PubMed İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397

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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.
Citation - WoS: 12
Citation - Scopus: 14
4D-QSAR Investigation and Pharmacophore Identification of Pyrrolo[2,1-C][1,4]Benzodiazepines Using Electron Conformational-Genetic Algorithm Method
(Taylor & Francis Ltd, 2016) Ozalp, A.; Yavuz, S. C.; Sabanci, N.; Copur, F.; Kokbudak, Z.; Saripinar, E.; 01. Abdullah Gül University
In this paper, we present the results of pharmacophore identification and bioactivity prediction for pyrrolo[2,1-c][1,4]benzodiazepine derivatives using the electron conformational-genetic algorithm (EC-GA) method as 4D-QSAR analysis. Using the data obtained from quantum chemical calculations at PM3/HF level, the electron conformational matrices of congruity (ECMC) were constructed by EMRE software. The ECMC of the lowest energy conformer of the compound with the highest activity was chosen as the template and compared with the ECMCs of the lowest energy conformer of the other compounds within given tolerances to reveal the electron conformational submatrix of activity (ECSA, i.e. pharmacophore) by ECSP software. A descriptor pool was generated taking into account the obtained pharmacophore. To predict the theoretical activity and select the best subset of variables affecting bioactivities, the nonlinear least square regression method and genetic algorithm were performed. For four types of activity including the GI(50), TGI, LC50 and IC50 of the pyrrolo[2,1-c][1,4] benzodiazepine series, the r(train)(2), r(test)(2) and q(2) values were 0.858, 0.810, 0.771; 0.853, 0.848, 0.787; 0.703, 0.787, 0.600; and 0.776, 0.722, 0.687, respectively.
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 - Scopus: 1
Alzheimer 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 University
Alzheimer'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.
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: 4
Citation - Scopus: 5
Analysis of Coronary Angiography Related Psychophysiological Responses
(BMC, 2011) Okkesim, Sukru; Kara, Sadik; Kaya, Mehmet G.; Asyali, Musa H.; 01. Abdullah Gül University
Background: Coronary angiography is an important tool in diagnosis of cardiovascular diseases. However, it is the administration is relatively stressful and emotionally traumatic for the subjects. The aim of this study is to evaluate psychophysiological responses induced by the coronary angiography instead of subjective methods such as a questionnaire. We have also evaluated the influence of the tranquilizer on the psychophysiological responses. Methods: Electrocardiography (ECG), Blood Volume Pulse (BVP), and Galvanic Skin Response (GSR) of 34 patients who underwent coronary angiography operation were recorded. Recordings were done at three phases: "1 hour before," "during," and "1 hour after" the coronary angiography test. Total of 5 features obtained from the physiological signals were compared across these three phases. Sixteen of the patients were administered 5 mg of a tranquilizer (Diazepam) before the operation and remaining 18 were not. Results: Our results indicate that there is a strong correlation between features (LF/HF, Bk, DN1/DN2, skin conductance level and seg_mean) in terms of reflecting psychophysiological responses. However only DN1/DN2 feature has statistically significant differences between angiography phases (for diazepam: p = 0.0201, for non_diazepam p = 0.0224). We also note that there are statistically significant differences between the diazepam and non-diazepam groups for seg_mean features in "before", "during" and "after" phases (p = 0.0156, 0.0282, and 0.0443, respectively). Conclusions: The most intense sympathetic activity is observed in the "during" angiography phase for both of the groups. The obtained features can be used in some clinical studies where generation of the customized/individual diagnoses styles and quantitative evaluation of psychophysiological responses is necessary.
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: 10
Citation - Scopus: 11
Analyzing the Genetic Diversity and Biotechnological Potential of Leuconostoc Pseudomesenteroides by Comparative Genomics
(Frontiers Media S.A., 2023) Gumustop, Ismail; Ortakci, Fatih; 01. Abdullah Gül University
Leuconostoc 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.
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.
Citation - WoS: 6
Citation - Scopus: 8
Anhedonia in Relation to Reward and Effort Learning in Young People With Depression Symptoms
(MDPI, 2023) Frey, Anna-Lena; Kaya, M. Siyabend; Adeniyi, Irina; McCabe, Ciara; 01. Abdullah Gül University; 06. İnsan ve Toplum Bilimleri Fakültesi; 06.02. Psikoloji
Anhedonia, a central depression symptom, is associated with impairments in reward processing. However, it is not well understood which sub-components of reward processing (anticipation, motivation, consummation, and learning) are impaired in association with anhedonia in depression. In particular, it is unclear how learning about different rewards and the effort needed to obtain them might be associated with anhedonia and depression symptoms. Therefore, we examined learning in young people (N = 132, mean age 20, range 17-25 yrs.) with a range of depression and anhedonia symptoms using a probabilistic instrumental learning task. The task required participants to learn which options to choose to maximize their reward outcomes across three conditions (chocolate taste, puppy images, or money) and to minimize the physical effort required to obtain the rewards. Additionally, we collected questionnaire measures of anticipatory and consummatory anhedonia, as well as subjective reports of "liking", "wanting" and "willingness to exert effort" for the rewards used in the task. We found that as anticipatory anhedonia increased, subjective liking and wanting of rewards decreased. Moreover, higher anticipatory anhedonia was significantly associated with lower reward learning accuracy, and participants demonstrated significantly higher reward learning than effort learning accuracy. To our knowledge, this is the first study observing an association of anhedonia with reward liking, wanting, and learning when reward and effort learning are measured simultaneously. Our findings suggest an impaired ability to learn from rewarding outcomes could contribute to anhedonia in young people. Future longitudinal research is needed to confirm this and reveal the specific aspects of reward learning that predict anhedonia. These aspects could then be targeted by novel anhedonia interventions.
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: 20
Citation - Scopus: 23
Apoptotic Effects of Non-Edible Parts of Punica Granatum on Human Multiple Myeloma Cells
(Sage Publications Ltd, 2016) Kiraz, Yagmur; Neergheen-Bhujun, Vidushi S.; Rummun, Nawraj; Baran, Yusuf; 01. Abdullah Gül University
Multiple myeloma is of great concern since existing therapies are unable to cure this clinical condition. Alternative therapeutic approaches are mandatory, and the use of plant extracts is considered interesting. Punica granatum and its derived products were suggested as potential anticancer agents due to the presence of bioactive compounds. Thus, polypenolic-rich extracts of the non-edible parts of P. granatum were investigated for their antiproliferative and apoptotic effects on U266 multiple myeloma cells. We demonstrated that there were dose-dependent decreases in the proliferation of U266 cells in response to P. granatum extracts. Also, exposure to the extracts triggered apoptosis with significant increases in loss of mitochondrial membrane potential in U266 cells exposed to the leaves and stem extracts, while the flower extract resulted in slight increases in loss of MMP. These results were confirmed by Annexin-V analysis. These results documented the cytotoxic and apoptotic effects of P. granatum extracts on human U266 multiple myeloma cells via disruption of mitochondrial membrane potential and increasing cell cycle arrest. The data suggest that the extracts can be envisaged in cancer chemoprevention and call for further exploration into the potential application of these plant parts.
Citation - WoS: 50
Citation - Scopus: 62
Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data
(MDPI, 2021) Yousef, Malik; Kumar, Abhishek; Bakir-Gungor, Burcu; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
In the last two decades, there have been massive advancements in high throughput technologies, which resulted in the exponential growth of public repositories of gene expression datasets for various phenotypes. It is possible to unravel biomarkers by comparing the gene expression levels under different conditions, such as disease vs. control, treated vs. not treated, drug A vs. drug B, etc. This problem refers to a well-studied problem in the machine learning domain, i.e., the feature selection problem. In biological data analysis, most of the computational feature selection methodologies were taken from other fields, without considering the nature of the biological data. Thus, integrative approaches that utilize the biological knowledge while performing feature selection are necessary for this kind of data. The main idea behind the integrative gene selection process is to generate a ranked list of genes considering both the statistical metrics that are applied to the gene expression data, and the biological background information which is provided as external datasets. One of the main goals of this review is to explore the existing methods that integrate different types of information in order to improve the identification of the biomolecular signatures of diseases and the discovery of new potential targets for treatment. These integrative approaches are expected to aid the prediction, diagnosis, and treatment of diseases, as well as to enlighten us on disease state dynamics, mechanisms of their onset and progression. The integration of various types of biological information will necessitate the development of novel techniques for integration and data analysis. Another aim of this review is to boost the bioinformatics community to develop new approaches for searching and determining significant groups/clusters of features based on one or more biological grouping functions.
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: 7
Citation - Scopus: 7
Assessment of Bohme Abrasion Value of Natural Stones Through Artificial Neural Networks (ANN)
(MDPI, 2022) Strzalkowski, Pawel; Koken, Ekin; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
This present study explored the Bohme abrasion value (BAV) of natural stones through artificial neural networks (ANNs). For this purpose, a detailed literature survey was conducted to collect quantitative data on the BAV of different natural stones from Turkey. As a result of the ANN analyses, several predictive models (M1-M13) were established by using the rock properties, such as the dry density (rho(d)), water absorption by weight (w(a)), Shore hardness value (SHV), pulse wave velocity (V-p), and uniaxial compressive strength (UCS) of rocks. The performance of the established predictive models was evaluated by using several statistical indicators, and the performance analyses indicated that four of the established models (M1, M5, M10, and M11) could be reliably used to estimate the BAV of natural stones. In addition, explicit mathematical formulations of the proposed ANN models were also introduced in this study to let users implement them more efficiently. In this context, the present study is believed to provide practical and straightforward information on the BAV of natural stones and can be declared a case study on how to model the BAV as a function of different rock properties.

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