PubMed İndeksli Yayınlar Koleksiyonu

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3Mont: A Multi-Omics Integrative Tool for Breast Cancer Subtype Stratification
(Public Library Science, 2025) Unlu Yazici, Miray; Marron, J. S.; Bakir-Gungor, Burcu; Zou, Fei; Yousef, Malik; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
Breast Cancer (BRCA) is a heterogeneous disease, and it is one of the most prevalent cancer types among women. Developing effective treatment strategies that address diverse types of BRCA is crucial. Notably, among different BRCA molecular sub-types, Hormone Receptor negative (HR-) BRCA cases, especially Basal-like BRCA sub-types, lack estrogen and progesterone hormone receptors and they exhibit a higher tumor growth rate compared to HR+ cases. Improving survival time and predicting prognosis for distinct molecular profiles is substantial. In this study, we propose a novel approach called 3-Multi-Omics Network and Integration Tool (3Mont), which integrates various -omics data by applying a grouping function, detecting pro-groups, and assigning scores to each pro-group using Feature importance scoring (FIS) component. Following that, machine learning (ML) models are constructed based on the prominent pro-groups, which enable the extraction of promising biomarkers for distinguishing BRCA sub-types. Our tool allows users to analyze the collective behavior of features in each pro-group (biological groups) utilizing ML algorithms. In addition, by constructing the pro-groups and equalizing the feature numbers in each pro-group using the FIS component, this process achieves a significant 20% speedup over the 3Mint tool. Contrary to conventional methods, 3Mont generates networks that illustrate the interplay of the prominent biomarkers of different -omics data. Accordingly, exploring the concerted actions of features in pro-groups facilitates understanding the dynamics of the biomarkers within the generated networks and developing effective strategies for better cancer sub-type stratification. The 3Mont tool, along with all supporting materials, can be found at https://github.com/malikyousef/3Mont.git.
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 Fakültesi
Novel 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.
Citation - WoS: 23
Citation - Scopus: 22
The 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 University
This 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.
Aguhyper: A Hyperledger-Based Electronic Health Record Management Framework
(PeerJ Inc, 2024) Dedeturk, Beyhan Adanur; Bakir-Gungor, Burcu; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
The increasing importance of healthcare records, particularly given the emergence of new diseases, emphasizes the need for secure electronic storage and dissemination. With these records dispersed across diverse healthcare entities, their physical maintenance proves to be excessively time-consuming. The prevalent management of electronic healthcare records (EHRs) presents inherent security vulnerabilities, including susceptibility to attacks and potential breaches orchestrated by malicious actors. To tackle these challenges, this article introduces AguHyper, a secure storage and sharing solution for EHRs built on a permissioned blockchain framework. AguHyper utilizes Hyperledger Fabric and the InterPlanetary Distributed File System (IPFS). Hyperledger Fabric establishes the blockchain network, while IPFS manages the off -chain storage of encrypted data, with hash values securely stored within the blockchain. Focusing on security, privacy, scalability, and data integrity, AguHyper ' s decentralized architecture eliminates single points of failure and ensures transparency for all network participants. The study develops a prototype to address gaps identi fi ed in prior research, providing insights into blockchain technology applications in healthcare. Detailed analyses of system architecture, AguHyper ' s implementation con fi gurations, and performance assessments with diverse datasets are provided. The experimental setup incorporates CouchDB and the Raft consensus mechanism, enabling a thorough comparison of system performance against existing studies in terms of throughput and latency. This contributes signi fi cantly to a comprehensive evaluation of the proposed solution and offers a unique perspective on existing literature in the fi eld.
Citation - WoS: 35
Citation - Scopus: 39
AirBNB 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 Fakültesi
This 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.
Citation - WoS: 110
Citation - Scopus: 114
Analysis of CO2 Emissions and Energy Consumption by Sources in MENA Countries: Evidence From Quantile Regressions
(Springer Heidelberg, 2021) Alharthi, Majed; Dogan, Eyup; Taskin, Dilvin; 01. Abdullah Gül University; 03.02. Ekonomi; 03. Yönetim Bilimleri Fakültesi
The development of economies and energy usage can significantly impact the carbon dioxide (CO2) emissions in the Middle East and North Africa (MENA) countries. Therefore, this study aims to analyze the factors that determine CO2 emissions in MENA under the environmental Kuznets curve (EKC) framework by applying novel quantile techniques on data for CO2 emissions, real income, renewable and non-renewable energy consumption, and urbanization over the period from 1990 to 2015. The results from the estimations suggest that renewable energy consumption significantly reduces the level of emissions; furthermore, its impact increases with higher quantiles. In addition, non-renewable energy consumption increases CO2 emissions, while its magnitude decreases with higher quantiles. The empirical results also confirm the validity of EKC hypothesis for the panel of MENA economies. Policymakers in the region should implement policies and regulations to promote the adoption and use of renewable energy to mitigate carbon emissions.
Citation - WoS: 60
Analysis 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 Fakültesi
The 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.
Citation - WoS: 1
Analysis 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 University
A 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.
Citation - WoS: 389
Citation - Scopus: 417
Analyzing the Environmental Kuznets Curve for the EU Countries: The Role of Ecological Footprint
(Springer Heidelberg, 2018) Destek, Mehmet Akif; Ulucak, Recep; Dogan, Eyup; 01. Abdullah Gül University; 03.02. Ekonomi; 03. Yönetim Bilimleri Fakültesi
A great majority of the environmental Kuznets curve (EKC) literature use CO2 emissions to proxy for environmental degradation. However, this is an important shortage in application of the EKC concept because environmental degradation cannot be captured by CO2 emissions only. By using a broader proxy, ecological footprint, this study aims to investigate the presence of environmental Kuznets curve hypothesis for the EU countries. The annual data from 1980 to 2013 is examined with second generation panel data methodologies which take into account the cross-sectional dependence among countries. The results show that there is U-shaped relationship between the real income and ecological footprint. In addition, non-renewable energy increases the environmental degradation while renewable energy and trade openness decrease the environmental degradation in the EU countries. Policy implications are further discussed.
Citation - WoS: 127
Citation - Scopus: 141
Analyzing 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 Fakültesi
In 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.
Citation - Scopus: 19
Analyzing the Nexus Between Environmental Sustainability and Clean Energy for the USA
(Springer, 2024) Dogan, Eyup; Si Mohammed, Kamel; Khan, Zeeshan Anis; BinSaeed, Rima Hassan; 01. Abdullah Gül University; 03.02. Ekonomi; 03. Yönetim Bilimleri Fakültesi
Environmental sustainability is a key target to achieve sustainable development goals (SDGs). However, achieving these targets needs tools to pave the way for achieving SDGs and COP28 targets. Therefore, the primary objective of the present study is to examine the significance of clean energy, research and development spending, technological innovation, income, and human capital in achieving environmental sustainability in the USA from 1990 to 2022. The study employed time series econometric methods to estimate the empirical results. The study confirmed the long-run cointegrating relationship among CO2 emissions, human capital, income, R&D, technological innovation, and clean energy. The results are statistically significant in the short run except for R&D expenditures. In the long run, the study found that income and human capital contribute to further aggravating the environment via increasing CO2 emissions. However, R&D expenditures, technological innovation, and clean energy help to promote environmental sustainability by limiting carbon emissions. The study recommends investment in technological innovation, clean energy, and increasing R&D expenditures to achieve environmental sustainability in the USA. © 2024 Elsevier B.V., All rights reserved.
Citation - WoS: 38
Citation - Scopus: 36
Analyzing the Nexus of COVID-19 and Natural Resources and Commodities: Evidence From Time-Varying Causality
(Elsevier Sci Ltd, 2022) Dogan, Eyup; Majeed, Muhammad Tariq; Luni, Tania; 01. Abdullah Gül University; 03.02. Ekonomi; 03. Yönetim Bilimleri Fakültesi
Even though a few studies have focused on natural resources and commodity sectors by considering the pandemic, they have only compared their status in pre-COVID19 to post-COVID19. None of the studies has directly examined the causal relationship between the pandemic, and natural resource index and the primary commodity-related sector indices. This study fills the gap of exploring the dynamic association between them by analyzing the causal relationship between the COVID19, and natural resources index and the primary commodity-related sectors (i.e., agribusiness, energy, and metals & mining) by applying a novel time-varying causality test on daily data from January 23, 2020, to November 12, 2021. The empirical results support the presence of time-varying causality from COVID19 to natural resources, agribusiness, energy and metals & mining. The results obtained from the rolling window algorithm support causal linkages between the variables however at several points it fails to capture the dynamics of linkages between the variables which is captured by the recursive window algorithm. The outcome is robust when the pandemic is proxied by either number of cases or deaths. Similarly, the findings obtained from heteroskedastic-robust specification also validate our findings. Several policy implications are further discussed in the study.
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 University
Candida 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.
Citation - WoS: 2
Citation - Scopus: 2
ARL13B 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. Biyomühendislik
The 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.
Citation - WoS: 3
Citation - Scopus: 1
Arousal 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 University
In 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.
Citation - WoS: 47
Citation - Scopus: 42
Atomically 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 University
Chiral 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.
Citation - WoS: 8
Citation - Scopus: 7
Berberine-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. Biyomühendislik
BackgroundGut 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.
Citation - WoS: 33
Citation - Scopus: 40
Big Data Acquired by Internet of Things-Enabled Industrial Multichannel Wireless Sensors Networks for Active Monitoring and Control in the Smart Grid Industry 4.0
(Elsevier, 2021) Faheem, Muhammad; Fizza, Ghulam; Ashraf, Muhammad Waqar; Butt, Rizwan Aslam; Ngadi, Md. Asri; Gungor, Vehbi Cagri; 01. Abdullah Gül University
Smart Grid Industry 4.0 (SGI4.0) defines a new paradigm to provide high-quality electricity at a low cost by reacting quickly and effectively to changing energy demands in the highly volatile global markets. However, in SGI4.0, the reliable and efficient gathering and transmission of the observed information from the Internet of Things (IoT)-enabled Cyberphysical systems, such as sensors located in remote places to the control center is the biggest challenge for the Industrial Multichannel Wireless Sensors Networks (IMWSNs). This is due to the harsh nature of the smart grid environment that causes high noise, signal fading, multipath effects, heat, and electromagnetic interference, which reduces the transmission quality and trigger errors in the IMWSNs. Thus, an efficient monitoring and real-time control of unexpected changes in the power generation and distribution processes is essential to guarantee the quality of service (QoS) re-quirements in the smart grid. In this context, this paper de-scribes the dataset contains measurements acquired by the IMWSNs during events monitoring and control in the smart grid. This work provides an updated detail comparison of our proposed work, including channel detection, channel assign-ment, and packets forwarding algorithms, collectively called CARP [1] with existing G-RPL [2] and EQSHC [3] schemes in the smart grid. The experimental outcomes show that the dataset and is useful for the design, development, testing, and validation of algorithms for real-time events monitoring and control applications in the smart grid. (C) 2021 The Authors. Published by Elsevier Inc.
Citation - WoS: 25
Citation - Scopus: 33
Big Datasets of Optical-Wireless Cyber-Physical Systems for Optimizing Manufacturing Services in the Internet of Things-Enabled Industry 4.0
(Elsevier, 2022) Faheem, Muhammad; Butt, Rizwan Aslam; 01. Abdullah Gül University
The Industry 4.0 revolution is aimed to optimize the product design according to the customers' demand, quality requirements and economic feasibility. Industry 4.0 employs advanced two-way communication technologies for optimizing the manufacturing process to increase the sales of the products and revenues to cope the existing global economy issues. In Industry 4.0, big data obtained from the Internet of Things (IoT)-enabled industrial Cyber-Physical Systems (CPS) plays an important role in enhancing the system service performance to boost the productivity with enhanced quality of customer experience. This paper presents the big datasets obtained from the Internet of things (IoT)-enabled Optical Wireless Sensor Networks (OWSNs) for optimizing service systems' performance in the electronics manufacturing Industry 4.0. The updated raw and analyzed big datasets of our published work [3] contain five values namely, data delivery, latency, congestion, throughput, and packet error rate in OWSNs. The obtained dataset are useful for optimizing the service system performance in the electronics manufacturing Industry 4.0. (c) 2022 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)
Citation - WoS: 1
Citation - Scopus: 1
Biochemical 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. Biyomühendislik
Pseudomonas 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.

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