Browsing by Subject "methodology"
Now showing 1 - 10 of 10
Results Per Page
Sort Options
Item Open Access Antibacterial electrospun poly(lactic acid) (PLA) nanofibrous webs incorporating triclosan/cyclodextrin inclusion complexes(2013) Kayaci F.; Umu O.C.O.; Tekinay, T.; Uyar, T.Solid triclosan/cyclodextrin inclusion complexes (TR/CD-IC) were obtained and then incorporated in poly(lactic acid) (PLA) nanofibers via electrospinning. α-CD, β-CD, and γ-CD were tested for the formation of TR/CD-IC by a coprecipitation method; however, the findings indicated that α-CD could not form an inclusion complex with TR, whereas β-CD and γ-CD successfully formed TR/CD-IC crystals, and the molar ratio of TR to CD was found to be 1:1. The structural and thermal characteristics of TR/CD-IC were investigated by 1H NMR, FTIR, XRD, DSC, and TGA studies. Then, the encapsulation of TR/β-CD-IC and TR/γ-CD-IC in PLA nanofibers was achieved. Electrospun PLA and PLA/TR nanofibers obtained for comparison were uniform, whereas the aggregates of TR/CD-IC crystals were present and distributed within the PLA fiber matrix as confirmed by SEM and XRD analyses. The antibacterial activity of these nanofibrous webs was investigated. The results indicated that PLA nanofibers incorporating TR/CD-IC showed better antibacterial activity against Staphylococcus aureus and Escherichia coli bacteria compared to PLA nanofibers containing only TR without CD-IC. Electrospun nanofibrous webs incorporating TR/CD-IC may be applicable in active food packaging due to their very high surface area and nanoporous structure as well as efficient antibacterial property. © 2013 American Chemical Society.Item Open Access A comprehensive methodology for determining the most informative mammographic features(2013) Wu, Y.; Alagoz O.; Ayvaci, M.U.S.; Munoz Del Rio, A.; Vanness, D.J.; Woods, R.; Burnside, E.S.This study aims to determine the most informative mammographic features for breast cancer diagnosis using mutual information (MI) analysis. Our Health Insurance Portability and Accountability Act-approved database consists of 44,397 consecutive structured mammography reports for 20,375 patients collected from 2005 to 2008. The reports include demographic risk factors (age, family and personal history of breast cancer, and use of hormone therapy) and mammographic features from the Breast Imaging Reporting and Data System lexicon. We calculated MI using Shannon's entropy measure for each feature with respect to the outcome (benign/malignant using a cancer registry match as reference standard). In order to evaluate the validity of the MI rankings of features, we trained and tested naïve Bayes classifiers on the feature with tenfold cross-validation, and measured the predictive ability using area under the ROC curve (AUC). We used a bootstrapping approach to assess the distributional properties of our estimates, and the DeLong method to compare AUC. Based on MI, we found that mass margins and mass shape were the most informative features for breast cancer diagnosis. Calcification morphology, mass density, and calcification distribution provided predictive information for distinguishing benign and malignant breast findings. Breast composition, associated findings, and special cases provided little information in this task. We also found that the rankings of mammographic features with MI and AUC were generally consistent. MI analysis provides a framework to determine the value of different mammographic features in the pursuit of optimal (i.e., accurate and efficient) breast cancer diagnosis. © 2013 Society for Imaging Informatics in Medicine.Item Open Access Electroless synthesis of 3nm wide alloy nanowires inside Tobacco mosaic virus(2012) Balci, S.; Hahn, K.; Kopold P.; Kadri, A.; Wege, C.; Kern, K.; Bittner, A.M.We show that 3nm wide cobaltiron alloy nanowires can be synthesized by simple wet chemical electroless deposition inside tubular Tobacco mosaic virus particles. The method is based on adsorption of Pd(II) ions, formation of a Pd catalyst, and autocatalytic deposition of the alloy from dissolved metal salts, reduced by a borane compound. Extensive energy-filtering TEM investigations at the nanoscale revealed that the synthesized wires are alloys of Co, Fe, and Ni. We confirmed by high-resolution TEM that our alloy nanowires are at least partially crystalline, which is compatible with typical Co-rich alloys. Ni traces bestow higher stability, presumably against corrosion, as also known from bulk CoFe. Alloy nanowires, as small as the ones presented here, might be used for a variety of applications including high density data storage, imaging, sensing, and even drug delivery. © 2012 IOP Publishing Ltd.Item Open Access Experimental observation of cavity formation in composite metamaterials(Optical Society of American (OSA), 2008) Caglayan H.; Bulu I.; Loncar, M.; Özbay, EkmelIn this paper, we investigated one of the promising applications of left-handed metamaterials: composite metamaterial based cavities. Four different cavity structures operating in the microwave regime were constructed, and we observed cavity modes on the transmission spectrum with different quality factors. The effective permittivity and permeability of the CMM structure and cavity structure were calculated by use of a retrieval procedure. Subsequently, in taking full advantage of the effective medium theory, we modeled CMM based cavities as one dimensional Fabry-Perot resonators with a subwavelength cavity at the center. We calculated the transmission from the Fabry-Perot resonator model using the one-dimensional transfer matrix method, which is in good agreement with the measured result. Finally, we investigated the Fabry-Perot resonance phase condition for a CMM based cavity, in which the condition was satisfied at the cavity frequency. Therefore, our results show that it is possible to treat metamaterial based cavities as one-dimensional Fabry-Perot resonators with a subwavelength cavity. © 2008 Optical Society of America.Item Open Access Generation of phospholipid vesicle-nanotube networks and transport of molecules therein(2011) Jesorka, A.; Stepanyants, N.; Zhang H.; Ortmen, B.; Hakonen, B.; Orwar O.We describe micromanipulation and microinjection procedures for the fabrication of soft-matter networks consisting of lipid bilayer nanotubes and surface-immobilized vesicles. These biomimetic membrane systems feature unique structural flexibility and expandability and, unlike solid-state microfluidic and nanofluidic devices prepared by top-down fabrication, they allow network designs with dynamic control over individual containers and interconnecting conduits. The fabrication is founded on self-assembly of phospholipid molecules, followed by micromanipulation operations, such as membrane electroporation and microinjection, to effect shape transformations of the membrane and create a series of interconnected compartments. Size and geometry of the network can be chosen according to its desired function. Membrane composition is controlled mainly during the self-assembly step, whereas the interior contents of individual containers is defined through a sequence of microneedle injections. Networks cannot be fabricated with other currently available methods of giant unilamellar vesicle preparation (large unilamellar vesicle fusion or electroformation). Described in detail are also three transport modes, which are suitable for moving water-soluble or membrane-bound small molecules, polymers, DNA, proteins and nanoparticles within the networks. The fabrication protocol requires ∼90 min, provided all necessary preparations are made in advance. The transport studies require an additional 60-120 min, depending on the transport regime. © 2011 Nature America, Inc. All rights reserved.Item Open Access GOPred: GO molecular function prediction by combined classifiers(2010) Saraç Ö.S.; Atalay V.; Cetin-Atalay, R.Functional protein annotation is an important matter for in vivo and in silico biology. Several computational methods have been proposed that make use of a wide range of features such as motifs, domains, homology, structure and physicochemical properties. There is no single method that performs best in all functional classification problems because information obtained using any of these features depends on the function to be assigned to the protein. In this study, we portray a novel approach that combines different methods to better represent protein function. First, we formulated the function annotation problem as a classification problem defined on 300 different Gene Ontology (GO) terms from molecular function aspect. We presented a method to form positive and negative training examples while taking into account the directed acyclic graph (DAG) structure and evidence codes of GO. We applied three different methods and their combinations. Results show that combining different methods improves prediction accuracy in most cases. The proposed method, GOPred, is available as an online computational annotation tool (http://kinaz.fen.bilkent.edu.tr/gopred). © 2010 Saraç et al.Item Open Access Method vs postmethod! : a survey on prospective EFL teachers' perspectives(Bilkent University, 2014) Tığlı, TufanThis descriptive study investigated the awareness level of ELT students regarding postmethod pedagogy, and the teaching methods in Turkey. Having emerged in the early 1990s, postmethod pedagogy has received mixed reactions in the ELT world. Based on the idea that the concept of method has a limiting impact on language teachers, postmethod condition suggests that method is an artificially planted term into the language classrooms; therefore, should no longer be regarded as a viable construct. While postmethod pedagogy calls for a closer inspection of local occurrences, its presence in local curricula among countries outside the European periphery remains questionable in that the innovative condition of postmethod is fairly new, and is still widely overshadowed by Communicative Approaches in educational contexts. By employing a quantitative approach, this study traced the echoes of methods and the postmethod condition in ELT departments in Turkey Eighty-eight ELT students from six different universities in Turkey participated in the study. An online survey with four sections was employed for the data collection stages of the study. Analyses of the data revealed that the Communicative Approaches are the widely preferred methods among third- and fourth-year ELT students in Turkey. Additionally, these students had negative perceptions towards the earlier methods of teaching English. Regarding the postmethod condition, the results indicated that Turkish ELT students still had strong links with the methods, and they were unwilling to abandon the guidance that ELT methods provided them. However, significant difference was observed between teacher groups regarding the Particularity principle of the postmethod condition. The findings of this descriptive study supported the existing literature in that while Communicative Approaches are the dominant methods of instruction in Turkey, which is an English as a Foreign Language setting, some complications remain among prospective teachers in implementing deep-end ELT methods to local agenda.Item Open Access Non-radiative resonance energy transfer in bi-polymer nanoparticles of fluorescent conjugated polymers(Optical Society of American (OSA), 2010) Ozel I.O.; Ozel, T.; Demir, Hilmi Volkan; Tuncel, D.This work demonstrates the comparative studies of non-radiative resonance energy transfer in bi-polymer nanoparticles based on fluorescent conjugated polymers. For this purpose, poly[(9,9-dihexylfluorene) (PF) as a donor (D) and poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) as an acceptor (A) have been utilized, from which four different bi-polymer nanoparticle systems are designed and synthesized. Both, steady-state fluorescence spectra and time-resolved fluorescence measurements indicate varying energy transfer efficiencies from the host polymer PF to the acceptor polymer MEH-PPV depending on the D-A distances and structural properties of the nanoparticles. The first approach involves the preparation of PF and MEH-PPV nanoparticles separately and mixing them at a certain ratio. In the second approach, first PF and MEH-PPV solutions are mixed prior to nanoparticle formation and then nanoparticles are prepared from the mixture. Third and fourth approaches involve the sequential nanoparticle preparation. In the former, nanoparticles are prepared to have PF as a core and MEH-PPV as a shell. The latter is the reverse of the third in which the core is MEH-PPV and the shell is PF. The highest energy transfer efficiency recorded to be 35% is obtained from the last system, in which a PF layer is sequentially formed on MEH-PPV NPs. © 2010 Optical Society of America.Item Open Access Photovoltaic nanocrystal scintillators hybridized on Si solar cells for enhanced conversion efficiency in UV(Optical Society of American (OSA), 2008) Mutlugun, E.; Soganci I.M.; Demir, Hilmi VolkanWe propose and demonstrate semiconductor nanocrystal based photovoltaic scintillators integrated on solar cells to enhance photovoltaic device parameters including spectral responsivity, open circuit voltage, short circuit current, fill factor, and solar conversion efficiency in the ultraviolet. Hybridizing (CdSe)ZnS core-shell quantum dots of 2.4 nm in diameter on multi-crystalline Si solar cells for the first time, we show that the solar conversion efficiency is enhanced 2 folds under white light illumination similar to the solar spectrum. Such nanocrystal scintillators provide the ability to extend the photovoltaic activity towards UV. © 2008 Optical Society of America.Item Open Access Texturing of titanium (Ti6Al4V) medical implant surfaces with MHz-repetition-rate femtosecond and picosecond Yb-doped fiber lasers(Optical Society of American (OSA), 2011) Erdoǧan, M.; Öktem, B.; Kalaycioǧlu H.; Yavaş, S.; Mukhopadhyay P.K.; Eken, K.; Özgören, K.; Aykaç, Y.; Tazebay, U.H.; Ilday F.O.We propose and demonstrate the use of short pulsed fiber lasers in surface texturing using MHz-repetition-rate, microjoule- and sub-microjoule-energy pulses. Texturing of titanium-based (Ti6Al4V) dental implant surfaces is achieved using femtosecond, picosecond and (for comparison) nanosecond pulses with the aim of controlling attachment of human cells onto the surface. Femtosecond and picosecond pulses yield similar results in the creation of micron-scale textures with greatly reduced or no thermal heat effects, whereas nanosecond pulses result in strong thermal effects. Various surface textures are created with excellent uniformity and repeatability on a desired portion of the surface. The effects of the surface texturing on the attachment and proliferation of cells are characterized under cell culture conditions. Our data indicate that picosecond-pulsed laser modification can be utilized effectively in low-cost laser surface engineering of medical implants, where different areas on the surface can be made cell-attachment friendly or hostile through the use of different patterns. © 2011 Optical Society of America.