Browsing by Subject "Synthesis"

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Open Access
Antibacterial electrospun nanofibers from triclosan/cyclodextrin inclusion complexes
(Elsevier, 2014) Celebioglu A.; Umu, O. C. O.; Tekinay, T.; Uyar, Tamer
The electrospinning of nanofibers (NF) from cyclodextrin inclusion complexes (CD-IC) with an antibacterial agent (triclosan) was achieved without using any carrier polymeric matrix. Polymer-free triclosan/CD-IC NF were electrospun from highly concentrated (160% CD, w/w) aqueous triclosan/CD-IC suspension by using two types of chemically modified CD; hydroxypropyl-beta-cyclodextrin (HPβCD) and hydroxypropyl-gamma-cyclodextrin (HPγCD). The morphological characterization of the electrospun triclosan/CD-IC NF by SEM elucidated that the triclosan/HPβCD-IC NF and triclosan/HPγCD-IC NF were bead-free having average fiber diameter of 520±250nm and 1100±660nm, respectively. The presence of triclosan and the formation of triclosan/CD-IC within the fiber structure were confirmed by 1H-NMR, FTIR, XRD, DSC, and TGA studies. The initial 1:1molar ratio of the triclosan:CD was kept for triclosan/HPβCD-IC NF after the electrospinning and whereas 0.7:1molar ratio was observed for triclosan/HPγCD-IC NF and some uncomplexed triclosan was detected suggesting that the complexation efficiency of triclosan with HPγCD was lower than that of HPβCD. The antibacterial properties of triclosan/CD-IC NF were tested against Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria. It was observed that triclosan/HPβCD-IC NF and triclosan/HPγCD-IC NF showed better antibacterial activity against both bacteria compared to uncomplexed pure triclosan.
Open Access
Deep learning for accelerated 3D MRI
(2021-08) Özbey, Muzaﬀer
Magnetic resonance imaging (MRI) oﬀers the ﬂexibility to image a given anatomic volume under a multitude of tissue contrasts. Yet, scan time considerations put stringent limits on the quality and diversity of MRI data. The gold-standard approach to alleviate this limitation is to recover high-quality images from data undersampled across various dimensions, most commonly the Fourier domain or contrast sets. A primary distinction among recovery methods is whether the anatomy is processed per volume or per cross-section. Volumetric models oﬀer enhanced capture of global contextual information, but they can suﬀer from sub-optimal learning due to elevated model complexity. Cross-sectional models with lower complexity oﬀer improved learning behavior, yet they ignore contextual information across the longitudinal dimension of the volume. Here, we introduce a novel progressive volumetrization strategy for generative models (ProvoGAN) that serially decomposes complex volumetric image recovery tasks into succes-sive cross-sectional mappings task-optimally ordered across individual rectilinear dimensions. ProvoGAN eﬀectively captures global context and recovers ﬁne-structural details across all dimensions, while maintaining low model complexity and improved learning behaviour. Comprehensive demonstrations on mainstream MRI reconstruction and synthesis tasks show that ProvoGAN yields superior per-formance to state-of-the-art volumetric and cross-sectional models.
Open Access
Deep learning for accelerated MR imaging
(2021-02) Dar, Salman Ul Hassan
Magnetic resonance imaging is a non-invasive imaging modality that enables multi-contrast acquisition of an underlying anatomy, thereby supplementing mul-titude of information for diagnosis. However, prolonged scan duration may pro-hibit its practical use. Two mainstream frameworks for accelerating MR image acquisitions are reconstruction and synthesis. In reconstruction, acquisitions are accelerated by undersampling in k-space, followed by reconstruction algorithms. Lately deep neural networks have oﬀered signiﬁcant improvements over tradi-tional methods in MR image reconstruction. However, deep neural networks rely heavily on availability of large datasets which might not be readily available for some applications. Furthermore, a caveat of the reconstruction framework in general is that the performance naturally starts degrading towards higher accel-eration factors where fewer data samples are acquired. In the alternative syn-thesis framework, acquisitions are accelerated by acquiring a subset of desired contrasts, and recovering the missing ones from the acquired ones. Current syn-thesis methods are primarily based on deep neural networks, which are trained to minimize mean square or absolute loss functions. This can bring about loss of intermediate-to-high spatial frequency content in the recovered images. Fur-thermore, the synthesis performance in general relies on similarity in relaxation parameters between source and target contrasts, and large dissimilarities can lead to artifactual synthesis or loss of features. Here, we tackle issues associated with reconstruction and synthesis approaches. In reconstruction, the data scarcity is-sue is addressed by pre-training a network on large readily available datasets, and ﬁne-tuning on just a few samples from target datasets. In synthesis, the loss of intermediate-to-high spatial frequency is catered for by adding adversarial and high-level perceptual losses on top of traditional mean absolute error. Fi-nally, a joint reconstruction and synthesis approach is proposed to mitigate the issues associated with both reconstruction and synthesis approaches in general. Demonstrations on MRI brain datasets of healthy subjects and patients indicate superior performance of the proposed techniques over the current state-of-the art ones.
Open Access
Design strategies for ratiometric chemosensors: modulation of excitation energy transfer at the energy donor site
(2009) Guliyev, R.; Coskun, A.; Akkaya, E. U.
Excitation energy transfer, when coupled to an ion-modulated ICT chromophore, creates novel opportunities in sensing. The direction of energy transfer and the point of ICT modulation can be varied as desired. In our previous work, we have shown that energy transfer efficiency between two energetically coupled fluorophores will be altered by the metal ion binding to the ICT chromophore carrying a ligand. There are two beneficial results: increased pseudo-Stokes shift and expanded dynamic range. Here, we explored the consequences of the modulation of energy transfer efficiency at the energy donor site, in a molecular design which has an ICT type metal ion-sensitive chromophore placed as the energy donor in the dyad. Clear advantages emerge compared to the acceptor site modulation: unaltered emission wavelength in the red end of the visible spectrum, while keeping a large Stokes shift and the ratiometric character. © 2009 American Chemical Society.
Open Access
Dispersion of multi-walled carbon nanotubes in an aqueous medium by water-dispersible conjugated polymer nanoparticles
(2010) Baykal, B.; Ibrahimova, V.; Er, G.; Bengü, E.; Tuncel, D.
Vertically aligned multi-walled carbon nanotubes (MWCNTs) synthesized by the alcohol catalytic CVD (ACCVD) technique are dispersed in water with the aid of water-dispersible conjugated polymer nanoparticles (CPNs). The interactions between CPNs and CNTs are studied with spectroscopy (UV-Vis, fluorescence and Raman) and electron microscopy techniques are used to confirm attachment of CPNs to the CNT sidewalls.
Open Access
edaGAN: Encoder-Decoder Attention Generative Adversarial Networks for multi-contrast MR image synthesis
(Institute of Electrical and Electronics Engineers, 2022-05-16) Dalmaz, Onat; Sağlam, Baturay; Gönç, Kaan; Çukur, Tolga
Magnetic resonance imaging (MRI) is the preferred modality among radiologists in the clinic due to its superior depiction of tissue contrast. Its ability to capture different contrasts within an exam session allows it to collect additional diagnostic information. However, such multi-contrast MRI exams take a long time to scan, resulting in acquiring just a portion of the required contrasts. Consequently, synthetic multi-contrast MRI can improve subsequent radiological observations and image analysis tasks like segmentation and detection. Because of this significant potential, multi-contrast MRI synthesis approaches are gaining popularity. Recently, generative adversarial networks (GAN) have become the de facto choice for synthesis tasks in medical imaging due to their sensitivity to realism and high-frequency structures. In this study, we present a novel generative adversarial approach for multi-contrast MRI synthesis that combines the learning of deep residual convolutional networks and spatial modulation introduced by an attention gating mechanism to synthesize high-quality MR images. We show the superiority of the proposed approach against various synthesis models on multi-contrast MRI datasets.
Open Access
Effects of perfluorination on thiophene and pyrrole oligomers
(2010) Salzner, U.
The effect of perfluorination on thiophene and pyrrole oligomers in neutral, cationic, and anionic states was investigated with density functional theory at the (TD)B3P86-30%/6-31G* level. For the title compounds fluorination leads to planarization. For pyrroles a band gap reduction of 0.58 eV results, as unsubstituted pyrroles are nonplanar and disordered in the solid state. For thiophene the band gap is slightly increased as long thiophene oligomers are almost planar. Ionization energies and electron affinities increase upon fluorination by 0.65 and 0.60 eV for polythiophene and by 0.45 and 0.90 eV for polypyrrole. Conduction band widths increase by 0.5 for polythiophene and by 0.7 eV for polypyrrole. Spectra of charged (doped) forms are almost identical to those of the parent systems. Like parent systems, fluorinated oligomers with chain lengths of more than six rings develop a third UV absorption that increases in strength and decreases in energy upon chain length increase.
Open Access
Generation of InN nanocrystals in organic solution through laser ablation of high pressure chemical vapor deposition-grown InN thin film
(Springer, 2012-07-27) Alkis, S.; Alevli, M.; Burzhuev, S.; Vural, H. A.; Okyay, Ali Kemal; Ortaç, B.
We report the synthesis of colloidal InN nanocrystals (InN-NCs) in organic solution through nanosecond pulsed laser ablation of high pressure chemical vapor deposition-grown InN thin film on GaN/sapphire template substrate. The size, the structural, the optical, and the chemical characteristics of InN-NCs demonstrate that the colloidal InN crystalline nanostructures in ethanol are synthesized with spherical shape within 5.9-25.3, 5.45-34.8, 3.24-36 nm particle-size distributions, increasing the pulse energy value. The colloidal InN-NCs solutions present strong absorption edge tailoring from NIR region to UV region.
Open Access
Green nanochemistry: metal oxide nanoparticles and porous thin films from bare metal powders
(Wiley-VCH Verlag, 2012) Redel, E.; Petrov, S.; Dag, Ö.; Moir, J.; Huai, C.; Mirtchev, P.; Ozin, G. A.
A universal, simple, robust, widely applicable and cost‐effective aqueous process is described for a controlled oxidative dissolution process of micrometer‐sized metal powders to form high‐purity aqueous dispersions of colloidally stable 3–8 nm metal oxide nanoparticles. Their utilization for making single and multilayer optically transparent high‐surface‐area nanoporous films is demonstrated. This facile synthesis is anticipated to find numerous applications in materials science, engineering, and nanomedicine.
Open Access
Laminin mimetic peptide nanofibers regenerate acute muscle defect
(Acta Materialia Inc, 2017) Cimenci, C. E.; Uzunalli, G.; Uysal, O.; Yergoz, F.; Umay, E. K.; Güler, Mustafa O.; Tekinay, A. B.
Skeletal muscle cells are terminally differentiated and require the activation of muscle progenitor (satellite) cells for their regeneration. There is a clinical need for faster and more efficient treatment methods for acute muscle injuries, and the stimulation of satellite cell proliferation is promising in this context. In this study, we designed and synthesized a laminin-mimetic bioactive peptide (LM/E-PA) system that is capable of accelerating satellite cell activation by emulating the structure and function of laminin, a major protein of the basal membrane of the skeletal muscle. The LM/E-PA nanofibers enhance myogenic differentiation in vitro and the clinical relevance of the laminin-mimetic bioactive scaffold system was demonstrated further by assessing its effect on the regeneration of acute muscle injury in a rat model. Laminin mimetic peptide nanofibers significantly promoted satellite cell activation in skeletal muscle and accelerated myofibrillar regeneration following acute muscle injury. In addition, the LM/E-PA scaffold treatment significantly reduced the time required for the structural and functional repair of skeletal muscle. This study represents one of the first examples of molecular- and tissue-level regeneration of skeletal muscle facilitated by bioactive peptide nanofibers following acute muscle injury. Significance Statement Sports, heavy lifting and other strength-intensive tasks are ubiquitous in modern life and likely to cause acute skeletal muscle injury. Speeding up regeneration of skeletal muscle injuries would not only shorten the duration of recovery for the patient, but also support the general health and functionality of the repaired muscle tissue. In this work, we designed and synthesized a laminin-mimetic nanosystem to enhance muscle regeneration. We tested its activity in a rat tibialis anterior muscle by injecting the bioactive nanosystem. The evaluation of the regeneration and differentiation capacity of skeletal muscle suggested that the laminin-mimetic nanosystem enhances skeletal muscle regeneration and provides a suitable platform that is highly promising for the regeneration of acute muscle injuries. This work demonstrates for the first time that laminin-mimetic self-assembled peptide nanosystems facilitate myogenic differentiation in vivo without the need for additional treatment.
Open Access
Liquid-phase synthesis of nanoparticles and nanostructured materials
(Elsevier, 2018) Karatutlu, A.; Barhoum, A.; Sapelkin, A.
Nanoparticles less than 100nm in size have attracted significant interest over the past 20 years due to their unique properties led by quantum size effect. This chapter evaluates the synthesis methods in liquid phase conducted under operation in high/room temperature and at vacuum/atmospheric environment for nanoparticles and nanostructured materials. We draw attention to the fact that various synthesis methods for formation of colloidally stable matrix-free nanoparticles are available. These methods including chemical stain etching, electrodeposition methods, direct-precipitation methods, sol-gel methods, colloidal synthesis methods, hot-injection synthesis methods, hydrothermal and solvothermal methods, microwave-assisted synthesis methods, ultrasonic synthesis methods, and laser ablation in liquid-phase.
Open Access
Mesoporous metallic rhodium nanoparticles
(Nature Publishing Group, 2017) Jiang B.; Li C.; Dag, Ö.; Abe, H.; Takei, T.; Imai, T.; Hossain, M. S. A.; Islam, M. T.; Wood, K.; Henzie, J.; Yamauchi, Y.
Mesoporous noble metals are an emerging class of cutting-edge nanostructured catalysts due to their abundant exposed active sites and highly accessible surfaces. Although various noble metal (e.g. Pt, Pd and Au) structures have been synthesized by hard- and soft-templating methods, mesoporous rhodium (Rh) nanoparticles have never been generated via chemical reduction, in part due to the relatively high surface energy of rhodium (Rh) metal. Here we describe a simple, scalable route to generate mesoporous Rh by chemical reduction on polymeric micelle templates [poly(ethylene oxide)-b-poly(methyl methacrylate) (PEO-b-PMMA)]. The mesoporous Rh nanoparticles exhibited a ∼1/42.6 times enhancement for the electrocatalytic oxidation of methanol compared to commercially available Rh catalyst. Surprisingly, the high surface area mesoporous structure of the Rh catalyst was thermally stable up to 400 °C. The combination of high surface area and thermal stability also enables superior catalytic activity for the remediation of nitric oxide (NO) in lean-burn exhaust containing high concentrations of O 2.
Open Access
A near IR di-styryl BODIPY-based ratiometric fluorescent chemosensor for Hg(II)
(Elsevier, 2010) Atilgan, S.; Kutuk, I.; Ozdemir, T.
A novel BODIPY-based near-IR emitting probe as a selective and sensitive fluorophore for Hg(II) is synthesized. This versatile BODIPY fluorophore is functionalized for long wavelength emission at the 3 and 5 positions via a condensation reaction in which two dithiodioxomonoaza-based crown-containing phenyl units are conjugated to the BODIPY core as a chelating unit. This designed fluorophore, employing an ICT sensor can be used effectively to detect Hg(II) cations by way of a hypsochromic shift (∼90 nm) in both the absorption and emission spectra. © 2009 Elsevier Ltd. All rights reserved.
Open Access
Phenylethynyl-BODIPY oligomers: bright dyes and fluorescent building blocks
(2009) Cakmak, Y.; Akkaya, E. U.
Boradiazaindacene dyes were converted into phenylethynyl-BODIPY oligomers via a cycle of reactions, notably including Sonogashira couplings. As expected, as the number, n, of repeating units increases, peak absorption and emission wavelengths are shifted to the red end of the visible spectrum, albeit with smaller increments as n increases. Decyl groups help to keep the solubility remarkably high, and in addition to being very bright red-emitting fluorophores, their rigid rod-like structures could allow their use as functional building blocks. © 2009 American Chemical Society.
Open Access
Poly-cyclodextrin cryogels with aligned porous structure for removal of polycyclic aromatic hydrocarbons (PAHs) from water
(Elsevier, 2017-08) Topuz, F.; Uyar, Tamer
Cyclodextrins (CDs) are sugar-based cyclic oligosaccharides, which form inclusion complexes with small guest molecules through their hydrophobic cavity. Here we successfully synthesized highly porous poly-cyclodextrin (poly-CD) cryogels, which were produced under cryogenic conditions by the cross-linking of amine-functional CDs with PEG-based diepoxide cross-linker. The poly-CD cryogels showed aligned porous network structures owing to the directional freezing of the matrix, of which the pore size and architecture exposed variations depending on the composition of the reactants. The cryogels were employed for the removal of genotoxic polycyclic aromatic hydrocarbons (PAHs) from aqueous solutions. They reached PAH sorption capacities as high as 1.25 mg PAH per gram cryogel. This high sorption performance is due to interactions between PAHs and the complete swollen network, and thus, is not restricted by interfacial adsorption. Given that the hydrophilic nature of the components, the sorption performance could only be attributed to the inclusion complex formation of CDs with PAH molecules. The poly-CD cryogels could be recycled with an exposure to ethanol and reused without any significant loss in the sorption capacity of PAHs.
Open Access
Prior-Guided image reconstruction for accelerated multi-contrast MRI via generative adversarial networks
(IEEE, 2020) Dar, Salman U.H.; Yurt, Mahmut; Shahdloo, Mohammad; Ildız, Muhammed Emrullah; Tınaz, Berk; Çukur, Tolga
Multi-contrast MRI acquisitions of an anatomy enrich the magnitude of information available for diagnosis. Yet, excessive scan times associated with additional contrasts may be a limiting factor. Two mainstream frameworks for enhanced scan efficiency are reconstruction of undersampled acquisitions and synthesis of missing acquisitions. Recently, deep learning methods have enabled significant performance improvements in both frameworks. Yet, reconstruction performance decreases towards higher acceleration factors with diminished sampling density at high-spatial-frequencies, whereas synthesis can manifest artefactual sensitivity or insensitivity to image features due to the absence of data samples from the target contrast. In this article, we propose a new approach for synergistic recovery of undersampled multi-contrast acquisitions based on conditional generative adversarial networks. The proposed method mitigates the limitations of pure learning-based reconstruction or synthesis by utilizing three priors: shared high-frequency prior available in the source contrast to preserve high-spatial-frequency details, low-frequency prior available in the undersampled target contrast to prevent feature leakage/loss, and perceptual prior to improve recovery of high-level features. Demonstrations on brain MRI datasets from healthy subjects and patients indicate the superior performance of the proposed method compared to pure reconstruction and synthesis methods. The proposed method can help improve the quality and scan efficiency of multi-contrast MRI exams.
Open Access
Progressively volumetrized deep generative models for data-efficient contextual learning of MR image recovery
(Elsevier BV, 2022-05) Yurt, Mahmut; Özbey, Muzaffer; Dar, Salman U.H.; Tınaz, Berk; Oğuz, Kader K.; Çukur, Tolga
Magnetic resonance imaging (MRI) offers the ﬂexibility to image a given anatomic volume under a multi- tude of tissue contrasts. Yet, scan time considerations put stringent limits on the quality and diversity of MRI data. The gold-standard approach to alleviate this limitation is to recover high-quality images from data undersampled across various dimensions, most commonly the Fourier domain or contrast sets. A primary distinction among recovery methods is whether the anatomy is processed per volume or per cross-section. Volumetric models offer enhanced capture of global contextual information, but they can suffer from suboptimal learning due to elevated model complexity. Cross-sectional models with lower complexity offer improved learning behavior, yet they ignore contextual information across the longitu- dinal dimension of the volume. Here, we introduce a novel progressive volumetrization strategy for gen- erative models (ProvoGAN) that serially decomposes complex volumetric image recovery tasks into suc- cessive cross-sectional mappings task-optimally ordered across individual rectilinear dimensions. Provo-GAN effectively captures global context and recovers ﬁne-structural details across all dimensions, while maintaining low model complexity and improved learning behavior. Comprehensive demonstrations on mainstream MRI reconstruction and synthesis tasks show that ProvoGAN yields superior performance to state-of-the-art volumetric and cross-sectional models.
Open Access
Quantum dot integrated LEDs using photonic and excitonic color conversion
(Elsevier, 2011-11-23) Demir, Hilmi Volkan; Nizamoglu, S.; Erdem, T.; Mutlugun, E.; Gaponik N.; Eychmüller A.
This review summarizes advantages, recent progress and challenges related to the quickly evolving research field of colloidal quantum dot integrated LEDs based on color conversion. We start with presenting a short general introduction to the field of solid state lighting and color conversion phenomena, which are essential for defining the requirements for high-quality general lighting. Subsequently we continue with a brief description of the synthesis of nanocrystal quantum dots and their optical properties together with the advantages of utilizing them in LEDs as color convertors. Following this basic background, we review the recent efforts on quantum dot integrated color-conversion LEDs, Förster resonance energy transfer (FRET) converted LEDs and FRET-enhanced LEDs. Finally, we conclude with a future outlook on semiconductor lighting and quantum dot integrated LEDs.
Open Access
A sensitive and selective ratiometric near IR fluorescent probe for zinc ions based on the distyryl-bodipy fluorophore
(2008) Atilgan, S.; Ozdemir, T.; Akkaya, E. U.
(Chemical Equation Presented) A novel distyryl-substituted boradiazaindacene (bodipy) dye with an emission peak moving hypsochromically from 730 to 680 nm on Zn(II) ion binding seems to be promising as one of the very few water-soluble fluorescent chemosensors emitting in the near IR region. © 2008 American Chemical Society.
Open Access
Sequence-specific self-sorting of the binding sites of a ditopic guest by cucurbituril homologues and subsequent formation of a hetero[4]pseudorotaxane
(2009) Celtek, G.; Artar, M.; Scherman, O. A.; Tuncel, D.
Ties us together: The selectivity and recognition behavior of cucurbit[n]uril (CB[n]) homologues (n = 6,7,8) towards a ditopic guest containing two distinct binding sites is explored. CB6, CB7, and CB8 recognize and self-sort the binding sites according to their size, shape, and chemical nature. In the presence of both CB6 and CB8 a hetero[4]pseudorotaxane is formed. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA.