACML-based access control approach for MAS platforms. The domain dependent behaviour and access control parameters in agent ontologies could be combined within a common XACML policy documents should be consistent to enforce policies for MAS. To obtain this conditions. Agent-based access control requirements and common XACML policy documents should be consistent to enforce policies for MAS. To obtain this condition, the translation of organizational policies and platform based policies have to be considered in derail and the verified policy features have to be enforced in MAS to provide access for resources.
Citation - WoS: 1
Automatic enforcement of location aware user based network access control policies
(World Scientific and Engineering Acad and Soc, 2008) Tuglular, Tugkan; Tuğlular, Tuğkan; Bilgisayar Mühendisliği Bölümü
Multiple interconnected network segments distributed across various locations, such as corporate networks, where users or employees constantly travel among segments and require to access servers, need to have network access control mechanisms that are able to adapt to these location changes. The idea of a firewall changing or adapting its rules depending on the location of users is presented by an architecture in this paper. This architecture proposes deployment of a policy server at the management level and policy agents at the firewall level, so that policy-driven network security management is enabled by specifying location aware user based network access control policies at the network security management and enforcing them at the managed firewalls. The architecture presented in this paper utilizes user VPN connection event triggers for dynamic policy configuration and automated policy deployment to firewalls. Location aware user based network access control policies, which are management level policies, are implemented using XACML. A network level policy is usually a configuration, or policy, file local to the firewall. The policy agent incorporated into the firewall performs the mapping from management level policy to firewall policy.
Citation - WoS: 1
Citation - Scopus: 5
Automation Architecture for Bayesian Network Based Test Case Prioritization and Execution
(Ieee, 2016) Ufuktepe, Ekincan; Tuglular, Tugkan; Tuğlular, Tuğkan; Bilgisayar Mühendisliği Bölümü
An automation architecture for Bayesian Network based test case prioritization is designed for software written in Java programming language following the approach proposed by Mirarab and Tahvildari [2]. The architecture is implemented as an integration of a series of tools and called Bayesian Network based test case prioritization and execution platform. The platform is triggered by a change in the source code, then it collects necessary information to be supplied to Bayesian Network and uses Bayesian Network evaluation results to run high priority unit tests.
Citation - WoS: 0
Autophagic and Apoptotic Effects of Tyrosine Kinase Inhibitors in Myeloid Leukemia: Comparison of Three Generation
(Amer Soc Hematology, 2012) Kayabasi, Cagla; Avci, Cigir Biray; Susluer, Sunde Yilmaz; Balci, Tugce; Baran, Yusuf; Saydam, Guray; Gunduz, Cumhur; Baran, Yusuf
[No Abstract Available]
Citation - Scopus: 3
Behavior-Driven Development of Software Product Lines
(Institute of Electrical and Electronics Engineers Inc., 2021) Tuglular, T.; Coskun, D.E.; Tuğlular, Tuğkan; Bilgisayar Mühendisliği Bölümü
Software product lines (SPLs) develop families of similar software products, which share a standard set of features, and they build in variety via optional features. That means customers can select features according to their needs and come up with a product configuration. Then the SPL is expected automatically to generate and test the software product for the chosen configuration. There are various SPL solutions for the automatic generation of software products, but those SPLs lack automatic testing of the generated product. To overcome this shortcoming, the SPL should automatically compose a test suite according to the selected features, automatically execute the test suite on the product, and automatically generate a test report delivered to the customer with the product. This paper proposes such an approach through behavior driven development. The proposed method is evaluated with a smart home SPL. © 2021 IEEE.
Citation - WoS: 8
Bioactive sphingolipids in docetaxel-induced apoptosis in human prostate cancer cells
(Elsevier France-editions Scientifiques Medicales Elsevier, 2012) Bassoy, Esen Yonca; Baran, Yusuf; Baran, Yusuf
In this study, we examined the possible roles of ceramide/sphingosine-1-phosphate and ceramide/glucosyleceramide signaling in docetaxel-induced apoptosis by examining expression levels of the glucosyleceramide synthase and sphingosine kinase-1 and ceramide synthase gene family. As confirmed by isobologram analysis, docetaxel in combination with agents that increase intracellular ceramide levels increased the cytotoxic and apoptotic effects of docetaxel synergistically. More importantly, RT-PCR results revealed that expression levels of glucosyleceramide synthase and sphingosine kinase-1 were downregulated and ceramide synthase genes were upregulated in response to docetaxel. This study identifies mechanisms underlying the involvement of ceramide metabolizing genes in docetaxel-induced apoptosis in prostate cancer cells. (c) 2012 Elsevier Masson SAS. All rights reserved.
Citation - WoS: 5
Bioactive Sphingolipids in Response to Chemotherapy: A Scope on Leukemias
(Bentham Science Publ Ltd, 2011) Ekiz, Huseyin Atakan; Baran, Yusuf; Baran, Yusuf
Sphingolipids are major constituents of the cells with emerging roles in the regulation of cellular processes. Deregulation of sphingolipid metabolism is reflected as various pathophysiological conditions including metabolic disorders and several forms of cancer. Ceramides, ceramide-1-phosphate (C1P), glucosyl ceramide (GluCer), sphingosine and sphingosine-1-phosphate (S1P) are among the bioactive sphingolipid species that have important roles in the regulation of cell death, survival and chemotherapeutic resistance. Some of those species are known to accumulate in the cells upon chemotherapy while some others are known to exhibit an opposite pattern. Even though the length of fatty acid chain has a deterministic effect, in general, upregulation of ceramides and sphingosine is known to induce apoptosis. However, S1P, C1P and GluCer are proliferative for cells and they are involved in the development of chemoresistance. Therefore, sphingolipid metabolism appears as a good target for the development of novel therapeutics or supportive interventions to increase the effectiveness of the chemotherapeutic drugs currently in hand. Some approaches involve manipulation of the synthesis pathways yielding the increased production of apoptotic sphingolipids while the proliferative ones are suppressed. Some others are trying to take advantage of cytotoxic sphingolipids like short chain ceramide analogs by directly delivering them to the malignant cells as a distinct chemotherapeutic intervention. Numerous studies in the literature show the feasibility of those approaches especially in acute and chronic leukemias. This review compiles the current knowledge about sphingolipids and their roles in chemotherapeutic response with the particular attention to leukemias.
Citation - WoS: 10
Citation - Scopus: 12
BODIPY-based organic color conversion layers for WLEDs
(Elsevier Sci Ltd, 2020) Yuce, Hurriyet; Guner, Tugrul; Dartar, Suay; Kaya, Beraat U.; Emrullahoglu, Mustafa; Demir, Mustafa M.; Demir, Mustafa
The usage of organic dyes in phosphor conversion layer of WLED is an attractive approach since they have high molar extinction coefficient and photostability. Various types of organic pigments have been employed for this purpose such as BODIPY, perylene diimide, Rhodamine B, pyrene, Nile red, etc. Among those, BODIPY-based organic dyes appear to be promising candidate for white light generation. In this work, for the first time, red and green emitting BODIPY-based organic molecules have been used as colour conversion layer. These molecules were associated with PMMA in DMF solution and the resulting solution was subjected to electrospinning. Colorful electrospun mats were embedded into PDMS matrix and their free-standing PDMS composite films were used as color conversion layers over blue LED to produce white light such that CRI of 95 and CCT of 4200 K was achieved. These values show that BODIPY-based organic molecules containing fiber composites are promising candidates to be used as color conversion layers for white light applications.
Citation - WoS: 3
Citation - Scopus: 9
Boolean Differentiation for Formalizing Myers' Cause-Effect Graph Testing Technique
(Ieee, 2015) Ayav, Tolga; Belli, Fevzi; Ayav, Tolga; Bilgisayar Mühendisliği Bölümü
Cause-Effect Graph Testing is a popular technique used for almost four decades. Based on Boolean algebra, this technique assists deriving test cases from a given specification informally written in a natural language. The present paper suggests Boolean differentiation for formalizing this technique. The new approach is applied to an example, borrowed from G. Myers, for demonstrating and analyzing its features. Evaluations show that the new approach outperforms Myers' approach in terms of the detected faults per test cases.
Citation - Scopus: 17
Brucellosis in pregnancy: results of multicenter ID-IRI study
(Springer Verlag, 2019) Inan,A.; Erdem,H.; Elaldi,N.; Gulsun,S.; Karahocagil,M.K.; Pekok,A.U.; Beeching,N.J.
Brucellosis in pregnant women is reported to be associated with obstetric complications (OCs), and adequate data for human brucellosis during pregnancy are largely lacking. We performed this multicenter retrospective cross-sectional study to evaluate the epidemiology, clinical course, treatment responses, and outcomes of brucellosis among pregnant women. The study period comprised a 14-year period from January 2002 to December 2015. All consecutive pregnant women diagnosed with brucellosis in 23 participating hospitals were included. Epidemiological, clinical, laboratory, therapeutic, and outcome data along with the assessment data of the neonate were collected using a standardized questionnaire. Data of 242 patients were analyzed. The OC rate was 14.0% (34/242) in the cohort. Of the 242 women, 219 (90.5%) delivered at term, 3 (1.2%) had preterm delivery, 15 (6.2%) aborted, and 5 (2.1%) had intrauterine fetal demise. Seventeen (7.0%) of the newborns were considered as low birth weight. Spontaneous abortion (6.1%) was the commonest complication. There were no maternal or neonatal deaths and pertinent sequelae or complications were not detected in the newborns. Splenomegaly (p = 0.019), nausea and/or vomiting (p < 0.001), vaginal bleeding (p < 0.001), anemia (blood hemoglobin < 11 g/dL; p < 0.001), high level of serum aspartate aminotransferase (> 41 IU/L; p = 0.025), oligohydramnios on ultrasonography (p = 0.0002), history of taking medication other than Brucella treatment during pregnancy (p = 0.027), and Brucella bacteremia (p = 0.029) were the significant factors associated with OCs. We recommend that pregnant women with OC or with fever should be investigated for brucellosis if they live in or have traveled to an endemic area. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.
Citation - WoS: 22
Caffeic acid phenethyl ester triggers apoptosis through induction of loss of mitochondrial membrane potential in CCRF-CEM cells
(Springer, 2011) Avci, Cigir Biray; Gunduz, Cumhur; Baran, Yusuf; Sahin, Fahri; Yilmaz, Sunde; Dogan, Zeynep Ozlem; Saydam, Guray; Baran, Yusuf
CAPE (caffeic acid phenethyl ester) is one of the most valuable and investigated component of propolis which is composed by honeybees. In the current study, we aimed at examining apoptotic effects of CAPE on CCRF-CEM leukemic cells and at determining the roles of mitochondrial membrane potential (MMP) in cell death. Trypan blue and XTT methods were used to evaluate the cytotoxicity. Apoptosis was examined by ELISA-based oligonucleotide and acridine orange/ethidium bromide dye techniques. Loss of mitochondrial membrane potential was evaluated using JC-1 dye by flow cytometric analysis and under fluorescent microscope. We detected the time- and dose-dependent increases in cytotoxic effect of CAPE on CCRF-CEM cells. ELISA and acridine orange/ethidium bromide results showed that apoptotic cell population increased significantly in CCRF-CEM cells exposed to increasing concentrations of CAPE. On the other hand, there was significant loss of MMP determined in response to CAPE in CCRF-CEM cells. This in vitro data by being supported with clinical data may open the way of the potential use of CAPE for the treatment of leukemia.
Citation - WoS: 350
Cell Proliferation and Cytotoxicity Assays
(Bentham Science Publ Ltd, 2016) Adan, Aysun; Kiraz, Yagmur; Baran, Yusuf; 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.

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