Izmir Institute of Technology
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Conference Object Citation Count: 6The 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 BölümüCurrently 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.Article Citation Count: 2252019 EACTS Expert Consensus on long-term mechanical circulatory support(European Association for Cardio-Thoracic Surgery, 2019) Potapov,E.V.; Antonides,C.; Crespo-Leiro,M.G.; Combes,A.; Färber,G.; Hannan,M.M.; Gustafsson,F.Long-term mechanical circulatory support (LT-MCS) is an important treatment modality for patients with severe heart failure. Different devices are available, and many - sometimes contradictory - observations regarding patient selection, surgical techniques, perioperative management and follow-up have been published. With the growing expertise in this field, the European Association for Cardio-Thoracic Surgery (EACTS) recognized a need for a structured multidisciplinary consensus about the approach to patients with LT-MCS. However, the evidence published so far is insufficient to allow for generation of meaningful guidelines complying with EACTS requirements. Instead, the EACTS presents an expert opinion in the LT-MCS field. This expert opinion addresses patient evaluation and preoperative optimization as well as management of cardiac and non-cardiac comorbidities. Further, extensive operative implantation techniques are summarized and evaluated by leading experts, depending on both patient characteristics and device selection. The faculty recognized that postoperative management is multidisciplinary and includes aspects of intensive care unit stay, rehabilitation, ambulatory care, myocardial recovery and end-of-life care and mirrored this fact in this paper. Additionally, the opinions of experts on diagnosis and management of adverse events including bleeding, cerebrovascular accidents and device malfunction are presented. In this expert consensus, the evidence for the complete management from patient selection to end-of-life care is carefully reviewed with the aim of guiding clinicians in optimizing management of patients considered for or supported by an LT-MCS device. © 2019 The Author(s).Article Citation Count: 9Achieving 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 BölümüMeeting 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.Conference Object Citation Count: 9Adaptive RTP rate control method(2011) Tos, U.; Ayav, T.; Ayav, Tolga; Bilgisayar Mühendisliği BölümüIn this paper, we present an adaptive method for maximizing network bandwidth utilization for the real-time applications. RTP protocol is chosen as the transport protocol and the network utilization is provided by increasing and decreasing the transmission rate of the RTP traffic. Our method employs a PID controller that keeps the RTP packet loss fraction at a predefined reference point. Packet loss fraction parameter is gathered from the RTCP receiver reports and fed into the PID controller that controls the transmission rate of the RTP traffic. Simulations are performed to demonstrate the effectiveness of the method under a bottleneck network configuration with background UDP traffic competing against the RTP traffic for the available bandwidth. © 2011 IEEE.Article Citation Count: 487Advanced heart failure: a position statement of the Heart Failure Association of the European Society of Cardiology(John Wiley and Sons Ltd, 2018) Crespo-Leiro,M.G.; Metra,M.; Lund,L.H.; Milicic,D.; Costanzo,M.R.; Filippatos,G.; Ruschitzka,F.This article updates the Heart Failure Association of the European Society of Cardiology (ESC) 2007 classification of advanced heart failure and describes new diagnostic and treatment options for these patients. Recognizing the patient with advanced heart failure is critical to facilitate timely referral to advanced heart failure centres. Unplanned visits for heart failure decompensation, malignant arrhythmias, co-morbidities, and the 2016 ESC guidelines criteria for the diagnosis of heart failure with preserved ejection fraction are included in this updated definition. Standard treatment is, by definition, insufficient in these patients. Inotropic therapy may be used as a bridge strategy, but it is only a palliative measure when used on its own, because of the lack of outcomes data. Major progress has occurred with short-term mechanical circulatory support devices for immediate management of cardiogenic shock and long-term mechanical circulatory support for either a bridge to transplantation or as destination therapy. Heart transplantation remains the treatment of choice for patients without contraindications. Some patients will not be candidates for advanced heart failure therapies. For these patients, who are often elderly with multiple co-morbidities, management of advanced heart failure to reduce symptoms and improve quality of life should be emphasized. Robust evidence from prospective studies is lacking for most therapies for advanced heart failure. There is an urgent need to develop evidence-based treatment algorithms to prolong life when possible and in accordance with patient preferences, increase life quality, and reduce the burden of hospitalization in this vulnerable patient population. © 2018 The Authors. European Journal of Heart Failure © 2018 European Society of CardiologyBook Citation Count: 15Advanced 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.Review Citation Count: 24Advances 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, MustafaIn 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.Book Part Citation Count: 4Advances in Model-Based Testing of Graphical User Interfaces(Elsevier Academic Press inc, 2017) Belli, Fevzi; Beyazit, Mutlu; Budnik, Christof J.; Tuglular, Tugkan; Tuğlular, Tuğkan; Bilgisayar Mühendisliği BölümüGraphical user interfaces (GUIs) enable comfortable interactions of the computer-based systems with their environment. Large systems usually require complex GUIs, which are commonly fault prone and thus are to be carefully designed, implemented, and tested. As a thorough testing is not feasible, techniques are favored to test relevant features of the system under test that will be specifically modeled. This chapter summarizes, reviews, and exemplifies conventional and novel techniques for model-based GUI testing.Article Citation Count: 15Aggregation of fillers blended into random elastomeric networks: Theory and comparison with experiments(2006) Demir M.M.; Menceloglu Y.Z.; Erman, B.A theoretical model describing aggregation of filler particles in amorphous elastomers is proposed. The model is based on a counting technique originally used in genome analysis to characterize the size and distribution of overlapping segments randomly placed on a DNA molecule. In the present model, the particles are first assumed to aggregate randomly upon mixing into the elastomer and then-sizes are calculated. The sizes and distributions of aggregates are also studied in the presence of attractive interparticle forces. Results of the proposed model are compared with experimental data on silica-filled end-linked poly(dimethyl-siloxane) networks. Comparison of the theory and experiment shows that the random aggregation assumption where no attractive forces exist between the particles is not valid and a significant attraction between the silica particles is needed in the theory to justify the experimental data obtained using atomic force microscopy. For filler content below 1.45 vol.-%, the model agrees, qualitatively, with experiment and shows the increase in cluster size with increasing amount of filler. It also explains the increase in the dispersion of aggregate sizes with increasing amount of filler. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA.Article Citation Count: 48Amidoxime functionalized Polymers of Intrinsic Microporosity (PIM-1) electrospun ultrafine fibers for rapid removal of uranyl ions from water(Elsevier Science Bv, 2019) Satilmis, Bekir; Isik, Tugba; Demir, Mustafa M.; Uyar, Tamer; Demir, MustafaThe Polymers of Intrinsic Microporosity (PIM-1) is considered as one of the most promising polymer candidates for adsorption applications owing to its high surface area and the ability to tailor the functionality for the targeted species. This study reports a facile method for the preparation of amidoxime functionalized PIM-1 fibrous membrane (AF-PIM-FM) by electrospinning technique and its practical use for the extraction of U(VI) ions from aqueous systems via column sorption under continuous flow. Fibrous membrane form of amidoxime functionalized PIM-1 (AF-PIM-FM) was prepared by electrospinning method owing to its excellent processability in dimethylformamide. Bead-free and uniform fibers were obtained as confirmed by SEM imaging and average fiber diameter was 1.69 +/- 0.34 mu m for AF-PIM-FM. In addition, electrospun PIM-1 fibrous membrane (PIM-FM) was prepared as a control group. Structural and thermal characterization of powder and membrane forms of the materials were performed using FT-IR, H-1 NMR, XPS, Elemental analyses, TGA, and DSC. The porosity of the samples was measured by N-2 sorption isotherms confirming amidoxime PIM-1 still maintain their porosity after functionalization. Amidoxime functionality along with membrane structure makes AF-PIM-FM a promising material for uranyl adsorption. First, a comparison between powder and membrane form of amidoxime functionalized PIM-1 was investigated using batch adsorption process. Although membrane form has shown slightly lower adsorption performance in the batch adsorption process, the advantage of using the membrane in column adsorption processes makes membrane form more feasible for real applications. In addition, amidoxime modification enhanced the uranium adsorption ability of PIM-FM up to 20 times. The effect of initial concentration and pH were investigated along with regeneration of the adsorbents. AF-PIM-FM was successfully used for five adsorption-desorption cycles without having any damage on the fibrous structure.Article Citation Count: 11The 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.Article Citation Count: 0AMWC 2013: Advanced Materials World Congress (izmir, Turkey, September 16-19, 2013)(2013) Demir, M.M.[No abstract available]Article Citation Count: 0Analysis 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, MetinThe 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.Article Citation Count: 12Anomalous transmittance of polystyrene-ceria nanocomposites at high particle loadings(Royal Soc Chemistry, 2013) Parlak, Onur; Demir, Mustafa M.; Demir, MustafaOptical nanocomposites based on transparent polymers and nanosized pigment particles have usually been produced at low particle concentrations due to the undesirable optical scattering of the pigment particles. However, the contribution of the particles to many physical properties is realized at high concentrations. In this study, nanocomposites were prepared with transparent polystyrene (PS) and organophilic CeO2 nanoparticles using various compositions in which the particle content was up to 95 wt%. The particles, capped by 3-methacryloxypropyltrimethoxysilane (MPS), were dispersed into PS and the transmittance of the spin-coated composite films was examined over the UV-visible region. When the particle concentration was <20 wt%, the transmittance of the films showed a first-order exponential decay as the Rayleigh scattering theory proposes. However, a positive deviation was observed from the decay function for higher particle contents. The improvement in transmittance may be a consequence of interference in the multiple scattering of light by the quasi-ordered internal microstructure that gradually develops as the particle concentration increases.Article Citation Count: 8An 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, YusufObjective(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.Article Citation Count: 52Anti-proliferative, apoptotic and signal transduction effects of hesperidin in non-small cell lung cancer cells(Springer, 2015) Cincin, Zeynep Birsu; Unlu, Miray; Kiran, Bayram; Bireller, Elif Sinem; Baran, Yusuf; Cakmakoglu, Bedia; Baran, YusufHesperidin, a glycoside flavonoid, is thought to act as an anti-cancer agent, since it has been found to exhibit both pro-apoptotic and anti-proliferative effects in several cancer cell types. The mechanisms underlying hesperidin-induced growth arrest and apoptosis are, however, not well understood. Here, we aimed to investigate the anti-proliferative and apoptotic effects of hesperidin on non-small cell lung cancer (NSCLC) cells and to investigate the mechanisms involved. The anti-proliferative and apoptotic effects of hesperidin on two NSCLC-derived cell lines, A549 and NCI-H358, were determined using a WST-1 colorimetric assay, a LDH cytotoxicity assay, a Cell Death Detection assay, an AnnexinV-FITC assay, a caspase-3 assay and a JC-1 assay, respectively, all in a time- and dose-dependent manner. As a control, non-cancerous MRC-5 lung fibroblasts were included. Changes in whole genome gene expression profiles were assessed using an Illumina Human HT-12v4 beadchip microarray platform, and subsequent data analyses were performed using an Illumina Genome Studio and Ingenuity Pathway Analyser (IPA). We found that after hesperidin treatment, A549 and NCI-H358 cells exhibited decreasing cell proliferation and increasing caspase-3 and other apoptosis-related activities, in conjunction with decreasing mitochondrial membrane potential activities, in a dose- and time-dependent manner. Through a GO analysis, by which changes in gene expression profiles were compared, we found that the FGF and NF-kappa B signal transduction pathways were most significantly affected in the hesperidin treated NCI-H358 and A549 NSCLC cells. Our results indicate that hesperidin elicits an in vitro growth inhibitory effect on NSCLC cells by modulating immune response-related pathways that affect apoptosis. When confirmed in vivo, hesperidin may serve as a novel anti-proliferative agent for non-small cell lung cancer.Article Citation Count: 17Apoptotic effects of non-edible parts of Punica granatum on human multiple myeloma cells(Sage Publications Ltd, 2016) Kiraz, Yagmur; Neergheen-Bhujun, Vidushi S.; Rummun, Nawraj; Baran, Yusuf; Baran, YusufMultiple myeloma is of great concern since existing therapies are unable to cure this clinical condition. Alternative therapeutic approaches are mandatory, and the use of plant extracts is considered interesting. Punica granatum and its derived products were suggested as potential anticancer agents due to the presence of bioactive compounds. Thus, polypenolic-rich extracts of the non-edible parts of P. granatum were investigated for their antiproliferative and apoptotic effects on U266 multiple myeloma cells. We demonstrated that there were dose-dependent decreases in the proliferation of U266 cells in response to P. granatum extracts. Also, exposure to the extracts triggered apoptosis with significant increases in loss of mitochondrial membrane potential in U266 cells exposed to the leaves and stem extracts, while the flower extract resulted in slight increases in loss of MMP. These results were confirmed by Annexin-V analysis. These results documented the cytotoxic and apoptotic effects of P. granatum extracts on human U266 multiple myeloma cells via disruption of mitochondrial membrane potential and increasing cell cycle arrest. The data suggest that the extracts can be envisaged in cancer chemoprevention and call for further exploration into the potential application of these plant parts.Article Citation Count: 20Apoptotic effects of non-edible parts of Punica granatum on human multiple myeloma cells(Springer Science and Business Media B.V., 2016) Baran, Yusuf; Neergheen-Bhujun,V.S.; Rummun,N.; Baran,Y.Multiple myeloma is of great concern since existing therapies are unable to cure this clinical condition. Alternative therapeutic approaches are mandatory, and the use of plant extracts is considered interesting. Punica granatum and its derived products were suggested as potential anticancer agents due to the presence of bioactive compounds. Thus, polypenolic-rich extracts of the non-edible parts of P. granatum were investigated for their antiproliferative and apoptotic effects on U266 multiple myeloma cells. We demonstrated that there were dose-dependent decreases in the proliferation of U266 cells in response to P. granatum extracts. Also, exposure to the extracts triggered apoptosis with significant increases in loss of mitochondrial membrane potential in U266 cells exposed to the leaves and stem extracts, while the flower extract resulted in slight increases in loss of MMP. These results were confirmed by Annexin-V analysis. These results documented the cytotoxic and apoptotic effects of P. granatum extracts on human U266 multiple myeloma cells via disruption of mitochondrial membrane potential and increasing cell cycle arrest. The data suggest that the extracts can be envisaged in cancer chemoprevention and call for further exploration into the potential application of these plant parts. © 2015, International Society of Oncology and BioMarkers (ISOBM).Article Citation Count: 30Apoptotic Effects of Quercitrin on DLD-1 Colon Cancer Cell Line(Frontiers Media Sa, 2015) Cincin, Zeynep Birsu; Unlu, Miray; Kiran, Bayram; Bireller, Elif Sinem; Baran, Yusuf; Cakmakoglu, Bedia; Baran, YusufQuercetin, which is the most abundant bioflavonoid compound, is mainly present in the glycoside form of quercitrin. Although different studies indicated that quercitrin is a potent antioxidant, the action of this compound is not well understood. In this study, we investigated whether quercitrin has apoptotic and antiproliferative effects in DLD-1 colon cancer cell lines. Time and dose dependent antiproliferative and apoptotic effects of quercitrin were subsequently determined by WST-1 cell proliferation assay, lactate dehydrogenase (LDH) cytotoxicity assay, detection of nucleosome enrichment factor, changes in caspase-3 activity, loss of mitochondrial membrane potential (MMP) and also the localization of phosphatidylserine (PS) in the plasma membrane. There were significant increases in caspase-3 activity, loss of MMP, and increases in the apoptotic cell population in response to quercitrin in DLD-1 colon cancer cells in a time- and dose-dependent manner. These results revealed that quercitrin has antiproliferative and apoptotic effects on colon cancer cells. Quercitrin activity supported with in vivo analyses could be a biomarker candicate for early colorectal carcinoma.Article Citation Count: 19Apoptotic 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, YusufAim: 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.
