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Integrating Computational and Experimental Insights Into Osmolyte-Driven Activation of Geobacillus Kaustophilus L-Asparaginase for Acrylamide Mitigation
No full textOsmolytes play a critical role in enhancing the stability and activity of enzymes for industrial applications. This study systematically investigated the effects of various osmolytes on the activity, optimal pH, temperature, stability, metal ion effects, storage, and acrylamide mitigation performance of L-asparaginase from the thermophilic Geobacillus kaustophilus (GkASNase). The experimental findings were further supported by computationally integrated tools such as homology modeling, docking, and molecular dynamics (MD) simulations. Among the selected osmolytes (maltose, sorbitol, trehalose, glycine, and sucrose), GkASNase showed the highest stability during 30 days of storage in the presence of maltose and arginine. Maltose increased GkASNase activity approximately 2-fold at 37 °C and 55 °C. In the presence of osmolytes, the Km values of GkASNase decreased and the Vmax values increased compared to controls at 37 °C and 55 °C. In the presence of osmolytes, the acrylamide mitigation performance of GkASNase increased by 1.7-fold in a 15 min reaction. The computational analysis indicates that L-asparagine as substrate enhances protein compactness and stability, while arginine as osmolyte increases flexibility and optimizes water distribution around the enzyme. These findings provide novel insights into enzyme stabilization that have implications for therapeutic and biotechnological applications. © 2025 Elsevier B.V
Extractivism Across Production and Social Reproduction: Classes of Labour in Rural Turkey
No full text[No abstract available]Department of Politics and International Relations, University of Sheffield; Department of Social Science; York University, Y
In Silico Identification and Evaluation of Antibiofilm Agents to Overcome Drug Resistance in Hepatocellular Carcinoma
No full textFrom Work to Leisure: "Transforming Kitchen Spaces, Technologies, and Practices in Türkiye, 1930s-2020s."
No full textKitchens are more than functional spaces; they reflect and shape cultural values, technologies, and ideals of modern life. Framing the kitchen as an orchestrating concept that brings together images, materials, and competencies, this article examines how idealized settings and tools have produced shifting narratives of modernity and redefined meanings, functions, and everyday practices in Türkiye from the 1930s to the present. It highlights the transformation of the kitchen from a moralizing space to one of entertainment and creativity across three eras: the ordered workshop of the 1930s, the cozy living room of the 1970s, and the technological hub of the 2000s. Drawing on archival research from a larger project on the social history of domestic technologies in T & uuml;rkiye, the article analyzes newspapers, magazines, TV commercials, social media, and films to reveal how domestic ideals have been negotiated through kitchen spaces.Turkiye Bilimsel ve Teknolojik Arastirma KurumuThis work was supported by Turkiye Bilimsel ve Teknolojik Arastirma Kurumu.Arts & Humanities Citation Inde
Investigation of the Potential of Antibiofilm Effective Agents to Overcome Drug Resistance Developed in Hepatocellular Carcinoma
No full textÖlümle sonuçlanan dördüncü en yaygın kanser türü olan karaciğer kanseri, en yaygın tür olan hepatosellüler karsinoma (HCC) için sınırlı tedavilere sahiptir. FDA onaylı, multi-kinaz inhibitörü sorafenib, ileri HCC'nin tedavisinin ilk aşamasında en çok tercih edilen ilaçtır. Günümüzde hastalara, önemli radyolojik ilerleme gözlenene kadar sorafenib tedavisi almaları ve ardından sorafenib'i başka bir FDA onaylı multi-kinaz inhibitörü olan regorafenib ile birlikte kullanmaları önerilmektedir. Ne yazık ki hastaların yaklaşık %70'i sorafenibe karşı gelişen direnç nedeniyle bu tedaviden fayda görememektedir. Metastatik karaciğer kanseri üzerine yapılan çalışmalar, gastrointestinal sistemden yayılan bağırsak mikrobiyotasını tümörle ilişkilendirmiş ve bağırsaklardan karaciğere bakteriyel geçişi göstermiştir. Tümör mikroçevresinde varlıklarını gösterebilen bakteriler, hayatta kalmak ve çoğalmak için genellikle biyofilm tabakası içeren bir habitat yaratır ve tümör hücreleri de bundan faydalanarak gelişebilir. Böyle bir tabaka ile korunmak, bakterilerin metabolik aktivitelerini mümkün olduğunca azaltarak antibiyotiklerin etkilerinden uzaklaşmasını da kolaylaştırır. Bu tezde, bakterilerin hayatta kalma şanslarını arttırmak için oluşturdukları biyofilm, hem oluşum mekanizması hem de içeriği açısından ele alınmıştır. Biyofilm oluşum sürecine katkıda bulunan temel proteinlerin inhibisyonu için küçük moleküllerden oluşan bir kütüphane oluşturulmuştur. Yüksek bağlanma afinitesine sahip potansiyel inhibitör moleküllerinin antibiyofilm etkileri moleküler yerleştirme ile gözlemlenmiştir. Ayrıca, FDA onaylı kemoterapi ilaçları sorafenib ve regorafenib'e dirençli HCC hedef proteinleri seçilmiştir. Bakteriyel biyofilm hedef proteinlerle moleküler yerleştirme sonucu en iyi sonucu veren küçük moleküller, HCC dirençli hedef proteinlerle yeniden moleküler yerleştirme yapılarak moleküler dinamik simülasyonlarla gözlemlenmiştir. Bu tez, geliştirilecek en etkili kombinatoryal tedavinin mekanizmalarını incelemeyi hedeflemektedir.The fourth most common cancer that results in death, liver cancer, has limited treatments for its most common type, hepatocellular carcinoma (HCC). The FDA-approved, multi-kinase inhibitor sorafenib is the main preferred drug in the first stage of treatment of advanced HCC. Today, patients are recommended to receive sorafenib treatment until significant radiological progression is observed. Then, sorafenib is used together with another FDA-approved multi-kinase inhibitor, regorafenib. Unfortunately, nearly 70% of patients do not benefit from this treatment due to the resistance that develops against sorafenib. Studies on metastatic liver cancer have been able to associate the intestinal microbiota spreading through the gastrointestinal tract with the tumor and show the bacterial transmission from the intestines to the liver. The bacteria that can show their presence in the tumor microenvironment create a habitat, generally including a biofilm layer, to survive and multiply, which the tumor cells can also benefit from to prosper. Being protected by such a layer also makes it easier for bacteria to get away from the effects of antibiotics by reducing their metabolic activities as much as possible. In this thesis, the biofilm that bacteria form to increase their chances of survival is discussed in terms of its formation mechanism and content. A library of small molecules has been created to inhibit key proteins contributing to biofilm formation. The antibiofilm effects of potential inhibitor molecules with high binding affinity have been observed with molecular docking. In addition, HCC target proteins suggested to be involved in resistance to FDA-approved chemotherapy drugs, sorafenib and regorafenib, were selected. The best results from the library docked with bacterial biofilm target proteins were re-docked with HCC-resistant proteins. Then, molecular dynamics simulations were performed with these proteins. This thesis aims to examine the mechanisms of the most effective combinatorial treatment to be developed
A Coalitional Perspective on Democratic Backsliding: Elite Coalitions and the Bureaucracy in Turkey
No full textThe rise of populism and the authoritarian shift has triggered a debate on the politics-administration nexus with a focus on the politics of democratic backsliding and the role of the bureaucracy. Recent studies have increasingly concentrated on the strategies of populist politicians to control the bureaucracy and the responses from the bureaucracy to these attempts. However, this dyadic approach to the politics-administration nexus remains limited in explaining fully the ramifications of democratic backsliding on bureaucracy. In this article, we propose a coalitional perspective on the politics of bureaucracy during the process of democratic backsliding. Illustrating the usefulness of this perspective through the Turkish context, the article highlights the role of intra-elite conflict and inter-elite competition in shaping the politics-administration nexus and explains why and how democratic backsliding has led to subordination, instrumentalization, and even deconstruction of bureaucracy in Turkey. As such, the article contributes to our understanding of the dynamics at play during the process of backsliding and the transformation of the politics-administration nexus.Social Science Citation Inde
Significant Reflection and Absorption Effects in the X-Ray Emission of the Intermediate Polar IGR J17195-4100
No full textContext. X-ray emission is emitted from shock-heated plasma in magnetic cataclysmic variables, particularly in intermediate polars, and is processed by absorption and scattering before reaching the observer. Aims. We investigate these effects in the X-ray emission of the intermediate polar IGR J17195-4100 by carrying out the X-ray spectral analysis, and examining spin modulation and hardness ratio. Methods. We present high-sensitivity broadband X-ray spectral analysis by combining NuSTAR and XMM-Newton observations in the 0.3-78.0 keV energy range. X-ray spectral analysis is performed using six composite models, including the angle-dependent reflection model (reflect), multi-temperature plasma emission models (CEVMKL, MKCFLOW), and photoionised and/or neutral partially covering absorption models (zxipcf, pcfabs) within XSPEC. We also examine the spin modulation in four energy ranges and the hardness ratio to determine the absorption and scattering effects. Results. We find that the spectrum is best modelled with a reflection amplitude (Ω) of 0.58+0.38-0.26, an ionisation parameter, log(ξ), of 1.46+0.44-0.23 with an equivalent hydrogen column density of 3.09+2.26-0.68 × 1022 cm-2, a neutral absorber, and a multi-temperature plasma temperature of 27.14+2.0-2.13 keV. In addition, we detect effects of electron scattering in the NuSTAR band, leading to a modulation amplitude of approximately a steady 9%, which rises to 15% after 20 keV. Conclusions. We stress that these effects significantly affect the X-ray emission of intermediate polars and should be considered to obtain a good representation of the intrinsic spectrum. © The Authors 2025.National Aeronautics and Space Administration, NASA; NuSTAR; Endocrine Society of Australia, ESA; European Regional Development Fund, ЕФРР; Istanbul Üniversitesi, (40017); Istanbul Üniversitesi; Agència de Gestió d'Ajuts Universitaris i de Recerca, AGAUR, (2023-FISDU-00225); Agència de Gestió d'Ajuts Universitaris i de Recerca, AGAUR; Ministerio de Economía y Competitividad, MEC, (PID2023-148661NB-I00); Ministerio de Economía y Competitividad, MEC; Generalitat de Catalunya, (SGR-386/2021); Generalitat de CatalunyaScience Citation Index Expande
Bilimsel İletişimde Dönüşüm: Açık Bilim, Yüksek Etkili Yayınlar ve Yapay Zeka
No full textBu sunum, 28 Ağustos 2025 tarihinde Kadir Has Üniversitesi’nde gerçekleştirilen ‘Bilimsel İletişimde Dönüşüm: Açık Bilim, Yüksek Etkili Yayınlar ve Yapay Zekâ’ başlıklı etkinlik kapsamında yapılmıştır
Exploring Challenges in Deep Learning of Single-Station Ground Motion Records
No full textContemporary deep learning models have demonstrated promising results across various applications within seismology and earthquake engineering. These models rely primarily on utilizing ground motion records for tasks such as earthquake event classification, localization, earthquake early warning systems, and structural health monitoring. However, the extent to which these models truly extract “deep” patterns from these complex time-series signals remains underexplored. In this study, our objective is to evaluate the degree to which auxiliary information, such as seismic phase arrival times or seismic station distribution within a network, dominates the process of deep learning from ground motion records, potentially hindering its effectiveness. Our experimental results reveal a strong dependence on the highly correlated Primary (P) and Secondary (S) phase arrival times. These findings expose a critical gap in the current research landscape, highlighting the lack of robust methodologies for deep learning from single-station ground motion recordings that do not rely on auxiliary inputs. © 2025 Elsevier B.V., All rights reserved.Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, TUBITAK, (121M732); Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, TUBITA
Effects of Imagining Someone Else Experience a Negative Autobiographical Memory on Phenomenological Experience
No full textWe investigated whether the phenomenological experience of a negative autobiographical memory changes when the self is presumably distanced from it. In session 1, participants described and phenomenologically rated an important negative event. One week later, in session 2, they imagined and described the event as if either a similar or a dissimilar friend experienced it. Afterward, they once more rated the original event that they described in session 1. Results showed increased observer perspective and decreased vividness, accessibility, and reliving of the original event after imagining that a friend experienced it. Importantly, when the negative event was imagined as experienced by a friend, preoccupation with overwhelming emotions related to the event, the event's emotional intensity, and its centrality to identity and life story also decreased. When the imagined friend was dissimilar, the emotional valence of the memory became more positive, and the emotional distance to the memory increased.Social Science Citation Inde