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Permanent URI for this collectionhttp://65.108.157.135:4000/handle/123456789/9

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Citation - WoS: 4
Citation - Scopus: 8
Advances 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 Bölümü
Graphical 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.
Citation - WoS: 12
Citation - Scopus: 14
Anomalous transmittance of polystyrene-ceria nanocomposites at high particle loadings
(Royal Soc Chemistry, 2013) Parlak, Onur; Demir, Mustafa M.; Demir, Mustafa
Optical 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.
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: 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 - WoS: 22
Biodiversity, drug discovery, and the future of global health: Introducing the biodiversity to biomedicine consortium, a call to action
(Univ Edinburgh, Global Health Soc, 2017) Neergheen-Bhujun, Vidushi; Awan, Almas Taj; Baran, Yusuf; Bunnefeld, Nils; Chan, Kit; Edison Dela Cruz, Thomas; Kagansky, Alexander; Baran, Yusuf
[No Abstract Available]
Citation - WoS: 15
Biodiversity: the overlooked source of human health
(Cell Press, 2023) Linhares, Yuliya; Kaganski, Alexander; Agyare, Christian; Kurnaz, Isil A.; Neergheen, Vidushi; Kolodziejczyk, Bartlomiej; Bueso, Yensi Flores
Biodiversity is the measure of the variation of lifeforms in a given ecological system. Biodiversity provides ecosystems with the robustness, stability, and re-silience that sustains them. This is ultimately essential for our survival because we depend on the services that natural ecosystems provide (food, fresh water, air, climate, and medicine). Despite this, human activity is driving an unprece-dented rate of biodiversity decline, which may jeopardize the life-support sys-tems of the planet if no urgent action is taken. In this article we show why biodiversity is essential for human health. We raise our case and focus on the biomedicine services that are enabled by biodiversity, and we present known and novel approaches to promote biodiversity conservation.
Citation - WoS: 109
Citation - Scopus: 123
Chitosan fiber-supported zero-valent iron nanoparticles as a novel sorbent for sequestration of inorganic arsenic
(Royal Soc Chemistry, 2013) Horzum, Nesrin; Demir, Mustafa M.; Nairat, Muath; Shahwan, Talal; Demir, Mustafa
This study proposes a new sorbent for the removal of inorganic arsenic from aqueous solutions. Monodispersed nano zero-valent iron (nZVI) particles were nucleated at the surface of electrospun chitosan fibers (average fiber diameter of 195 +/- 50 nm) by liquid phase reduction of FeCl3 using NaBH4. The material was characterized using SEM, TGA, XPS, XRD, and FTIR. The diameter of iron nanoparticles was found to vary between 75-100 nm. A set of batch experiments were carried out to elucidate the efficiency of the composite sorbent toward fixation of arsenite and arsenate ions. The ion concentrations in the supernatant solutions were determined using inductively coupled plasma-mass spectrometry (ICP-MS). The results revealed that the chitosan fiber supported nZVI particles is an excellent sorbent material for inorganic arsenic uptake at concentrations ranging from 0.01 to 5.00 mg L-1 over a wide range of pH values. Based on XPS analysis, As(III) was found to undergo oxidation to As(V) upon sorption, while As(V) retained its oxidation state. By virtue of the successful combination of the electrospun fibers' mechanical integrity and the large reactivity of dispersed nZVI particles, the applicability of the resulting sorbent material in arsenic sorption holds broad promise.
Citation - WoS: 11
Citation - Scopus: 11
Controlled surface mineralization of metal oxides on nanofibers
(Royal Soc Chemistry, 2015) Horzum, Nesrin; Mari, Margherita; Wagner, Manfred; Fortunato, Giuseppino; Popa, Ana-Maria; Demir, Mustafa M.; Munoz-Espi, Rafael; Demir, Mustafa
We report a versatile approach for the preparation of metal oxide/polymer hybrid nanofibers by in situ formation of metal oxide nanoparticles on surface-functionalized polymer fibers. Poly (styrene-covinylphosphonic acid) fibers were produced by electrospinning and used as supports for the in situ formation of ceria nanocrystals without further thermal treatment. The crystallization of ceria was induced by the addition of an alkaline solution to fibers loaded with the corresponding precursor. The formation of the inorganic material at the fiber surface was investigated by transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). The extension of the approach to prepare polymer/titania hybrid nanofibers demonstrates its versatility.
Citation - WoS: 15
Controlling Spontaneous Emission of CdSe Nanoparticles Dispersed in Electrospun Fibers of Polycarbonate Urethane
(Amer Chemical Soc, 2009) Demir, Mustafa M.; Soyal, Duygu; Unlu, Caner; Kus, Mahmut; Ozcelik, Serdar; Demir, Mustafa
Luminescent fibrous composite films consisting of submicrometer diameter fibers were prepared by electrospinning of segmented polycarbonate urethane (PCU) in dimethyl formamide and tri-n-octylphosphine oxide (TOPO)-capped CdSe nanocrystals (5 nm in diameter) in toluene. Using a pair of conductive electrodes separated with an air gap, we successfully produced randomly deposited and uniaxially aligned electrospun fibers. The surface structure of the electrospun fibers was studied using atomic force microscopy (AFM) and was compared to the corresponding film prepared by casting. In cast film, tapping mode AFM imaging suggests that hard urethane segments organize into rodlike morphology dispersed in soft polycarbonate. When PCU/CdSe dispersions were subjected to electrospinning, copolymer domains were forced to arrange into lamella along the fiber axis due to elongational flow and high stretching. Molecular orientation in the domains of the composite fibers was confirmed by polarized infrared spectroscopy. We demonstrated that formation of the oriented domains by electrospinning develops a hierarchical structure, which consequently modifies spectral properties because new multiple sharp lines appeared in the photoluminescence (PL) spectra of the fibers. In contrast to randomly deposited fibers, the PL intensity of uniaxially aligned fibers was found to be angle dependent. We propose that the elongated internal structure within the fibers controls the spontaneous emission of CdSe nanoparticles dispersed throughout the electrospun mat. A discussion on the nature of the controlled spontaneous emission is provided.
Citation - WoS: 12
Citation - Scopus: 17
Design of Polymeric Antiscalants Based on Functional Vinyl Monomers for (Fe, Mg) Silicates
(Amer Chemical Soc, 2017) Topcu, Gokhan; Celik, Asli; Baba, Alper; Demir, Mustafa M.; Demir, Mustafa
Silica/silicate scaling is one of a few detrimental problems that cause high economical loss in the geothermal and petroleum fields. The prevention of silica/silicate has been attempted using antiscalants with functional groups, particularly -NH2; however, metal silicates are commonly found in the fields, and the antiscalants developed thus far are not effective against these compounds. In this work, polymeric antiscalants have been developed by merging two or-snore functional-comonomers consisting of various chelating groups for metal cations. Homo- and copolymers of acrylamide (AM), the sodium salt of vinyl sulfonic acid (VSA), and vinyl phosphonic acid (VPA) were synthesized to examine their antiscaling performance against metal silicate scaling. Lab-scale metal silicates were obtained in a pressured autoclave reactor. The, antiscalants were tested at various dosages (25, 50, and 100 ppm), and their effects were investigated from the leftover decaritates after isolation of the solid precipitates. The polymeric antiscalants were found to be particularly effective against metal silicates and ineffective against simple silica precipitates. Acidic groups may be coordinating the metal cations, which prevents the-formation of precipitates. Among these acidic comonomers; VSA-containing polymers, in particular, increased the solubility-of metal silicates.
Citation - WoS: 2
Development of AB3-Type Novel Phthalocyanine and Porphyrin Photosensitizers Conjugated with Triphenylphosphonium for Higher Photodynamic Efficacy
(Amer Chemical Soc, 2022) Onal, Emel; Tuncel, Ozge; Vatansever, Ipek Erdogan; Albakour, Mohamad; Celik, Gizem Gumusgoz; Kucuk, Tugba; Ozcelik, Serdar
There are a number of lipophilic cations that can be chosen; the triphenylphosphonium (TPP) ion is particularly unique for mitochondrion targeting, mainly due to its simplicity in structure and ease to be linked to the target molecules. In this work, mitochondrion-targeted AB3-type novel phthalocyanine and porphyrin photosensitizers (PSs) were synthesized and their photophysical photochemical properties were defined. Fluores-cence quantum yields (phi F) are 0.009, 0.14, 0.13, and 0.13, and the singlet-oxygen quantum yields (phi Delta) are 0.27, 0.75, 0.57, and 0.58 for LuPcPox(OAc), AB3TPP-Pc, AB3TPP-Por-C4, and AB3TPP-Por-C6, respectively. To evaluate the photodynamic efficacy of the TPP-conjugated PS cell viabilities of A549 and BEAS-2B lung cells were comparatively measured and IC-50 values were determined. AB3TPP-Por-C4, AB3TPP-Por-C6, and AB3TPP-Pc compounds compared to the reference molecules ZnPc and H2TPP were found to be highly cytotoxic (sub-micromolar concentration) under the light. LuPcPox(OAc) is the most effective molecule regarding cell killing (the activity). The cell killing of the TPP-conjugated porphyrin derivatives exhibits a similar response compared to LuPcPox(OAc) when the light absorbing factor of the PS is normalized at 660 nm: TPP-conjugated porphyrins absorb less light (lower extinction coefficient) but produce more radical species (higher singlet-oxygen quantum yield) and therefore effectively kill the cells. The singlet oxygen-producing capacity of AB3TPP-Pc is almost 3 times higher compared to LuPcPox(OAc) and 50% more efficient with respect to ZnPc, suggesting that TPP-conjugated phthalocyanine may serve as a good photosensitizer for photodynamic therapy (PDT). The high singlet oxygen generation capacity of these novel TPP-conjugated porphyrin and phthalocyanine PS suggests that they might be useful for PDT requiring lower photosensitizer concentration and reduced energy deposited through less light exposure.
Citation - WoS: 0
Dietary Garlic Prevents Development of Diabesity in Mice
(Federation Amer Soc Exp Biol, 2009) Tu, Chen-Pei David; Akgul, Bunyamin; Lin, Kai-Wei; Pan, Huei-Ju; Chen, Yen-Hui; Lu, Tzu-Huan; Chen, Yuan-Tsong; Akgül, Bünyamin
[No Abstract Available]
Citation - WoS: 0
Dietary garlic prevents development of or alleviates diabetes and obesity in mice
(Federation Amer Soc Exp Biol, 2011) Tu, Chen-Pei David; Yang, Hui-Mei Ou; Lin, Kai-Wei; Akgul, Bunyamin; Chen, Yen-Hui; Lu, Tzu-Huan; Chen, Yuan-Tsong; Akgül, Bünyamin
[No Abstract Available]
Citation - WoS: 35
Effect of Molecular Architecture on Cell Interactions and Stealth Properties of PEG
(Amer Chemical Soc, 2017) Ozer, Imran; Tomak, Aysel; Zareie, Hadi M.; Baran, Yusuf; Bulmus, Volga; Baran, Yusuf
PEGylation, covalent attachment of PEG to therapeutic biomolecules, in which suboptimal pharmacokinetic profiles limiting their therapeutic utility are of concern, is a widely applied technology. However, this technology has been challenged by reduced bioactivity of biomolecules upon PEGylation and immunogenicity of PEG triggering immune response and abrogating clinical efficacy, which collectively necessitate development of stealth polymer alternatives. Here we demonstrate that comb-shape poly[oligo(ethylene glycol) methyl ether methacrylate](POEGMA); a stealth polymer alternative, has a more compact structure than PEG and self-organize into nanoparticles in a molecular weight dependent manner. Most notably, we show that comb shape POEGMA promotes significantly higher cellular uptake and exhibits less steric hindrance imposed on the conjugated biomolecule than PEG. Collectively, comb-shape POEGMA offers a versatile alternative to PEG for stealth polymer-biomolecule conjugation applications.
Citation - WoS: 10
Effects of cell-mediated osteoprotegerin gene transfer and mesenchymal stem cell applications on orthodontically induced root resorption of rat teeth
(Oxford Univ Press, 2017) Amuk, Nisa Gul; Kurt, Gokmen; Baran, Yusuf; Seyrantepe, Volkan; Yandim, Melis Kartal; Adan, Aysun; Sonmez, Mehmet Fatih; Baran, Yusuf
Aim: The aim of this study is to evaluate and compare therapeutic effects of mesenchymal stem cell (MSCs) and osteoprotegerin (OPG) gene transfer applications on inhibition and/or repair of orthodontically induced inflammatory root resorption (OIIRR). Materials and methods: Thirty Wistar rats were divided into four groups as untreated group (negative control), treated with orthodontic appliance group (positive control), MSCs injection group, and OPG transfected MSCs [gene therapy (GT) group]. About 100 g of orthodontic force was applied to upper first molar teeth of rats for 14 days. MSCs and transfected MSC injections were performed at 1st, 6th, and 11th days to the MSC and GT group rats. At the end of experiment, upper first molar teeth were prepared for genetical, scanning electron microscopy (SEM), fluorescent microscopy, and haematoxylin eosin-tartrate resistant acid phosphatase staining histological analyses. Number of total cells, number of osteoclastic cells, number of resorption lacunae, resorption area ratio, SEM resorption ratio, OPG, RANKL, Cox-2 gene expression levels at the periodontal ligament (PDL) were calculated. Paired t-test, Kruskal-Wallis, and chi-square tests were performed. Results: Transferred MSCs showed marked fluorescence in PDL. The results revealed that number of osteoclastic cells, resorption lacunae, resorption area ratio, RANKL, and Cox-2 were reduced after single MSC injections significantly (P < 0.05). GT group showed the lowest number of osteoclastic cells (P < 0.01), number of resorption lacunae, resorption area ratio, and highest OPG expression (P < 0.001). Conclusions: Taken together all these results, MSCs and GT showed marked inhibition and/or repair effects on OIIRR during orthodontic treatment on rats.
Citation - WoS: 0
EFFECTS OF HESPERIDIN ON NON-SMALL CELL LUNG CANCER CELLS
(int inst Anticancer Research, 2014) Bireller, Elif Sinem; Cincin, Zeynep Birsu; Unlu, Miray; Kiran, Bayram; Baran, Yusuf; Cakmakoglu, Bedia; Baran, Yusuf
[No Abstract Available]
Citation - WoS: 15
Citation - Scopus: 16
Electrospun amino-functionalized PDMS as a novel SPME sorbent for the speciation of inorganic and organometallic arsenic species
(Royal Soc Chemistry, 2013) Boyaci, Ezel; Horzum, Nesrin; Cagir, Ali; Demir, Mustafa M.; Eroglu, Ahmet E.; Demir, Mustafa
Sol-gel based amine-functionalized SPME fibers (PDMS-weak anion exchanger) were prepared and used for direct mode extraction of dimethylarsinic acid (DMA), monomethylarsonic acid (MMA), and arsenate (As(V)) from aqueous solutions followed by HPLC-ICPMS determination. Two different methods of coating were employed: (i) electrospinning and (ii) dip coating. Electrospinning was used for the first time for preparation of sol-gel based SPME fibers and was found to be superior in terms of extracted amount of arsenicals, coating homogeneity, accessibility of amine groups on the surface, and preparation time for a single fiber. Various parameters such as solution pH, extraction time, agitation speed, extraction temperature, and ionic strength were studied. Optimum extraction conditions were determined as pH of 5.0, extraction time of 30 min, agitation speed of 700 rpm, and extraction temperature of 20 degrees C. Extraction ability of the novel coating decreased by the addition of NaCl as a consequence of the competition between anionic arsenic species and chloride ions for active sites of the weak anion exchanger. This novel sol-gel coating prepared by electrospinning was found to be promising for SPME applications. Vibrational spectroscopy revealed the alignment of PDMS chains by elongational force under electrospinning process. The chain alignment accordingly orients the pendant amino functional groups perpendicular to the fiber surface, which may develop the free active functional groups available to the medium and lead to the enhancement of the extraction performance. Moreover, the proposed coating strategy through electrospinning might be able to break new ground for various applications in analytical chemistry as well as other disciplines.
Citation - WoS: 4
Citation - Scopus: 9
End-to-end security implementation for mobile devices using TLS protocol
(Springer France, 2006) Kayayurt, Baris; Tuglular, Tugkan; Tuğlular, Tuğkan; Bilgisayar Mühendisliği Bölümü
End-to-end security has been an emerging need for mobile devices with the widespread use of personal digital assistants and mobile phones. Transport Layer Security Protocol (TLS) is an end-to-end security protocol that is commonly used on the Internet, together with its predecessor, SSL protocol. By implementing TLS protocol in the mobile world, the advantage of the proven security model of this protocol can be utilized. The main design goals of mobile end-to-end security protocol are maintainability and extensibility. Cryptographic operations are performed with a free library, Bouncy Castle Cryptography Package. The object oriented architecture of proposed end-to-end security protocol implementation makes the replacement of this library with another cryptography package easier. The implementation has been experimented with different cases, which represent use of different cryptographic algorithms.
Citation - WoS: 0
Enhanced light-matter interaction in a hybrid photonic-plasmonic cavity (vol 127, 907, 2021)
(Springer Heidelberg, 2022) Gokbulut, Belkis; Inanc, Arda; Topcu, Gokhan; Ozcelik, Serdar; Demir, Mustafa M.; Inci, M. Naci; Demir, Mustafa
[No Abstract Available]
Citation - WoS: 6
Enhanced Spontaneous Emission Rate in a Low-Q Hybrid Photonic-Plasmonic Nanoresonator
(Amer Chemical Soc, 2019) Gokbulut, Belkis; Inanc, Arda; Topcu, Gokhan; Unluturk, Secil S.; Ozcelik, Serdar; Demir, Mustafa M.; Inci, M. Naci; Demir, Mustafa
In this paper, CdTe quantum dots (QDs)-doped single electrospun polymer nanofibers are partially coated with gold nanoparticles to form distinct hybrid photonic-plasmonic nanoresonators to investigate the critical role of the cavity-confined hybrid mode on the modification of the spontaneous emission dynamics of the fluorescent emitters in low-Q photonic cavities. A total enhancement factor of 11.2 is measured via a time-resolved experimental technique, which shows that there is an increase of about three times in the spontaneous emission rate for the QDs-doped gold nanoparticle-decorated nanofibers as they are compared with those uncoated ones. The physical mechanism affecting the spontaneous emission rate of the encapsulated QDs in such a hybrid photonic-plasmonic nanoresonator is explained to be due to regeneration of the mode field in the nanofiber cavity upon the interaction of the dipoles with the surface plasmons of distinctive gold nanoparticles that surround the outer surface of the nanofiber.

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