Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Dysfunctional K+ Homeostasis as a Driver for Brain Inflammation(Multidisciplinary Digital Publishing Institute (MDPI), 2024) Ozsoy, Nagihan; Dallas, Mark L.The central nervous system (CNS) relies on precise regulation of potassium ion (K+) concentrations to maintain physiology. This regulation involves complex cellular and molecular mechanisms that work in concert to regulate both intracellular and extracellular K+ levels. Inflammation, a key physiological response, encompasses a series of cell-specific events leading to inflammasome activation. Perturbations in K+-sensitive processes can result in either chronic or uncontrolled inflammation, highlighting the intricate relationship between K+ homeostasis and inflammatory signalling. This review explores molecular targets that influence K+ homeostasis and have been implicated in inflammatory cascades, offering potential therapeutic avenues for managing inflammation. We examine both cell-specific and common molecular targets across different cell types, providing a comprehensive overview of the interplay between K+ regulation and inflammation in the CNS. By elucidating these mechanisms, we identify leads for drug discovery programmes aimed at modulating inflammatory responses. Additionally, we highlight potential consequences of targeting individual molecular entities for therapeutic purposes, emphasizing the need for a nuanced approach in developing anti-inflammatory strategies. This review considers current knowledge on K+-sensitive inflammatory processes within the CNS, offering critical insights into the molecular underpinnings of inflammation and potential therapeutic interventions. Our findings underscore the importance of considering K+ homeostasis in the development of targeted therapies for inflammatory conditions within the CNS. © 2025 Elsevier B.V., All rights reserved.Article Citation - Scopus: 1Assessing the Density of Wood in Heritage Buildings’ Elements Through Expedited Semi-Destructive Techniques(Multidisciplinary Digital Publishing Institute (MDPI), 2025) Henriques, Dulce F.; Sen, Ali Umut; Gomes, Maria da GloriaFeatured Application The research presented and justified in this text aims to provide agents involved in the conservation and refurbishment of old timber elements in buildings with a correlation table for interpreting the readings obtained with penetration resistance testing equipment.Abstract Historically, wood has been among the main materials used in heritage buildings. However, the species and mechanical properties of these elements are often unknown. This uncertainty complicates safety assessment calculations, aggravated by the natural variability of the wood properties. The aim of this work is to assess the density of wooden elements in service using semi-destructive techniques that retain the integrity of structural elements. This research had two phases. First, penetration resistance tests were carried out on laboratory scale on Pinus sylvestris L. wood samples taken from 18th, 19th, and 20th century heritage buildings in Lisbon, Portugal. Later, a field study was carried out on wooden elements from the same buildings, involving needle penetration, core drilling, and moisture content determination tests. The laboratory test results showed a strong correlation between the needle penetration depth and wood density, with an R2 value of 0.76. The results of the field study indicated that the density estimated by the needle penetration test correlated effectively with the measured density of extracted cores after moisture correction, with an R2 of 0.99. In conclusion, the experimental results confirm that penetration resistance and moisture tests are reliable and practical for estimating wood density under in-service conditions.Article Yeast-Produced Human Recombinant Lysosomal Β-Hexosaminidase Efficiently Rescues Gm2 Ganglioside Accumulation in Tay–Sachs Disease(Multidisciplinary Digital Publishing Institute (MDPI), 2025) Inci, O.K.; Leal, A.F.; Ates, N.; Súarez, D.A.; Espejo-Mojica, A.J.; Alméciga-Diaz, C.J.; Seyrantepe, V.Background: Tay–Sachs disease (TSD) is an autosomal recessive lysosomal storage disorder characterized by the accumulation of GM2 ganglioside due to mutations in the HEXA gene, which encodes the α-subunit of β-Hexosaminidase A. This accumulation leads to significant neuropathological effects and premature death in affected individuals. No effective treatments exist, but enzyme replacement therapies are under investigation. In our previous work, we demonstrated the internalization and efficacy of human recombinant lysosomal β-hexosaminidase A (rhHex-A), produced in the methylotrophic yeast Pichia pastoris, in reducing lipids and lysosomal mass levels in fibroblasts and neural stem cells derived from patient-induced pluripotent stem cells (iPSCs). In this study, we further evaluated the potential of rhHex-A to prevent GM2 accumulation using fibroblast and neuroglia cells from a TSD patient alongside a relevant mouse model. Methods: Fibroblasts and neuroglial cell lines derived from a murine model and TSD patients were treated with 100 nM rhHexA for 72 h. After treatment, cells were stained by anti-GM2 (targeting GM2 ganglioside; KM966) and anti-LAMP1 (lysosomal-associated membrane protein 1) colocalization staining and incubated with 50 nM LysoTracker Red DND-99 to label lysosomes. In addition, GM2AP and HEXB expression were analyzed to assess whether rhHex-A treatment affected the levels of enzymes involved in GM2 ganglioside degradation. Results: Immunofluorescence staining for LysoTracker and colocalization studies of GM2 and Lamp1 indicated reduced lysosomal mass and GM2 levels. Notably, rhHex-A treatment also affected the expression of the HEXB gene, which is involved in GM2 ganglioside metabolism, highlighting a potential regulatory interaction within the metabolic pathway. Conclusions: Here, we report that rhHex-A produced in yeast can efficiently degrade GM2 ganglioside and rescue lysosomal accumulation in TSD cells. © 2025 by the authors.Article Understanding the Impact of Deep Learning Models on Building Information Modeling Systems: a Study on Generative Artificial Intelligence Tools †(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Yönder,V.M.The power of the relationship between building information modeling (BIM) systems and advanced artificial intelligence models holds considerable weight for users of BIM. This relationship allows the generation, analysis, and deduction of insights from substantial construction digital data. This research explores the relationship between generative artificial intelligence (generative AI), deep neural nets, and the BIM systems, including its users. This study examines the correlation between generative artificial intelligence and BIM methodology by conducting a case study. Furthermore, this paper investigates the conceptual and practical use of generative AI components (e.g., text-to-image models, diffusion networks, deep neural networks, large language model, and generative adversarial network) in BIM systems via bibliometric analysis. © 2023 by the author.Article Citation - Scopus: 4An Investigation of Shopping Mall Design Requirements †(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Çavka,H.B.Shopping malls may be considered as controversial structures since they sometimes fail to comply with the expectations of the project stakeholders throughout the project life cycle. New mall projects often attract the attention of people since such a structure has a potential to reshape the neighborhood it is located in; however, the impact is usually negative. On the other hand, the parties involved in mall projects may be subject to criticism from both the public and the industry during the design, construction, and operation. In this study we conducted semi-structured interviews with five managers of an international company that provides real estate services worldwide, and mainly focuses on managing shopping centers within the context of Turkiye. During the interviews, we collected insights on shopping mall design and criteria that have an impact on the operational success or failure. We analyzed the interview data to understand the shopping mall design requirements from the experts’ perspectives. We summarized our investigation under three main categories as location, shop and brand mix, and design. Analyzed data indicates that the requirements and use of shopping malls evolve and change over time. The change is driven by things such as changing habits and expectations of the users and new marketing approaches. Understanding such changes is essential for designers and investors to propose new design approaches and space compositions in order to be able to adapt to the changes. Through our analysis of the collected data, we provided insights on requirements and new trends that affect the design of malls. As further explained in this paper, our analysis indicates a number of important topics during design such as the need to design to fit ever-changing spatial needs, providing feel-good environment for users, correct placement of spaces and stores related to each other, designing circulation that supports commercial activities, and designing with a consideration of operation and maintenance. According to the collected data, the trend of shopping mall design is towards integration of hybrid uses, free forms, more open spaces, increased emphasis on gastronomy, and enabling socializing while leveraging technology and being more sustainable. © 2023 by the author.Article Citation - Scopus: 1Strategy for Revalorization of Cheese Whey Streams To Produce Phenyllactic Acid †(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Meruvu,H.Cheese whey (CW) is the residual liquid waste from cheese manufacturing industries, and it is rich in diverse nutrients with the potential for usage as a growth matrix for sustaining lactic acid bacteria (LAB) fermentation. Lactic acid (LA), phenyllactic acid (PLA), and their derivatives are green chemicals that can be produced by LAB metabolism with the revalorization of CW. LA and PLA are known for their antimicrobial properties, immunoregulatory functions, and production of biobased polymers (biodegradable plastics) like poly lactic acid and poly-phenyl lactic acid; hence, they find numerous applications in agricultural/food-based, pharmaceutical, biochemistry, or medical fields, as well as in antibiotic supplements in livestock feeds for animal husbandry. Herewith, we discuss our experimental strategy/concept (that can be implemented) for the microbial fermentation of cheese whey streams using robust LAB co-cultures to produce 3-PLA through sequential steps, adding a note upon their possible applications hereof. It is proposed that various food matrices, like raw cow milk, fermented cow milk, and fermented table olives, will be screened for the isolation of robust lactic acid bacteria that can be used as starter cultures for the fermentation of cheese whey liquids for producing augmented levels of LA and/or PLA. Moreover, we discuss the feasibility of practically producing PLA using an orchestrated assemblage of simple procedures, viz., isolating robust LAB strains from natural food matrices, tailoring LAB growth using a selective medium sustenance, adopting adaptive evolution procedures for improving resistance to higher temperatures and tolerance to lactic acid and/or cheese whey (low-cost substrate), and using FTIR and HPLC tools for analyzing the PLA content produced. Two Lactobacillus isolates (CM30_001 and CMW_10−3), sourced from raw cow milk and fermented cow milk whey, were found to produce 3-PLA contents of 39 mg/L and 32 mg/L in batch fermentation, using this proposed strategy. © 2023 by the author.Article Citation - Scopus: 20Estrus Detection and Dairy Cow Identification With Cascade Deep Learning for Augmented Reality-Ready Livestock Farming(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Arıkan, İ.; Ayav, T.; Seçkin, A.Ç.; Soygazi, F.Accurate prediction of the estrus period is crucial for optimizing insemination efficiency and reducing costs in animal husbandry, a vital sector for global food production. Precise estrus period determination is essential to avoid economic losses, such as milk production reductions, delayed calf births, and disqualification from government support. The proposed method integrates estrus period detection with cow identification using augmented reality (AR). It initiates deep learning-based mounting detection, followed by identifying the mounting region of interest (ROI) using YOLOv5. The ROI is then cropped with padding, and cow ID detection is executed using YOLOv5 on the cropped ROI. The system subsequently records the identified cow IDs. The proposed system accurately detects mounting behavior with 99% accuracy, identifies the ROI where mounting occurs with 98% accuracy, and detects the mounting couple with 94% accuracy. The high success of all operations with the proposed system demonstrates its potential contribution to AR and artificial intelligence applications in livestock farming. © 2023 by the authors.Article Citation - WoS: 3Citation - Scopus: 3Assessment of Mutual Variation of Near-Surface Air Temperature, Land Surface Temperature and Driving Urban Parameters at Urban Microscale(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Gerçek,D.; Güven,İ.T.The Urban Heat Island (UHI) effect is of critical concern for cities’ adaptation to climate change. The UHI effect shows substantial intra-urban variation at the city microscale, causing disparities in thermal comfort and energy consumption. Therefore, air temperature assessment should be prioritized for effective heat mitigation and climate adaptation. However, meteorological stations’ spatial distribution is far from meeting the scale that the UHI and its driving parameters operate. This limitation hampers demonstrating the intra-city variability of UHI and its origin of sources; for example, most studies employ Land Surface Temperature (LST), usually without demonstrating the relationship between UHI and LST. The current body of knowledge on urban climate implies a much better understanding and more detailed information on the spatial pattern of UHI and the driving factors to provide decision-makers with tools to develop effective UHI mitigation and adaptation strategies. In an attempt to address the adequacy of the use of LST and UPs in describing the intra-city variability of UHI, this study investigates the relationship between LST daytime and nighttime, and air temperature (Ta) daytime and nighttime, and driving urban parameters (UPs) of UHI together. Although it is well recognized that the intensity of the UHI is characterized by Ta, particularly at night, so-called nocturnal UHI, the use of remotely sensed LST is common, owing to the lack of spatially detailed Ta data in cities. Our findings showed that nocturnal UHI is weakly correlated with nighttime LST with a Pearson correlation (r) of 0.335 at p > 0.05 and that it is not correlated with daytime LST for the case study, highlighting the need for Ta observations for representing the intra-urban variation of nocturnal UHI. Among UPs, Sky View Factor (SVF), Building Volume Density (BVD), and Road Network Density (RND) explained 69% of the variability of Ta nighttime that characterizes nocturnal UHI. Therefore, UPs that performed well in estimating nocturnal UHI may be used in the absence of densely distributed Ta measurements. In a further investigation of the urban cooling phenomenon based on UHI diurnal changes, a particular region with high nighttime temperatures spoiled the Ta daytime and nighttime coherence. This region is characterized by high Mean Building Height (MBH), BFD, and BVD that re-emits heat, low SVF that prevents urban cooling, and high RND that releases extra heat at night. These particular UPs can be of prior interest for urban cooling. The present study, exploring the relationships of LST and Ta in a diurnal context, offers a further understanding of the preference of LST, Ta, or UPs to characterize UHI. Ta, in relation to major causative factors (UPs), provides insights into addressing the localities most vulnerable to the UHI effect and possible strategies targeting heat mitigation for sustainability and climate change resilience. © 2023 by the authors.