Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Role of Long Non-Coding RNA X-Inactive Transcript (XIST) in Neuroinflammation and Myelination: Insights From Cerebral Organoids and Implications for Multiple Sclerosis(MDPI, 2025) Pepe, Nihan Aktas; Acar, Busra; Zararsiz, Gozde Erturk; Guner, Serife Ayaz; Sen, AlaattinBackground/Objectives: X-inactive-specific transcript (XIST) is a factor that plays a role in neuroinflammation. This study investigated the role of XIST in neuronal development, neuroinflammation, myelination, and therapeutic responses within cerebral organoids in the context of Multiple Sclerosis (MS) pathogenesis. Methods: Human cerebral organoids with oligodendrocytes were produced from XIST-silenced H9 cells, and the mature organoids were subsequently treated with either FTY720 or DMF. Gene expression related to inflammation and myelination was subsequently analyzed via qRT-PCR. Immunofluorescence staining was used to assess the expression of proteins related to inflammation, myelination, and neuronal differentiation. Alpha-synuclein protein levels were also checked via ELISA. Finally, transcriptome analysis was conducted on the organoid samples. Results: XIST-silenced organoids presented a 2-fold increase in the expression of neuronal stem cells, excitatory neurons, microglia, and mature oligodendrocyte markers. In addition, XIST silencing increased IL-10 mRNA expression by 2-fold and MBP and PLP1 expression by 2.3- and 0.6-fold, respectively. Although XIST silencing tripled IBA1 protein expression, it did not affect organoid MBP expression. FTY720, but not DMF, distinguished MBP and IBA1 expression in XIST-silenced organoids. Furthermore, XIST silencing reduced the concentration of alpha-synuclein from 300 to 100 pg/mL, confirming its anti-inflammatory role. Transcriptomic and gene enrichment analyses revealed that the differentially expressed genes are involved in neural development and immune processes, suggesting the role of XIST in neuroinflammation. The silencing of XIST modified the expression of genes associated with inflammation, myelination, and neuronal growth in cerebral organoids, indicating a potential involvement in the pathogenesis of MS. Conclusions: XIST may contribute to the MS pathogenesis as well as neuroinflammatory diseases such as and Alzheimer's and Parkinson's diseases and may be a promising therapeutic target.Article Citation - WoS: 5Citation - Scopus: 6A Comparative Study of Metaheuristic Feature Selection Algorithms for Respiratory Disease Classification(MDPI, 2024) Gürkan Kuntalp, D.; Özcan, N.; Düzyel, Okan; Kababulut, F.Y.; Kuntalp, M.The correct diagnosis and early treatment of respiratory diseases can significantly improve the health status of patients, reduce healthcare expenses, and enhance quality of life. Therefore, there has been extensive interest in developing automatic respiratory disease detection systems. Most recent methods for detecting respiratory disease use machine and deep learning algorithms. The success of these machine learning methods depends heavily on the selection of proper features to be used in the classifier. Although metaheuristic-based feature selection methods have been successful in addressing difficulties presented by high-dimensional medical data in various biomedical classification tasks, there is not much research on the utilization of metaheuristic methods in respiratory disease classification. This paper aims to conduct a detailed and comparative analysis of six widely used metaheuristic optimization methods using eight different transfer functions in respiratory disease classification. For this purpose, two different classification cases were examined: binary and multi-class. The findings demonstrate that metaheuristic algorithms using correct transfer functions could effectively reduce data dimensionality while enhancing classification accuracy. © 2024 by the authors.Review Citation - WoS: 19Citation - Scopus: 22Water Dams: From Ancient To Present Times and Into the Future(MDPI, 2024) Angelakis, Andreas N.; Baba, Alper; Valipour, Mohammad; Dietrich, Jorg; Fallah-Mehdipour, Elahe; Krasilnikoff, Jens; Ahmed, Abdelkader T.Since ancient times, dams have been built to store water, control rivers, and irrigate agricultural land to meet human needs. By the end of the 19th century, hydroelectric power stations arose and extended the purposes of dams. Today, dams can be seen as part of the renewable energy supply infrastructure. The word dam comes from French and is defined in dictionaries using words like strange, dike, and obstacle. In other words, a dam is a structure that stores water and directs it to the desired location, with a dam being built in front of river valleys. Dams built on rivers serve various purposes such as the supply of drinking water, agricultural irrigation, flood control, the supply of industrial water, power generation, recreation, the movement control of solids, and fisheries. Dams can also be built in a catchment area to capture and store the rainwater in arid and semi-arid areas. Dams can be built from concrete or natural materials such as earth and rock. There are various types of dams: embankment dams (earth-fill dams, rock-fill dams, and rock-fill dams with concrete faces) and rigid dams (gravity dams, rolled compacted concrete dams, arch dams, and buttress dams). A gravity dam is a straight wall of stone masonry or earthen material that can withstand the full force of the water pressure. In other words, the pressure of the water transfers the vertical compressive forces and horizontal shear forces to the foundations beneath the dam. The strength of a gravity dam ultimately depends on its weight and the strength of its foundations. Most dams built in ancient times were constructed as gravity dams. An arch dam, on the other hand, has a convex curved surface that faces the water. The forces generated by the water pressure are transferred to the sides of the structure by horizontal lines. The horizontal, normal, and shear forces resist the weight at the edges. When viewed in a horizontal section, an arch dam has a curved shape. This type of dam can also resist water pressure due to its particular shape that allows the transfer of the forces generated by the stored water to the rock foundations. This article takes a detailed look at hydraulic engineering in dams over the millennia. Lessons should be learned from the successful and unsuccessful applications and operations of dams. Water resource managers, policymakers, and stakeholders can use these lessons to achieve sustainable development goals in times of climate change and water crisis.Article An Analysis of Visitors’ Perceptions of Shopping Malls †(MDPI, 2023) Çavka, Hasan BurakShopping malls have been a significant part of our daily lives for decades. Their significance is derived from the use of these spaces based on great numbers of people, as well as the role malls play in culture. On the other hand, the design of malls has been constantly evolving according to the needs of users and the market. This study is based on survey data that we collected from ninety visitors of a shopping mall located in Izmir, Turkiye. Through the survey, we collected data on topics such as the participants’ visit frequency and reasons for visiting the mall, architectural and spatial features they favor and/or dislike, their opinions on where they perceive malls in everyday life, and their opinions on alternative spaces to malls. The data collection was finalized right before the pandemic, which significantly changed the way we think about public spaces, as well as malls, in relation to architecture. Analyzing collected data provides further insight into surveyed customers’ perception of spaces, the design of shopping malls, the use of the space, the preferred design features, as well as design features that drive customers away from the mall. The analysis was later compared and linked to studies in the literature. These research findings have the potential to be used in studies that evaluate mall design and space use, as well as in studies that compare the post-pandemic perception of spaces and the use of shopping malls. © 2023 by the author.Article Iron-Promoted 1,5-Substitution Reaction of Endocyclic Enyne Oxiranes With Memgbr: a Stereoselective Method for the Synthesis of Exocyclic 2,4,5-Trienol Derivatives(MDPI, 2023) Kuş, Melih; Omur, Cenk; Karaca, Sila; Artok, LeventThe iron-promoted 1,5-substitution reaction of endocyclic oxiranes with MeMgBr yields exocyclic 2,4,5-trienols with high diastereomeric ratios of up to 100:0. However, for the method's success, the oxirane ring must have a trans-configuration. The reactions exhibit strong stereoselectivity concerning the methylation mode and the configuration of the resulting exocyclic double bond. Enantiomerically pure enyne oxiranes can be synthesized through Sharpless asymmetric dihydroxylation and subsequent manipulations. With these reagents, it has been possible to produce exocyclic 2,4,5-trienols in enantiopure forms. Importantly, this process maintains chirality without degradation during the center-to-axis transfer of chirality.Article Citation - WoS: 1Citation - Scopus: 1Light-Dark and Activity Rhythm Therapy (l-Dart) To Improve Sleep in People With Schizophrenia Spectrum Disorders: a Single-Group Mixed Methods Study of Feasibility, Acceptability and Adherence(MDPI, 2023) Faulkner, Sophie; Didikoğlu, Altuğ; Byrne, Rory; Drake, Richard; Bee, PennyPeople with a diagnosis of schizophrenia often have poor sleep, even when their psychotic symptoms are relatively well managed. This includes insomnia, sleep apnoea, hypersomnia, and irregular or non-24 h sleep-wake timing. Improving sleep would better support recovery, yet few evidence-based sleep treatments are offered to this group. This paper presents a mixed methods feasibility and acceptability study of Light-Dark and Activity Rhythm Therapy (L-DART). L-DART is delivered by an occupational therapist over 12 weeks. It is highly personalisable to sleep phenotypes and circumstances. Ten participants with schizophrenia spectrum diagnoses and sleep problems received L-DART; their sleep problems and therapy goals were diverse. We measured recruitment, attrition, session attendance, and adverse effects, and qualitatively explored acceptability, engagement, component delivery, adherence, activity patterns, dynamic light exposure, self-reported sleep, wellbeing, and functioning. Recruitment was ahead of target, there was no attrition, and all participants received the minimum 'dose' of sessions. Acceptability assessed via qualitative reports and satisfaction ratings was good. Adherence to individual intervention components varied, despite high participant motivation. All made some potentially helpful behaviour changes. Positive sleep and functioning outcomes were reported qualitatively as well as in outcome measures. The findings above support testing the intervention in a larger randomised trial ISRCTN11998005.Article Citation - WoS: 4Citation - Scopus: 3Atomic-Scale Insights Into Carbon Dioxide Hydrogenation Over Bimetallic Iron-Cobalt Catalysts: a Density Functional Theory Study(MDPI, 2023) Tuncer, Dilan; Kızılkaya, Ali CanThe conversion of carbon dioxide to fuels and chemicals is a promising long-term approach for mitigating CO2 emissions. Despite extensive experimental efforts, a fundamental understanding of the bimetallic catalytic structures that selectively produce the desired products is still lacking. Here, we report on a computational surface science approach into the effect of the Fe doping of Co(111) surfaces in relation to CO2 hydrogenation to C1 products. Our results indicate that Fe doping increases the binding strength of surface species but slightly decreases the overall catalytic activity due to an increase in the rate-limiting step of CO dissociation. FeCo(111) surfaces hinder hydrogenation reactions due to lower H coverages and higher activation energies. These effects are linked to the Lewis basic character of the Fe atoms in FeCo(111), leading to an increased charge on the adsorbates. The main effect of Fe doping is identified as the inhibition of oxygen removal from cobalt surfaces, which can be expected to lead to the formation of oxidic phases on bimetallic FeCo catalysts. Overall, our study provides comprehensive mechanistic insights related to the effect of Fe doping on the catalytic behavior and structural evolution of FeCo bimetallic catalysts, which can contribute to the rational design of bimetallic catalysts.Article Citation - WoS: 4Citation - Scopus: 4A New Shapley-Based Feature Selection Method in a Clinical Decision Support System for the Identification of Lung Diseases(MDPI, 2023) Kababulut, Fevzi Yasin; Kuntalp, Damla Gurkan; Düzyel, Okan; Özcan, Nermin; Kuntalp, MehmetThe aim of this study is to propose a new feature selection method based on the class-based contribution of Shapley values. For this purpose, a clinical decision support system was developed to assist doctors in their diagnosis of lung diseases from lung sounds. The developed systems, which are based on the Decision Tree Algorithm (DTA), create a classification for five different cases: healthy and disease (URTI, COPD, Pneumonia, and Bronchiolitis) states. The most important reason for using a Decision Tree Classifier instead of other high-performance classifiers such as CNN and RNN is that the class contributions of Shapley values can be seen with this classifier. The systems developed consist of either a single DTA classifier or five parallel DTA classifiers each of which is optimized to make a binary classification such as healthy vs. others, COPD vs. Others, etc. Feature sets based on Power Spectral Density (PSD), Mel Frequency Cepstral Coefficients (MFCC), and statistical characteristics extracted from lung sound recordings were used in these classifications. The results indicate that employing features selected based on the class-based contribution of Shapley values, along with utilizing an ensemble (parallel) system, leads to improved classification performance compared to performances using either raw features alone or traditional use of Shapley values.Article Citation - WoS: 15Citation - Scopus: 16Formulation of Gluten-Free Cookies Utilizing Chickpea, Carob, and Hazelnut Flours Through Mixture Design(MDPI, 2023) Doğruer, Ilgın; Başer, Filiz; Güleç, Şükrü; Tokatlı, Figen; Özen, BanuLegume flours, which offer high nutritional quality, present viable options for gluten-free bakery products. However, they may have an objectionable flavor and taste for some consumers. In this study, it was aimed to improve the gluten-free cookie formulation by incorporating carob and hazelnut flours to pre-cooked chickpea flour and to investigate the techno-functional properties of the formulated cookies. The flours used in the formulations were assessed for their chemical and physical properties. This study employed a mixture design (simplex-centroid) to obtain the proportions of the flours to be used in the cookie formulations. The rheological characteristics of the doughs and the technological attributes of the baked cookies were determined. The addition of the hazelnut and carob flours had the overall effect of reducing the rheological characteristics of the cookie doughs. Furthermore, the textural attribute of the hardness of the baked cookies decreased as the ratio of hazelnut flour in the formulations was raised. The analysed results and sensory evaluation pointed to a formulation consisting of 30% pre-cooked chickpea/30% carob/30% hazelnut flours, which exhibited improved taste and overall acceptability scores. A total of 16.82 g/100 g of rapidly digestible starch, 5.36 g/100 g of slowly digestible starch, and 8.30 g/100 g of resistant starch exist in this particular cookie. As a result, combinations of chickpea, hazelnut, and carob flours hold promise as good alternatives for gluten-free cookie ingredients and warrant further exploration in the development of similar products.Review Citation - WoS: 3Citation - Scopus: 3Evolution of Tunneling Hydro-Technology: From Ancient Times To Present and Future(MDPI, 2023) Angelakis, Andreas N.; Passchier, Cees W.; Valipour, Mohammad; Krasilnikoff, Jens A.; Tzanakakis, Vasileios A.; Ahmed, Abdelkader T.; Baba, Alper; Kumar, Rohitashw; Capodaglio, Andrea G.; Dercas, Nicholas; Bilgiç, EsraWater tunnels are one of the oldest hydro-technologies for extracting water resources and/or transmitting them through water distribution systems. In the past, human societies have used tunneling for various purposes, including development, as a measure to enable underground resource extraction and the construction of transportation networks in challenging landscapes and topographies. The development of hydro-technology potentially involves the construction of tunnels to feed aqueducts, irrigation and waste water systems. Thus, the ability to make and maintain tunnels became an important component in creating lasting and sustainable water systems, which increased water supply and security, minimized construction costs, and reduced environmental impact. Thus, this review asks how, when and why human societies of the past included tunneling for the development of lasting water supply systems. This review presents a comprehensive overview across time and space, covering the history of tunneling in hydro technology from antiquity to the present, and it ponders how past experiences could impact on future hydro-technological projects involving tunneling. A historical review of tunnel systems enhances our understanding of the potential, performance, challenges, and prospects associated with the use of hydro-techniques. In the past, as the different examples in time and space demonstrate, tunneling was often dedicated to solving local problems of supply and disposal. However, across the world, some features were repeated, including the need for carving through the living rock or digging to create tunnels covered with stone slabs. Also, the world-wide use of extensive and costly tunnel systems indicates the high level of investment which human societies are willing to make for securing control over and with its water resources. This study helps us to gather inspiration from proven technologies of the past and more recent knowledge of water tunnel design and construction. As we face global warming and its derivate problems, including problems of water scarcity and flooding, the ability to create and maintain tunnels remains an important technology for the future.