PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
Browse
Browsing PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection by Title
Now showing 1 - 20 of 1417
- Results Per Page
- Sort Options
Article Citation - WoS: 6Citation - Scopus: 71,2-Diborolanes With Strong Donor Substituents: Synthesis and High Antimicrobial Activity(Academic Press, 2021) Şahin, Yüksel; Özgener, Hüseyin; Poyrazoğlu Çoban, Esin; Sevinçek, Resul; Bıyık, Halil H.; Özgener, Hüseyin; Aygün, Muhittin; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology1,2-diborolanes with strong and without strong donor substituents have been described, and are also referred to as 1,2-diboracyclopentane. The 1,2-diaryl/alkyl-amino-1,2-diboracyclopentanes 2, 3, and 4 were obtained in good yield after the reaction of 1,2-dichloro-1,2-diboracyclopentane 1 with ArNHLi and Me3Si-NR2. The structures of these new derivatives were characterized by nuclear magnetic resonance spectroscopy. The molecular structures of 2b, 2c, 2e, 4, and 5f were also determined by single-crystal X-ray diffraction. The newly synthesized 1,2-borolanes are stable in air and showed particularly high activity against some Gram-positive bacteria. © 2020 Elsevier Inc.Article Citation - WoS: 52Citation - Scopus: 581.55 Å-Resolution Structure of Ent-Copalyl Diphosphate Synthase and Exploration of General Acid Function by Site-Directed Mutagenesis(Elsevier, 2014) Köksal, Mustafa; Köksal, Mustafa; Christianson, David W.; Peters, Reuben John; Potter, Kevin; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyBackground The diterpene cyclase ent-copalyl diphosphate synthase (CPS) catalyzes the first committed step in the biosynthesis of gibberellins. The previously reported 2.25 Å resolution crystal structure of CPS complexed with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate (1) established the αβγ domain architecture, but ambiguities regarding substrate analog binding remained. Method Use of crystallization additives yielded CPS crystals diffracting to 1.55 Å resolution. Additionally, active site residues that hydrogen bond with D379, either directly or through hydrogen bonded water molecules, were probed by mutagenesis. Results This work clarifies structure-function relationships that were ambiguous in the lower resolution structure. Well-defined positions for the diphosphate group and tertiary ammonium cation of 1, as well as extensive solvent structure, are observed. Conclusions Two channels involving hydrogen bonded solvent and protein residues lead to the active site, forming hydrogen bonded "proton wires" that link general acid D379 with bulk solvent. These proton wires may facilitate proton transfer with the general acid during catalysis. Activity measurements made with mutant enzymes indicate that N425, which donates a hydrogen bond directly to D379, and T421, which hydrogen bonds with D379 through an intervening solvent molecule, help orient D379 for catalysis. Residues involved in hydrogen bonds with the proton wire, R340 and D503, are also important. Finally, conserved residue E211, which is located near the diphosphate group of 1, is proposed to be a ligand to Mg2 + required for optimal catalytic activity. General significance This work establishes structure-function relationships for class II terpenoid cyclases.Article Citation - WoS: 10Citation - Scopus: 143D Bioprinting of mouse pre-osteoblasts and human MSCs using bioinks consisting of gelatin and decellularized bone particles(Iop Publishing Ltd, 2024) Kara, Aylin; Kara, Aylin; Distler, Thomas; Tıhmınlıoğlu, Funda; Akkineni, Ashwini Rahul; Tihminlioglu, Funda; Gelinsky, Michael; Boccaccini, Aldo R.; 03.02. Department of Chemical Engineering; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyOne of the key challenges in biofabrication applications is to obtain bioinks that provide a balance between printability, shape fidelity, cell viability, and tissue maturation. Decellularization methods allow the extraction of natural extracellular matrix, preserving tissue-specific matrix proteins. However, the critical challenge in bone decellularization is to preserve both organic (collagen, proteoglycans) and inorganic components (hydroxyapatite) to maintain the natural composition and functionality of bone. Besides, there is a need to investigate the effects of decellularized bone (DB) particles as a tissue-based additive in bioink formulation to develop functional bioinks. Here we evaluated the effect of incorporating DB particles of different sizes (<= 45 and <= 100 mu m) and concentrations (1%, 5%, 10% (wt %)) into bioink formulations containing gelatin (GEL) and pre-osteoblasts (MC3T3-E1) or human mesenchymal stem cells (hTERT-MSCs). In addition, we propose a minimalistic bioink formulation using GEL, DB particles and cells with an easy preparation process resulting in a high cell viability. The printability properties of the inks were evaluated. Additionally, rheological properties were determined with shear thinning and thixotropy tests. The bioprinted constructs were cultured for 28 days. The viability, proliferation, and osteogenic differentiation capacity of cells were evaluated using biochemical assays and fluorescence microscopy. The incorporation of DB particles enhanced cell proliferation and osteogenic differentiation capacity which might be due to the natural collagen and hydroxyapatite content of DB particles. Alkaline phosphatase activity is increased significantly by using DB particles, notably, without an osteogenic induction of the cells. Moreover, fluorescence images display pronounced cell-material interaction and cell attachment inside the constructs. With these promising results, the present minimalistic bioink formulation is envisioned as a potential candidate for bone tissue engineering as a clinically translatable material with straightforward preparation and high cell activity.Correction 3D modelling of surface spreading and underground dam groundwater recharge: Egri creek subbasin, Turkey(Springer, 2023) Şahin, Yavuz; Tayfur, Gökmen; Tayfur, Gökmen; 03.03. Department of Civil Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyArticle Citation - WoS: 4Citation - Scopus: 43d Modelling of Surface Spreading and Underground Dam Groundwater Recharge: Egri Creek Subbasin, Turkey(Springer, 2023) Şahin, Yavuz; Tayfur, Gökmen; Tayfur, Gökmen; 03.03. Department of Civil Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThis study investigated surface spreading and underground dam recharge methods to replenish groundwater in Turkey's Egri Creek Sub-basin of the Kucuk Menderes River Basin. A three-dimensional numerical model was employed for this purpose. Field and lab data are provided to the model for realistic simulations. Pumping test results were used to determine the aquifer parameters. The laboratory works involved sieve analysis, permeability tests, and porosity and water content prediction. The numerical model's boundary conditions were determined from the geological and hydrogeological characteristics of the study area. Initial conditions were expressed regarding water content and pressure head in the vadose zone. The numerical model was satisfactorily validated by simulating water levels in three different pumping wells in the study area. Seven different scenarios, each having a different pool size, were investigated for the surface spreading recharge method. The results showed that a pool size of 30 x 30 m with a 6-m depth basin was the most optimal choice, raising the groundwater level to about 29.3 m. On the other hand, it was found that an underground dam could raise the levels by an average of 9.5 m, which might not be significant to warrant the construction.Article Citation - WoS: 47Citation - Scopus: 543d Printed Gelatin/Decellularized Bone Composite Scaffolds for Bone Tissue Engineering: Fabrication, Characterization and Cytocompatibility Study(Elsevier, 2022-06) Kara, Aylin; Tıhmınlıoğlu, Funda; Distler, Thomas; Kara, Aylin; Polley, Christian; Schneidereit, Dominik; Seitz, Hermann; Friedrich, Oliver; Tıhmınlıoğlu, Funda; Boccaccini, Aldo R; 03.02. Department of Chemical Engineering; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThree-dimensional (3D) printing technology enables the design of personalized scaffolds with tunable pore size and composition. Combining decellularization and 3D printing techniques provides the opportunity to fabricate scaffolds with high potential to mimic native tissue. The aim of this study is to produce novel decellularized bone extracellular matrix (dbECM)-reinforced composite-scaffold that can be used as a biomaterial for bone tissue engineering. Decellularized bone particles (dbPTs, ∼100 μm diameter) were obtained from rabbit femur and used as a reinforcement agent by mixing with gelatin (GEL) in different concentrations. 3D scaffolds were fabricated by using an extrusion-based bioprinter and crosslinking with microbial transglutaminase (mTG) enzyme, followed by freeze-drying to obtain porous structures. Fabricated 3D scaffolds were characterized morphologically, mechanically, and chemically. Furthermore, MC3T3-E1 mouse pre-osteoblast cells were seeded on the dbPTs reinforced GEL scaffolds (GEL/dbPTs) and cultured for 21 days to assess cytocompatibility and cell attachment. We demonstrate the 3D-printability of dbPTs-reinforced GEL hydrogels and the achievement of homogenous distribution of the dbPTs in the whole scaffold structure, as well as bioactivity and cytocompatibility of GEL/dbPTs scaffolds. It was shown that Young's modulus and degradation rate of scaffolds were enhanced with increasing dbPTs content. Multiphoton microscopy imaging displayed the interaction of cells with dbPTs, indicating attachment and proliferation of cells around the particles as well as into the GEL-particle hydrogels. Our results demonstrate that GEL/dbPTs hydrogel formulations have potential for bone tissue engineering.Book Part Citation - Scopus: 444 Current Challenges in Mirnomics(Humana Press, 2022) Akgül, Bünyamin; Allmer, Jens; Stadler, Peter F.; Akgül, Bünyamin; Hawkins, Liam J.; Hadj-Moussa, Hanane; Storey, Kenneth B.; Ergin, Kemal; Allmer, Jens; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyMature microRNAs (miRNAs) are short RNA sequences about 18–24 nucleotide long, which provide the recognition key within RISC for the posttranscriptional regulation of target RNAs. Considering the canonical pathway, mature miRNAs are produced via a multistep process. Their transcription (pri-miRNAs) and first processing step via the microprocessor complex (pre-miRNAs) occur in the nucleus. Then they are exported into the cytosol, processed again by Dicer (dsRNA) and finally a single strand (mature miRNA) is incorporated into RISC (miRISC). The sequence of the incorporated miRNA provides the function of RNA target recognition via hybridization. Following binding of the target, the mRNA is either degraded or translation is inhibited, which ultimately leads to less protein production. Conversely, it has been shown that binding within the 5? UTR of the mRNA can lead to an increase in protein product. Regulation of homeostasis is very important for a cell; therefore, all steps in the miRNA-based regulation pathway, from transcription to the incorporation of the mature miRNA into RISC, are under tight control. While much research effort has been exerted in this area, the knowledgebase is not sufficient for accurately modelling miRNA regulation computationally. The computational prediction of miRNAs is, however, necessary because it is not feasible to investigate all possible pairs of a miRNA and its target, let alone miRNAs and their targets. We here point out open challenges important for computational modelling or for our general understanding of miRNA-based regulation and show how their investigation is beneficial. It is our hope that this collection of challenges will lead to their resolution in the near future. © 2022, Springer Science+Business Media, LLC, part of Springer Nature.Article Citation - WoS: 48Citation - Scopus: 485-Fluorouracil Signaling Through a Calcium-Calmodulin Pathway Is Required for P53 Activation and Apoptosis in Colon Carcinoma Cells(Nature Publishing Group, 2013-09) Can, G.; Baran, Yusuf; Akpınar, B.; Baran, Yusuf; Zhivotovsky, B.; Olsson, M.; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology5-Fluorouracil (5-FU) is an anti-metabolite that is in clinical use for treatment of several cancers. In cells, it is converted into three distinct fluoro-based nucleotide analogs, which interfere with DNA synthesis and repair, leading to genome impairment and, eventually, apoptotic cell death. Current knowledge states that in certain cell types, 5-FU-induced stress is signaling through a p53-dependent induction of tumor necrosis factor-receptor oligomerization required for death-inducing signaling complex formation and caspase-8 activation. Here we establish a role of calcium (Ca 2+) as a messenger for p53 activation in response to 5-FU. Using a combination of pharmacological and genetic approaches, we show that treatment of colon carcinoma cells stimulates entry of extracellular Ca 2+ through long lasting-type plasma membrane channels, which further directs posttranslational phosphorylation of at least three p53 serine residues (S15, S33 and S37) by means of calmodulin (CaM) activity. Obstructing this pathway by the Ca 2+ -chelator BAPTA (1,2-bis(o-aminophenoxy)ethane- N,N,N',N'-tetraacetic acid) or by inhibitors of CaM efficiently reduces 5-FU-induced caspase activities and subsequent cell death. Moreover, ectopic expression of p53 S15A in HCT116 p53 -/- cells confirmed the importance of a Ca 2+ -CaM-p53 axis in 5-FU-induced extrinsic apoptosis. The fact that a widely used therapeutic drug, such as 5-FU, is operating via this pathway could provide new therapeutic intervention points, or specify new combinatorial treatment regimes. © 2013 Macmillan Publishers Limited.Article Citation - WoS: 31Citation - Scopus: 346-Bicycloaryl Substituted (s)- and (r)-5,6 Asymmetric Synthesis, and Anti-Proliferative Properties(Elsevier Ltd., 2009-01) Kasaplar, Pınar; Çağır, Ali; Yılmazer, Özgür; Çağır, Ali; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology(R)-Goniothalamin, is a member of styryl lactones, possesses selective cytotoxicity against cancer cell lines. In this work, replacement of styryl substituent with 2-naphthyl and 3-quinoyl gave new analogues which may have less conformational changes compared to the lead compound. Anti-proliferative tests indicated that 2-naphthyl substituted (R)-5,6-dihydro-2H-pyran-2-one has slightly better cytotoxicity than (R)-goniothalamin. To clarify the effect of 2-naphthyl substituent additional aryl substituted (R)-5,6-dihydro-2H-pyran-2-ones have been synthesized enantioselectively and tested against PC-3 and MCF-7 cell lines.Article Citation - WoS: 43Citation - Scopus: 46Aas, Xrpd, Sem/Eds, and Ftir Characterization of Zn2+ Retention by Calcite, Calcite–kaolinite, and Calcite–clinoptilolite Minerals(Elsevier Ltd., 2005-04-08) Shahwan, Talal; Eroğlu, Ahmet Emin; Zünbül, Banu; Shahwan, Talal; Tunusoğlu, Özge; Eroğlu, Ahmet Emin; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn this study, the sorption behavior of Zn2+ on calcite, kaolinite, and clinoptilolite, in addition to mixtures of calcite with kaolinite and clinoptilolite, was investigated at various loadings and mixture compositions using atomic absorption spectroscopy, scanning electron microscopy/energy dispersive X-ray spectroscopy, X-ray powder diffraction, and Fourier transform infrared techniques. According to the obtained results, within the experimental operating conditions, the sorption capacity was enhanced with increasing amount of calcite in both types of mixtures. Under neutral–alkaline pH conditions and high loadings, the order of Zn2+ retention was observed as calcite > clinoptilolite > kaolinite. The experiments on the retention of Zn2+ by pure calcite under conditions of oversaturation showed that the uptake process proceeds via an initial adsorption mechanism (possibly ion-exchange type) followed by a slower mechanism that leads to the overgrowth of the hydrozincite phase, Zn5(OH)6(CO3)2.Article Abnormally Accumulated Gm2 Ganglioside Contributes To Skeletal Deformity in Tay-Sachs Mice(Springer Heidelberg, 2024) Demir, Secil Akyildiz; Seyrantepe, Volkan; Seyrantepe, Volkan; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyTay-Sachs Disease is a rare lysosomal storage disorder caused by mutations in the HEXA gene, responsible for the degradation of ganglioside GM2. In addition to progressive neurodegeneration, Tay-Sachs patients display bone anomalies, including kyphosis. Tay-Sachs disease mouse model (Hexa-/-Neu3-/-) shows both neuropathological and clinical abnormalities of the infantile-onset disease phenotype. In this study, we investigated the effects of GM2 accumulation on bone remodeling activity. Here, we evaluated the bone phenotype of 5-month-old Hexa-/-Neu3-/- mice with age-matched control groups using gene expression analysis, bone plasma biomarker analysis, and micro-computed tomography. We demonstrated lower plasma alkaline phosphatase activity and calcium levels with increased tartrate-resistant acid phosphatase levels, indicating reduced bone remodeling activity in mice. Consistently, gene expression analysis confirmed osteoblast reduction and osteoclast induction in the femur of mice. Micro-computed tomography and analysis show reduced trabecular bone volume, mineral density, number, and thickness in Hexa-/-Neu3-/- mice. In conclusion, we demonstrated that abnormal GM2 ganglioside accumulation significantly triggers skeletal abnormality in Tay-Sachs mice. We suggest that further investigation of the molecular basis of bone structure anomalies is necessary to elucidate new therapeutic targets that prevent the progression of bone symptoms and improve the life standards of Tay-Sachs patients.Article Citation - WoS: 19Citation - Scopus: 22Absence of Superoxide Dismutase Activity Causes Nuclear Dna Fragmentation During the Aging Process(Academic Press Inc., 2014-02) Muid, Khandaker Ashfaqul; Koç, Ahmet; Karakaya, Hüseyin Çaglar; Koç, Ahmet; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologySuperoxide dismutases (SOD) serve as an important antioxidant defense mechanism in aerobic organisms, and deletion of these genes shortens the replicative life span in the budding yeast Saccharomyces cerevisiae. Even though involvement of superoxide dismutase enzymes in ROS scavenging and the aging process has been studied extensively in different organisms, analyses of DNA damages has not been performed for replicatively old superoxide dismutase deficient cells. In this study, we investigated the roles of SOD1, SOD2 and CCS1 genes in preserving genomic integrity in replicatively old yeast cells using the single cell comet assay. We observed that extend of DNA damage was not significantly different among the young cells of wild type, sod1Δ and sod2Δ strains. However, ccs1Δ mutants showed a 60% higher amount of DNA damage in the young stage compared to that of the wild type cells. The aging process increased the DNA damage rates 3-fold in the wild type and more than 5-fold in sod1Δ, sod2Δ, and ccs1Δ mutant cells. Furthermore, ROS levels of these strains showed a similar pattern to their DNA damage contents. Thus, our results confirm that cells accumulate DNA damages during the aging process and reveal that superoxide dismutase enzymes play a substantial role in preserving the genomic integrity in this process.Article Citation - WoS: 93Citation - Scopus: 111The Accelerating Effects of the Microorganisms on Biodeterioration of Stone Monuments Under Air Pollution and Continental-Cold Climatic Conditions in Erzurum, Turkey(Elsevier Ltd., 2006-07) Nuhoğlu, Yaşar; İpekoğlu, Başak; Ensar, Oğuz; Uslu, Hakan; Özbek, Ahmet; İpekoğlu, Başak; Ocak, İjlal; Hasenekoğlu, İsmet; 02.01. Department of Conservation and Restoration of Cultural Heritage; 02. Faculty of Architecture; 01. Izmir Institute of TechnologyThe aim of this research was to determine the accelerating effects of microorganisms on the biodeterioration of stone under air pollution and continental-cold climatic region in Erzurum, Turkey. Studies have been carried out on specimens of the Rustempasa Bazaar, the Lalapasa Mosque, the Erzurum Castle Mosque, the Double Minarets-Madrasah, the Great Mosque and the Haji Mehmet Fountain aged from 441 to 823 years old. The results showed that vegetative and reproductive (generative) forms of the microorganisms could develop during the winter months when the night time average temperature was even - 25 °C. Also the reproductive forms had developed and the whole stone surface was covered with a biofilm caused by the microorganisms. Silicon, aluminum, calcium, potassium, titanium, magnesium, zinc, sulfur, iron, sodium, and niobium were found in the stones of the historical buildings with varying amounts through the SEM-EDS analysis. Some of these elements could be used as an energy resource for the microorganisms together with the air pollutants such as sulfur dioxide, nitrogen oxides and particles on the stone surfaces. Of 21 isolates, 15 species from 6 bacterium genera and 5 species from 5 fungi genera plus 1 fungi genera were identified on the deteriorated stone surfaces even during the coldest months by microbial identification system (MIS) and these findings were tested by SEM investigations.Article Citation - WoS: 34Citation - Scopus: 36Acclimation To Heat During Incubation. 2. Embryo Composition and Residual Egg Yolk Sac Fatty Acid Profiles in Chicks(Elsevier, 2008-06) Yalçın, S.; Uysal, İlke; Bağdatlıoğlu, Neriman; Bruggeman, V.; Babacanoglu, E.; Uysal, İlke; Buyse, J.; Decuypere, E.; Siegel, P. B.; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThe aim of the research was to evaluate embryo composition and changes in egg yolk fatty acid composition during embryonic development as a function of incubation temperature and age of breeders. Eggs obtained from a common breeder stock at 3 ages: 32 (younger), 42 (mid age), and 65 (older) wk were divided into 2 groups and placed into 2 incubators: the control and the second where eggs were heat-acclimated (HA) at 38.5°C for 6 h daily from d 10 to 18 of incubation. Body composition of embryos and chicks were measured on d 14, 18, and at hatch, respectively. Fatty acid profiles of yolk and residual egg yolk sac of chicks were analyzed before incubation and at hatch, respectively. Moisture content of embryos was highest on d 14 and then decreased regardless of parental age and incubation temperature. Moisture content of chicks at hatch from 42- and 65-wk parents were lower than those of chicks from 32-wk parents, whereas the trend in chick fat content was opposite. Incubation temperature had no effect on composition of chicks. Consistently lower cis-4,7,10,13,16,19- eicosapentaenoic (docosahexaenoic acid, DHA; 22:6n-3) and cis-11,14,17- eicosatrienoic (20:3n-3) fatty acids in the residual yolk sac of chicks than in egg yolks before incubation may have resulted from preferential uptake from the yolk. The DHA content in the residual yolk sac was considerably higher in chicks from older parents incubated at HA, whereas, in contrast, levels of 18:3n-3 were lower. Also, chicks from younger parents in the HA treatment had lower transported 18:3n-3 and higher levels of transported DHA. It may be concluded that this process observed during the high incubation temperature may be related to a protective strategy and thus contributes to postnatal heat adaptation.Article Citation - WoS: 4Citation - Scopus: 7Adding Pneumatic Compression Therapy in Lower Extremity Lymphedema Increases Compliance of Treatment, While Decreasing the Infection Rate(Mary Ann Liebert, Inc, 2022) Soran, Atilla; Sezgin, Efe; Toktaş, Osman; Grassi, Ariel; Sezgin, Efe; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyBackground: Lymphedema (LE) is a chronic condition that requires lifelong treatment. Although pneumatic compression therapy (PCT) is one treatment option, current algorithms consider it as an adjunct to standard LE. The purpose of this study is to evaluate the importance of adapting PCT for lower extremity LE (LEL) in relation to patient compliance and rate of infection. Materials and Methods: Patients diagnosed with LEL were followed prospectively. Patient demographics, comorbidities, treatment modality, compliance, infection due to LE, and hospitalization were recorded. LEL patients with no-PCT were also recorded in the same time period to evaluate the treatment compliance and the need for physical therapy visits. The no-PCT group received the standard LE care, whereas the PCT group received the standard LE care plus a new-generation pneumatic compression device. Results: A total of 69 patients were enrolled in this study. The PCT group had 50 patients and no-PCT group had 19 patients. The PCT group had median 58.5 months of LE symptoms, while non-PCT patients had median 23 months of LE symptoms (p = 0.11). Infection rates decreased by 32% and hospitalizations due to infection decreased by 14% after PCT treatment had been initiated. Physical therapy needs decreased by 24% after PCT use. At median 18 months, follow-up compliance for PCT was 84%, but compliance for manual lymphatic drainage was almost half (53%) in no-PCT group. Conclusions: PCT leads to a decrease in infection rate, hospital admissions, and physical therapy (PT) visits in clinically significant LEL. Although there is no cost calculation in this study, it can be correlated to significant cost savings due to a reduction of infection and hospitalization and the need for PT visits. Adoption of PCT offers a superior value proposition to not only patients but also the health care system. Cost analysis should be followed.Article Citation - WoS: 16Citation - Scopus: 21Adhesive Bonding Strategies To Fabricate High-Strength and Transparent 3d Printed Microfluidic Device(American Institute of Physics, 2020) Keçili, Seren; Tekin, Hüseyin Cumhur; Tekin, Hüseyin Cumhur; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyRecently, the use of 3D printing technologies has become prevalent in microfluidic applications. Although these technologies enable low-cost, rapid, and easy fabrication of microfluidic devices, fabricated devices suffer from optical opaqueness that inhibits their use for microscopic imaging. This study investigates bonding strategies using polydimethylsiloxane (PDMS) and printer resin as interlayer materials to fabricate high-strength optically transparent 3D-printed microfluidic devices. First, we fabricated microfluidic structures using a stereolithography 3D printer. We placed 3D-printed structures on interlayer materials coated surfaces. Then, we either let these 3D-printed structures rest on the coated slides or transferred them to new glass slides. We achieved bonding between 3D-printed structures and glass substrates with UV exposure for resin and with elevated temperature for PDMS interlayer materials. Bonding strength was investigated for different interlayer material thicknesses. We also analyzed the bright-field and fluorescence imaging capability of microfluidic devices fabricated using different bonding strategies. We achieve up to twofold (9.1 bar) improved bonding strength and comparable fluorescence sensitivity with respect to microfluidic devices fabricated using the traditional plasma activated PDMS-glass bonding method. Although stereolithography 3D printer allows fabrication of enclosed channels having dimensions down to similar to 600 mu m, monolithic transparent microfluidic channels with 280 x 110 mu m(2) cross section can be realized using adhesive interlayers. Furthermore, 3D-printed microfluidic chips can be integrated successfully with Protein-G modified substrates using resin interlayers for detection of fluorescent-labeled immunoglobulin down to similar to 30 ng/ml. Hence, this strategy can be applied to fabricate high-strength and transparent microfluidic chips for various optical imaging applications including biosensing.Article Citation - WoS: 7Citation - Scopus: 10Adjuvant Potency of Astragaloside Vii Embedded Cholesterol Nanoparticles for H3n2 Influenza Vaccine(TÜBİTAK, 2020) Genç, Rukan; Bedir, Erdal; Yakuboğulları, Nilgün; Yakuboğulları, Nilgün; Nalbantsoy, Ayşe; Coven, Fethiye; Bedir, Erdal; 01.01. Units Affiliated to the Rectorate; 03.01. Department of Bioengineering; 01. Izmir Institute of Technology; 03. Faculty of EngineeringAdjuvants are substances that increase the immune response to a given antigen. In the development of novel vaccine adjuvants/systems, saponins are one of the most attractive molecules due to their altered immunomodulatory activities. In this study, we tried to develop PEG (polyethylene glycol)/cholesterol-based lipid nanoparticles (LNPs) to deliver the Astragaloside VII (AST-VII) and potentiate adjuvant properties of AST-VII for the influenza vaccine. In the formation of PEG/cholesterol/AST-VII-based LNPs (PEG300: Chol-AST-VII LNPs), 3 different primary solvents (acetone, ethanol, and chloroform) were evaluated, employing their effects on hydrodynamic particle size, distribution, surface chemistry, and colloidal stability. Prepared nanoparticles were simply admixtured with inactivated influenza antigen (H3N2) and applied to PMA (phorbol 12-myristate 13-acetate)-ionomycin treated human whole blood to evaluate their cytokine release profile. PEG300: Chol-AST-VII LNPs (80.2 +/- 7.7 nm) were obtained using chloroform as a desolvation agent. Co-treatment of PMA-ionomycin with AST-VII and PEG300: Chol-AST-VII LNPs significantly increased the levels of IL-2 and IFN-gamma, compared to PMA-ionomycin alone. In the presence of H3N2, AST-VII was able to augment IL-17A, while PEG300: Chol-AST-VII LNPs stimulated the production of IFN-gamma. Hemolysis was only observed in PEG300: Chol-AST-VII LNPs (250 mu g/mL) treatment. AST-VII and AST-VII-integrated LNPs could be used as efficacious adjuvants for an inactivated H3N2 vaccine in vitro, and cytokine response through Th1/Th17 route was reported.Article Citation - WoS: 1Citation - Scopus: 1Adsorption and Diffusion Characteristics of Lithium on Hydrogenated ?- and Ss-Silicene(Beilstein-Institut Zur Forderung der Chemischen Wissenschaften, 2017-08) İyikanat, Fadıl; Şahin, Hasan; Kandemir, Ali; Bacaksız, Cihan; Şahin, Hasan; 04.04. Department of Photonics; 04. Faculty of Science; 01. Izmir Institute of TechnologyUsing first-principles density functional theory calculations, we investigate adsorption properties and the diffusion mechanism of a Li atom on hydrogenated single-layer α- and β-silicene on a Ag(111) surface. It is found that a Li atom binds strongly on the surfaces of both α- and β-silicene, and it forms an ionic bond through the transfer of charge from the adsorbed atom to the surface. The binding energies of a Li atom on these surfaces are very similar. However, the diffusion barrier of a Li atom on H-α-Si is much higher than that on H-β-Si. The energy surface calculations show that a Li atom does not prefer to bind in the vicinity of the hydrogenated upper-Si atoms. Strong interaction between Li atoms and hydrogenated silicene phases and low diffusion barriers show that α- and β-silicene are promising platforms for Li-storage applications.Article Citation - WoS: 70Citation - Scopus: 86Adsorption of Olive Leaf (olea Europaea L.) Antioxidants on Silk Fibroin(American Chemical Society, 2007-02) Bayçın, Deniz; Ülkü, Semra; Altıok, Evren; Bayraktar, Oğuz; Ülkü, Semra; Bayraktar, Oğuz; 03.02. Department of Chemical Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThe adsorption isotherms of oleuropein and rutin were evaluated at different temperatures, pH values, and solid/liquid ratios. The experimental data of adsorption isotherms were well fitted to a Langmuir model. The maximum adsorption capacities were determined as 108 mg of oleuropein/g of silk fibroin and 21 mg of rutin/g of silk fibroin. After adsorption of oleuropein and rutin, the antioxidant capacity of silk fibroin increased from 1.93 to 3.61 mmol of TEAC/g. Silk fibroin also gained antimicrobial activity against Staphylococcus aureus and Klebsiella pneumoniae after adsorption of olive leaf antioxidants. In a desorption process, 81% of rutin and 85% of oleuropein were removed from the adsorbent surface in 70% aqueous ethanol solution. Consequently, silk fibroin was found to be a promising biomaterial for the production of functional food or dietary supplements and for the purification of oleuropein and rutin from olive leaf extracts.Article Citation - WoS: 64Citation - Scopus: 81Advanced Backcross Qtl Analysis of a Lycopersicon Esculentum X L. Pennellii Cross and Identification of Possible Orthologs in the Solanaceae(Springer Verlag, 2004-02) Frary, Anne; Frary, Anne; Fulton, Theresa M.; Zamir, Dani; Tanksley, Steven D.; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn this study, the advanced backcross QTL (AB-QTL) mapping strategy was used to identify loci for yield, processing and fruit quality traits in a population derived from the interspecific cross Lycopersicon esculentum E6203 x Lycopersicon pennellii accession LA1657. A total of 175 BC2 plants were genotyped with 150 molecular markers and BC2F1 plots were grown and phenotyped for 25 traits in three locations in Israel and California, U.S.A. A total of 84 different QTLs were identified, 45% of which have been possibly identified in other wild-species-derived populations of tomato. Moreover, three fruit-weight/size and shape QTLs (fs2b.1, fw3.1/fsz3.1 andfs8.1) appear to have putative orthologs in the related solanaceous species, pepper and eggplant. For the 23 traits for which allelic effects could be deemed as favorable or unfavorable, 26% of the identified loci had L. pennellii alleles that enhanced the performance of the elite parent. Alleles that could be targeted for further introgression into cultivated tomato were also identified.
