PubMed İndeksli Yayınlar Koleksiyonu
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Article Achieving Extreme Solubility and Green Solvent-Processed Organic Field-Effect Transistors: A Viable Asymmetric Functionalization of [1]Benzothieno[3,2-B][1]Benzothiophenes(American Chemical Society, 2025) Yıldız, T.A.; Deneme, İ.; Usta, H.; 01. Abdullah Gül University; 10. Rektörlük; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik FakültesiNovel structural engineering strategies for solubilizing high-mobility semiconductors are critical, which enables green solvent processing for eco-friendly, sustainable device fabrication, and unique molecular properties. Here, we introduce a viable asymmetric functionalization approach, synthesizing monocarbonyl [1]benzothieno[3,2-b][1]benzothiophene molecules on a gram scale in two transition-metal-free steps. An unprecedented solubility of up to 176.0 mg·mL–1(at room temperature) is achieved, which is the highest reported to date for a high-performance organic semiconductor. The single-crystal structural analysis reveals a herringbone motif with multiple edge-to-face interactions and nonclassical hydrogen bonds involving the carbonyl unit. The asymmetric backbones adopt an antiparallel arrangement, enabling face-to-face π-π interactions. The mono(alkyl-aryl)carbonyl-BTBT compound, m-C6PhCO-BTBT enables formulations in varied green solvents, including acetone and ethanol, all achieving p-channel top-contact/bottom-gate OFETs in ambient conditions. Charge carrier mobilities of up to 1.87 cm2/V·s (μeff≈ 0.4 cm2/V·s; Ion/Ioff≈ 107–108) were achieved. To the best of our knowledge, this is one of the highest OFET performances achieved using a green solvent. Hansen solubility parameters (HSP) analysis, combined with Scatchard–Hildebrand regular solution theory and single-crystal packing analysis, elucidates this exceptional solubility and reveals unique relationships between molecular structure, interaction energy densities, cohesive energetics, and solute–solvent distances (Ra). An optimal solute–green solvent interaction distance in HSP space proves critical for green solvent-processed thin-film properties. This asymmetric functionalization approach, with demonstrated unique solubility insights, provides a foundation for designing green solvent-processable π-conjugated systems, potentially advancing innovation in sustainable (opto)electronics and bioelectronics. © 2025 Elsevier B.V., All rights reserved.Article Citation - WoS: 23Citation - Scopus: 22The Age Structure, Stringency Policy, Income, and Spread of Coronavirus Disease 2019: Evidence From 209 Countries(Frontiers Media S.A., 2021) Bilgili, Faik; Dundar, Munis; Kuskaya, Sevda; Lorente, Daniel Balsalobre; Unlu, Fatma; Gencoglu, Pelin; Mugaloglu, Erhan; 01. Abdullah Gül UniversityThis article aims at answering the following questions: (1) What is the influence of age structure on the spread of coronavirus disease 2019 (COVID-19)? (2) What can be the impact of stringency policy (policy responses to the coronavirus pandemic) on the spread of COVID-19? (3) What might be the quantitative effect of development levelincome and number of hospital beds on the number of deaths due to the COVID-19 epidemic? By employing the methodologies of generalized linear model, generalized moments method, and quantile regression models, this article reveals that the shares of median age, age 65, and age 70 and older population have significant positive impacts on the spread of COVID-19 and that the share of age 70 and older people in the population has a relatively greater influence on the spread of the pandemic. The second output of this research is the significant impact of stringency policy on diminishing COVID-19 total cases. The third finding of this paper reveals that the number of hospital beds appears to be vital in reducing the total number of COVID-19 deaths, while GDP per capita does not affect much the level of deaths of the COVID-19 pandemic. Finally, this article suggests some governmental health policies to control and decrease the spread of COVID-19.Article Citation - WoS: 35Citation - Scopus: 39AirBNB and COVID-19: Space-Time Vulnerability Effects in Six World-Cities(Elsevier Sci Ltd, 2022) Kourtit, Karima; Nijkamp, Peter; Osth, John; Turk, Umut; 01. Abdullah Gül University; 03.02. Ekonomi; 03. Yönetim Bilimleri FakültesiThis study examines the COVID-19 vulnerability and subsequent market dynamics in the volatile hospitality market worldwide, by focusing in particular on individual Airbnb bookings-data for six world-cities in various continents over the period January 2020-August 2021. This research was done by: (i) looking into factual survival rates of Airbnb accommodations in the period concerned; (ii) examining place-based impacts of intracity location on the economic performance of Airbnb facilities; (iii) estimating the price responses to the pandemic by means of a hedonic price model. In our statistical analyses based on large volumes of time- and space-varying data, multilevel logistic regression models are used to trace `corona survivability footprints' and to estimate a hedonic price-elasticity-of-demand model. The results reveal hardships for the Airbnb market as a whole as well as a high volatility in prices in most cities. Our study highlights the vulnerability and `corona echoeffects' on Airbnb markets for specific accommodation segments in several large cities in the world. It adds to the tourism literature by testing the geographic distributional impacts of the corona pandemic on customers' choices regarding type and intra-urban location of Airbnb accommodations.Article Citation - WoS: 3Citation - Scopus: 3Alantolactone Ameliorates Graft Versus Host Disease in Mice(Elsevier, 2024) Odabas, Gul Pelin; Aslan, Kubra; Suna, Pinar Alisan; Kendirli, Perihan Kader; Erdem, Serife; Cakir, Mustafa; Unal, Ekrem; 01. Abdullah Gül UniversityThe anti-inflammatory and immunosuppressive drugs which are used in the treatment of Graft-versus-Host Disease (GVHD) have limited effects in controlling the severity of the disease. In this study, we aimed to investigate the prophylactic effect of Alantolactone (ALT) in a murine model of experimental GVHD. The study included 4 BALB/c groups as hosts: Naive (n = 7), Control GVHD (n = 16), ALT-GVHD (n = 16), and Syngeneic transplantation (n = 10). Busulfan (20 mg/kg/day) for 4 days followed by cyclophosphamide (100 mg/kg/day) were administered for conditioning. Allogeneic transplantation was performed with cells collected from mismatched female C57BL/6, and GVHD development was monitored by histological and flow cytometric assays. Additionally, liver biopsies were taken from GVHD patient volunteers between ages 2-18 (n = 4) and non-GVHD patients between ages 2-50 (n = 5) and cultured ex vivo with ALT, and the supernatants were used for ELISA. ALT significantly ameliorated histopathological scores of the GVHD and improved GVHD clinical scores. CD8+ T cells were shown to be reduced after ALT treatment. More importantly, ALT treatment skewed T cells to a more naive phenotype (CD62L+ CD44-). ALT did not alter Treg cell number or frequency. ALT treatment appears to suppress myeloid cell lineage (CD11c+). Consistent with reduced myeloid lineage, liver and small intestine levels of GM-CSF were reduced in ALT-treated mice. IL-6 gene expression was significantly reduced in the intestinal tissue. Ex vivo ALT-treated liver biopsy samples from GVHD patients showed a trend of decrease in proinflammatory cytokines but there was no statistical significance. Collectively, the data indicated that ALT may have immunomodulatory actions in a preclinical murine GVHD model.Article Citation - Scopus: 1Alzheimer Disease Associated Loci: APOE Single Nucleotide Polymorphisms in Marmara Region(MDPI, 2024) Ismail, Aya Badeea; Dundar, Mehmet Sait; Erguzeloglu, Cemre Ornek; Ergoren, Mahmut Cerkez; Alemdar, Adem; Sag, Sebnem Ozemri; Temel, Sehime Gulsun; 01. Abdullah Gül UniversityAlzheimer's disease (AD) is a major global health challenge, especially among individuals aged 65 or older. According to population health studies, Turkey has the highest AD prevalence in the Middle East and Europe. To accurately determine the frequencies of common and rare APOE single nucleotide polymorphisms (SNPs) in the Turkish population residing in the Marmara Region, we conducted a retrospective study analyzing APOE variants in 588 individuals referred to the Bursa Uludag University Genetic Diseases Evaluation Center. Molecular genotyping, clinical exome sequencing, bioinformatics analysis, and statistical evaluation were employed to identify APOE polymorphisms and assess their distribution. The study revealed the frequencies of APOE alleles as follows: epsilon 4 at 9.94%, epsilon 2 at 9.18%, and epsilon 3 at 80.68%. The gender-based analysis in our study uncovered a tendency for females to exhibit a higher prevalence of mutant genotypes across various SNPs. The most prevalent haplotype observed was epsilon 3/epsilon 3, while rare APOE SNPs were also identified. These findings align with global observations, underscoring the significance of genetic diversity and gender-specific characteristics in comprehending health disparities and formulating preventive strategies.Article Citation - WoS: 60Analysis of the Best Available Techniques for Wastewaters from a Denim Manufacturing Textile Mill(Academic Press Ltd- Elsevier Science Ltd, 2017) Yukseler, H.; Uzal, N.; Sahinkaya, E.; Kitis, M.; Dilek, F. B.; Yetis, U.; 01. Abdullah Gül University; 02.03. İnşaat Mühendisliği; 02. Mühendislik FakültesiThe present study was undertaken as the first plant scale application and evaluation of Best Available Techniques (BAT) within the context of the Integrated Pollution Prevention and Control/Industrial Emissions Directive to a textile mill in Turkey. A "best practice example" was developed for the textile sector; and within this context, BAT requirements for one of the World's leading denim manufacturing textile mills were determined. In order to achieve a sustainable wastewater management; firstly, a detailed wastewater characterization study was conducted and the possible candidate wastewaters to be reused within the mill were identified. A wastewater management strategy was adopted to investigate the possible reuse opportunities for the dyeing and finishing process wastewaters along with the composite mill effluent. In line with this strategy, production processes were analysed in depth in accordance with the BAT Reference Document not only to treat the generated wastewaters for their possible reuse, but also to reduce the amount of water consumed and wastewater generated. As a result, several applicable BAT options and strategies were determined such as reuse of dyeing wastewaters after treatment, recovery of caustic from alkaline finishing wastewaters, reuse of biologically treated composite mill effluent after membrane processes, minimization of wash water consumption in the water softening plant, reuse of concentrate stream from reverse osmosis plant, reducing water consumption by adoption of counter-current washing in the dyeing and finishing processes. The adoption of the selected in-process BAT options for the minimization of water use provided a 30% reduction in the total specific water consumption of the mill. The treatability studies adopted for both segregated and composite wastewaters indicated that nanofiltration is satisfactory in meeting the reuse criteria for all the wastewater streams considered. (C) 2017 Elsevier Ltd. All rights reserved.Article Citation - WoS: 1Analysis of the in Vitro Nanoparticle-Cell Interactions via a Smoothing-Splines Mixed-Effects Model(Taylor & Francis Ltd, 2016) Dogruoz, Elifnur; Dayanik, Savas; Budak, Gurer; Sabuncuoglu, Ihsan; 01. Abdullah Gül UniversityA mixed-effects statistical model has been developed to understand the nanoparticle (NP)-cell interactions and predict the rate of cellular uptake of NPs. NP-cell interactions are crucial for targeted drug delivery systems, cell-level diagnosis, and cancer treatment. The cellular uptake of NPs depends on the size, charge, chemical structure, and concentration of NPs, and the incubation time. The vast number of combinations of these variable values disallows a comprehensive experimental study of NP-cell interactions. A mathematical model can, however, generalize the findings from a limited number of carefully designed experiments and can be used for the simulation of NP uptake rates, to design, plan, and compare alternative treatment options. We propose a mathematical model based on the data obtained from in vitro interactions of NP-healthy cells, through experiments conducted at the Nanomedicine and Advanced Technologies Research Center in Turkey. The proposed model predicts the cellular uptake rate of silica, polymethyl methacrylate, and polylactic acid NPs, given the incubation time, size, charge and concentration of NPs. This study implements the mixed-model methodology in the field of nanomedicine for the first time, and is the first mathematical model that predicts the rate of cellular uptake of NPs based on sound statistical principles. Our model provides a cost-effective tool for researchers developing targeted drug delivery systems.Article Citation - WoS: 10Citation - Scopus: 11Analyzing the Genetic Diversity and Biotechnological Potential of Leuconostoc Pseudomesenteroides by Comparative Genomics(Frontiers Media S.A., 2023) Gumustop, Ismail; Ortakci, Fatih; 01. Abdullah Gül UniversityLeuconostoc pseudomesenteroides is a lactic acid bacteria species widely exist in fermented dairy foods, cane juice, sourdough, kimchi, apple dumpster, caecum, and human adenoid. In the dairy industry, Ln. pseudomesenteroides strains are usually found in mesophilic starter cultures with lactococci. This species plays a crucial role in the production of aroma compounds such as acetoin, acetaldehyde, and diacetyl, thus beneficially affecting dairy technology. We performed genomic characterization of 38 Ln. pseudomesenteroides from diverse ecological niches to evaluate this species' genetic diversity and biotechnological potential. A mere similar to 12% of genes conserved across 38 Ln. pseudomesenteroides genomes indicate that accessory genes are the driving force for genotypic distinction in this species. Seven main clades were formed with variable content surrounding mobile genetic elements, namely plasmids, transposable elements, IS elements, prophages, and CRISPR-Cas. All but three genomes carried CRISPR-Cas system. Furthermore, a type IIA CRISPR-Cas system was found in 80% of the CRISPR-Cas positive strains. AMBR10, CBA3630, and MGBC116435 were predicted to encode bacteriocins. Genes responsible for citrate metabolism were found in all but five strains belonging to cane juice, sourdough, and unknown origin. On the contrary, arabinose metabolism genes were only available in nine strains isolated from plant-related systems. We found that Ln. pseudomesenteroides genomes show evolutionary adaptation to their ecological environment due to niche-specific carbon metabolism and forming closely related phylogenetic clades based on their isolation source. This species was found to be a reservoir of type IIA CRISPR-Cas system. The outcomes of this study provide a framework for uncovering the biotechnological potential of Ln. pseudomesenteroides and its future development as starter or adjunct culture for dairy industry.Article Citation - WoS: 127Citation - Scopus: 141Analyzing the Nexus Between Energy Transition, Environment and ICT: A Step Towards COP26 Targets(Academic Press Ltd- Elsevier Science Ltd, 2023) Tzeremes, Panayiotis; Dogan, Eyup; Alavijeh, Nooshin Karimi; 01. Abdullah Gül University; 03.02. Ekonomi; 03. Yönetim Bilimleri FakültesiIn line with the Sustainable Development Goals and the recent COP26 summit, energy transition, low carbon emissions and technology have become extremely important subjects in the agenda of governments and poli-cymakers. The present study thus discusses the nexus between energy transition, economic growth, CO2 emis-sions and information and communications technology (ICT) in BRICS countries applying the novel GMM-PVAR method proposed on the annual data for the period 2000-2017. This method is strong to the issue of endogeneity which is commonly faced in the context of panel data analysis but mostly ignored in the literature. The findings of this research demonstrate that carbon emissions have a positive and significant effect on energy transition; similarly, raising economic growth augments the consumption of energy transition. Furthermore, ICT is found to be a significant choice in the development of energy transition and the solution of environmental challenges. Overall, technological factors in addition to economic and environmental factors also have great roles in the development of renewable energy and energy transition. Thus, results from this study call for government supports to develop ICT across the BRICS countries.Article Antifungal Efficacy of 3D-Cultured Palatal Mesenchymal Stem Cells and Their Secreted Factors Against Candida albicans(American Chemical Society, 2025) Bicer, M.; Öztürk, E.; Sener, F.; Hakki, S.S.; Fidan, O.; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik; 01. Abdullah Gül UniversityCandida albicans is among the life-threatening fungal species and the primary contributor to hospital-acquired systemic infections, accounting for nearly 70% of all fungal infections worldwide. The current treatment primarily relies on azoles, pyrimidine analogs, polyenes, and echinocandins. However, growing antifungal resistance highlights the urgent need for the development of alternative treatments against C. albicans. Mesenchymal stem cells (MSCs) offer huge therapeutic potential for the treatment of C. albicans-associated diseases. In this study, palatal adipose tissue-derived MSCs (PAT-MSCs) and PAT-MSCs cultured in 3D biomaterial using nanofibrillar cellulose were tested against C. albicans strains ATCC 10231 and ATCC MYA 2876 using an in vitro antifungal activity assay. In addition, the conditioned medium from both PAT-MSCs and PAT-MSCs cultured in 3D hydrogel biomaterial (CM-PAT-MSCs-3D) were evaluated for their antifungal activities. The combined effect of PAT-MSCs and their secreted factors was also investigated. The expression of five antimicrobial peptide (AMP)-encoding genes was analyzed by quantitative real-time PCR. The expression of antimicrobial peptides was further confirmed via immunocytochemical staining. PAT-MSCs significantly inhibited the growth of C. albicans strains at varying inoculum concentrations (500 and 2000 CFU). Similarly, a comparable antifungal effect was observed when Candida strains were treated with PAT-MSC secreted factors alone. Statistical analysis revealed significant differences between the antifungal activities of PAT-MSCs and CM-PAT-MSCs. Lastly, the combination of PAT-MSCs and CM-PAT-MSC-3D led to a marked reduction in fungal growth, with inhibition rates of 99.75% and 99.91% for C. albicans ATCC 10231 and ATCC MYA-2876, respectively, at 500 CFU inocula. At 2000 CFU inocula, inhibition rates were 99.54% and 99.91%, respectively (****P ≤ 0.0001). These antifungal activities were further confirmed by using RT-PCR and immunocytochemical analysis. Our findings underscore a perspective on the potent antifungal activity of secreted factors from PAT-MSCs cultured within a 3D hydrogel matrix, specifically against various strains of C. albicans. Particularly, the combination of PAT-MSCs with their secreted factors represents a promising therapeutic platform, potentially offering a safer and more effective alternative to conventional antifungal treatments. © 2025 Elsevier B.V., All rights reserved.Article Citation - WoS: 2Citation - Scopus: 2ARL13B Regulates Juxtaposed Cilia-Cilia Elongation in BBSome Dependent Manner in Caenorhabditis Elegans(Cell Press, 2025) Turan, Merve Gul; Kantarci, Hanife; Cevik, Sebiha; Kaplan, Oktay I.; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.02. Moleküler Biyoloji ve Genetik; 04.01. BiyomühendislikThe interaction of cilia with various cellular compartments, such as axons, has emerged as a new form of cellular communication. Cilia often extend in proximity to cilia from neighboring cells. However, the mechanisms driving this process termed juxtaposed cilia-cilia elongation (JCE) remain unclear. We use fluorescence-based visualization to study the mechanisms of coordinated cilia elongation in sensory neurons of Caenorhabditis elegans. Conducting a selective gene-based screening strategy reveals that ARL-13/ARL13B and MKS-5/RPGRIP1L are essential for JCE. We demonstrate that ARL-13 modulates JCE independently of cilia length. Loss of NPHP-2/inversin along with HDAC-6 enhances the cilia misdirection phenotype of arl-13 mutants, while disruption of the BBSome complex, but not microtubule components, partially suppresses the JCE defects in arl-13 mutants. We further show changes in the phospholipid compositions in arl-13 mutants. We suggest that ARL-13 contributes to JCE, in part, through the modulation of the ciliary membrane.Article Citation - WoS: 3Citation - Scopus: 1Arousal State Transitions Occlude Sensory-Evoked Neurovascular Coupling in Neonatal Mice(Nature Portfolio, 2023) Gheres, Kyle W. W.; Unsal, Hayreddin S. S.; Han, Xu; Zhang, Qingguang; Turner, Kevin L. L.; Zhang, Nanyin; Drew, Patrick J. J.; 01. Abdullah Gül UniversityIn the adult sensory cortex, increases in neural activity elicited by sensory stimulation usually drive vasodilation mediated by neurovascular coupling. However, whether neurovascular coupling is the same in neonatal animals as adults is controversial, as both canonical and inverted responses have been observed. We investigated the nature of neurovascular coupling in unanesthetized neonatal mice using optical imaging, electrophysiology, and BOLD fMRI. We find in neonatal (postnatal day 15, P15) mice, sensory stimulation induces a small increase in blood volume/BOLD signal, often followed by a large decrease in blood volume. An examination of arousal state of the mice revealed that neonatal mice were asleep a substantial fraction of the time, and that stimulation caused the animal to awaken. As cortical blood volume is much higher during REM and NREM sleep than the awake state, awakening occludes any sensory-evoked neurovascular coupling. When neonatal mice are stimulated during an awake period, they showed relatively normal (but slowed) neurovascular coupling, showing that that the typically observed constriction is due to arousal state changes. These result show that sleep-related vascular changes dominate over any sensory-evoked changes, and hemodynamic measures need to be considered in the context of arousal state changes. A combination of optical imaging, electrophysiology, and BOLD fMRI in unanesthetized neonatal mice reveals that sleep-related vascular changes dominate over sensory-evoked changes.Article Citation - WoS: 47Citation - Scopus: 42Atomically Precise Gold Nanoclusters at the Molecular-to Transition With Intrinsic Chirality From Surface Layers(Nature Portfolio, 2023) Liu, Li-Juan; Alkan, Fahri; Zhuang, Shengli; Liu, Dongyi; Nawaz, Tehseen; Guo, Jun; He, Jian; 01. Abdullah Gül UniversityChiral metal nanoclusters prepared from achiral ligands generally contain chiral kernel structures. Here, the authors report an alternative type of gold nanoclusters whose intrinsic chirality arises solely from the arrangement of the organic components on their surface. The advances in determining the total structure of atomically precise metal nanoclusters have prompted extensive exploration into the origins of chirality in nanoscale systems. While chirality is generally transferrable from the surface layer to the metal-ligand interface and kernel, we present here an alternative type of gold nanoclusters (138 gold core atoms with 48 2,4-dimethylbenzenethiolate surface ligands) whose inner structures are not asymmetrically induced by chiral patterns of the outermost aromatic substituents. This phenomenon can be explained by the highly dynamic behaviors of aromatic rings in the thiolates assembled via pi - pi stacking and C - H center dot center dot center dot pi interactions. In addition to being a thiolate-protected nanocluster with uncoordinated surface gold atoms, the reported Au-138 motif expands the size range of gold nanoclusters having both molecular and metallic properties. Our current work introduces an important class of nanoclusters with intrinsic chirality from surface layers rather than inner structures and will aid in elucidating the transition of gold nanoclusters from their molecular to metallic states.Article Citation - WoS: 8Citation - Scopus: 7Berberine-Containing Natural-Medicine With Boiled Peanut-Oit Induces Sustained Peanut-Tolerance Associated With Distinct Microbiota Signature(Frontiers Media S.A., 2023) Srivastava, Kamal; Cao, Mingzhuo; Fidan, Ozkan; Shi, Yanmei; Yang, Nan; Nowak-Wegrzyn, Anna; Li, Xiu-Min; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. BiyomühendislikBackgroundGut microbiota influence food allergy. We showed that the natural compound berberine reduces IgE and others reported that BBR alters gut microbiota implying a potential role for microbiota changes in BBR function. ObjectiveWe sought to evaluate an oral Berberine-containing natural medicine with a boiled peanut oral immunotherapy (BNP) regimen as a treatment for food allergy using a murine model and to explore the correlation of treatment-induced changes in gut microbiota with therapeutic outcomes. MethodsPeanut-allergic (PA) mice, orally sensitized with roasted peanut and cholera toxin, received oral BNP or control treatments. PA mice received periodic post-therapy roasted peanut exposures. Anaphylaxis was assessed by visualization of symptoms and measurement of body temperature. Histamine and serum peanut-specific IgE levels were measured by ELISA. Splenic IgE(+)B cells were assessed by flow cytometry. Fecal pellets were used for sequencing of bacterial 16S rDNA by Illumina MiSeq. Sequencing data were analyzed using built-in analysis platforms. ResultsBNP treatment regimen induced long-term tolerance to peanut accompanied by profound and sustained reduction of IgE, symptom scores, plasma histamine, body temperature, and number of IgE(+) B cells (p <0.001 vs Sham for all). Significant differences were observed for Firmicutes/Bacteroidetes ratio across treatment groups. Bacterial genera positively correlated with post-challenge histamine and PN-IgE included Lachnospiraceae, Ruminococcaceae, and Hydrogenanaerobacterium (all Firmicutes) while Verrucromicrobiacea. Caproiciproducens, Enterobacteriaceae, and Bacteroidales were negatively correlated. ConclusionsBNP is a promising regimen for food allergy treatment and its benefits in a murine model are associated with a distinct microbiota signature.Article Citation - WoS: 1Citation - Scopus: 1Biochemical Characterization and Genome Analysis of Pseudomonas Loganensis Sp. Nov., a Novel Endophytic Bacterium(Wiley, 2025) Karaman, Melisa Z.; Yetiman, Ahmet E.; Zhan, Jixun; Fidan, Ozkan; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. BiyomühendislikPseudomonas species are highly adaptable, thriving in diverse environments and exhibiting remarkable genetic and metabolic diversity. While some strains are pathogenic, others have significant ecological and industrial applications. Bioinformatics and biochemical analyses, including antibiotic sensitivity testing, revealed that Pseudomonas loganensis sp. nov. can tolerate NaCl concentrations up to 5% and pH ranges between 5 and 9. Antibiogram results corroborated genome data, demonstrating resistance to vancomycin, ampicillin, methicillin, oxacillin, and penicillin G. Phylogenetic analysis based on 16S rRNA, rpoB, rpoD, and gyrB genes, combined with average nucleotide identity (ANI) comparisons, confirmed P. loganensis sp. nov. as a novel species within the Pseudomonas genus. Genome analysis further revealed the presence of turnerbactin and carotenoid gene clusters. Turnerbactin, known to contribute to nitrogen fixation in plants, highlights the strain's potential as a biofertilizer. Additionally, the carotenoid gene cluster suggests potential applications in industrial carotenoid production. The discovery of a trehalose synthase (treS) gene indicates the capability for one-step conversion of maltose into trehalose, underscoring its potential utility in trehalose production.Editorial Citation - WoS: 28Citation - Scopus: 45Biodiversity, 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; 01. Abdullah Gül UniversityArticle Citation - WoS: 43Citation - Scopus: 44Boronic Acid Moiety as Functional Defect in UiO-66 and Its Effect on Hydrogen Uptake Capacity and Selective Co2 Adsorption: a Comparative Study(Amer Chemical Soc, 2018) Erkartal, Mustafa; Sen, Unal; 01. Abdullah Gül UniversityHerein, we use linker fragmentation approach to introduce boronic acid moieties as functional defects into Zr-based metal organic frameworks (MOFs, UiO-66). Our findings show that the amount of permanently incorporated boronic acid containing ligand is directly dependent on the synthesis method. The accessible boronic acid moieties in the pore surfaces significantly improve the hydrogen uptake values, which are 3.10 and 3.44 wt % at 21 bar, 77 K for dimethylformamide (DMF)/H2O and DMF/HCI synthesis methods, respectively. Also, CO2 selectivity of the resulting MOFs over N-2 and CH4 significantly increases due to the quadrupolar interaction between active surfaces and CO2 molecules. To the best of our knowledge, both hydrogen storage and selectivity of CO2 for UiO-66 are the highest reported values in the literature to date. Furthermore, another striking result that emerged from the high-pressure hydrogen uptake isotherms is the direct correlation between the defects and hysteric adsorption behavior, which may result in the shift from rigidity to flexibility of the framework due to the uncoordinated sites.Article Citation - Scopus: 5Building a Challenging Medical Dataset for Comparative Evaluation of Classifier Capabilities(Elsevier Ltd, 2024) Bozkurt, Berat; Coskun, Kerem; Bakal, Gokhan; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik FakültesiSince the 2000s, digitalization has been a crucial transformation in our lives. Nevertheless, digitalization brings a bulk of unstructured textual data to be processed, including articles, clinical records, web pages, and shared social media posts. As a critical analysis, the classification task classifies the given textual entities into correct categories. Categorizing documents from different domains is straightforward since the instances are unlikely to contain similar contexts. However, document classification in a single domain is more complicated due to sharing the same context. Thus, we aim to classify medical articles about four common cancer types (Leukemia, Non-Hodgkin Lymphoma, Bladder Cancer, and Thyroid Cancer) by constructing machine learning and deep learning models. We used 383,914 medical articles about four common cancer types collected by the PubMed API. To build classification models, we split the dataset into 70% as training, 20% as testing, and 10% as validation. We built widely used machine-learning (Logistic Regression, XGBoost, CatBoost, and Random Forest Classifiers) and modern deep-learning (convolutional neural networks - CNN, long short-term memory - LSTM, and gated recurrent unit - GRU) models. We computed the average classification performances (precision, recall, F-score) to evaluate the models over ten distinct dataset splits. The best-performing deep learning model(s) yielded a superior F1 score of 98%. However, traditional machine learning models also achieved reasonably high F1 scores, 95% for the worst-performing case. Ultimately, we constructed multiple models to classify articles, which compose a hard-to-classify dataset in the medical domain. © 2024 Elsevier B.V., All rights reserved.Article Citation - WoS: 52Citation - Scopus: 54Cadmium-Free and Efficient Type-II InP/ZnO Quantum Dots and Their Application for Leds(Amer Chemical Soc, 2021) Eren, Guncem Ozgun; Sadeghi, Sadra; Jalali, Houman Bahmani; Ritter, Maximilian; Han, Mertcan; Baylam, Isinsu; Nizamoglu, Sedat; 01. Abdullah Gül UniversityIt is a generally accepted perspective that type-II nanocrystal quantum dots (QDs) have low quantum yield due to the separation of the electron and hole wavefunctions. Recently, high quantum yield levels were reported for cadmium-based typeII QDs. Hence, the quest for finding non-toxic and efficient type-II QDs is continuing. Herein, we demonstrate environmentally benign type-II InP/ZnO/ZnS core/shell/shell QDs that reach a high quantum yield of similar to 91%. For this, ZnO layer was grown on core InP QDs by thermal decomposition, which was followed by a ZnS layer via successive ionic layer adsorption. The small-angle Xray scattering shows that spherical InP core and InP/ZnO core/ shell QDs turn into elliptical particles with the growth of the ZnS shell. To conserve the quantum efficiency of QDs in device architectures, InP/ZnO/ZnS QDs were integrated in the liquid state on blue light-emitting diodes (LEDs) as down-converters that led to an external quantum efficiency of 9.4% and a power conversion efficiency of 6.8%, respectively, which is the most efficient QD-LED using type-II QDs. This study pointed out that cadmium-free type-II QDs can reach high efficiency levels, which can stimulate novel forms of devices and nanomaterials for bioimaging, display, and lighting.Article Citation - WoS: 16Citation - Scopus: 17Can Laws Be a Potential PET Image Texture Analysis Approach for Evaluation of Tumor Heterogeneity and Histopathological Characteristics in NSCLC(Springer, 2018) Karacavus, Seyhan; Yilmaz, Bulent; Tasdemir, Arzu; Kayaalti, Omer; Kaya, Eser; Icer, Semra; Ayyildiz, Oguzhan; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik MühendisliğiWe investigated the association between the textural features obtained from F-18-FDG images, metabolic parameters (SUVmax(,) SUVmean, MTV, TLG), and tumor histopathological characteristics (stage and Ki-67 proliferation index) in non-small cell lung cancer (NSCLC). The FDG-PET images of 67 patients with NSCLC were evaluated. MATLAB technical computing language was employed in the extraction of 137 features by using first order statistics (FOS), gray-level co-occurrence matrix (GLCM), gray-level run length matrix (GLRLM), and Laws' texture filters. Textural features and metabolic parameters were statistically analyzed in terms of good discrimination power between tumor stages, and selected features/parameters were used in the automatic classification by k-nearest neighbors (k-NN) and support vector machines (SVM). We showed that one textural feature (gray-level nonuniformity, GLN) obtained using GLRLM approach and nine textural features using Laws' approach were successful in discriminating all tumor stages, unlike metabolic parameters. There were significant correlations between Ki-67 index and some of the textural features computed using Laws' method (r = 0.6, p = 0.013). In terms of automatic classification of tumor stage, the accuracy was approximately 84% with k-NN classifier (k = 3) and SVM, using selected five features. Texture analysis of FDG-PET images has a potential to be an objective tool to assess tumor histopathological characteristics. The textural features obtained using Laws' approach could be useful in the discrimination of tumor stage.
