PubMed İndeksli Yayınlar Koleksiyonu
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Editorial Citation - WoS: 0Citation - Scopus: 0Miniaturized Soft Growing Robots for Minimally Invasive Surgeries: Challenges and Opportunities(Iop Publishing Ltd, 2025) Stroppa, Fabıo; Saraç Stroppa, Mine; Sarac, Mine; Mechatronics Engineering; Computer EngineeringAdvancements in assistive robots have significantly transformed healthcare procedures in recent years. Clinical continuum robots have enhanced minimally invasive surgeries, offering benefits to patients such as reduced blood loss and a short recovery time. However, controlling these devices is difficult due to their limited accuracy in three-dimensional deflections and challenging localization, particularly in confined spaces like human internal organs. Consequently, there has been growing research interest in employing miniaturized soft growing robots, a promising alternative that provides enhanced flexibility and maneuverability. In this work, we extensively investigated issues concerning their designs and interactions with humans in clinical contexts. We took insights from the open challenges of the generic soft growing robots to examine implications for miniaturization, actuation, and biocompatibility. We proposed technological concepts and provided detailed discussions on leveraging existing technologies, such as smart sensors, haptic feedback, and artificial intelligence, to ensure the safe and efficient deployment of the robots. Finally, we offer an array of opinions from a biomedical engineering perspective that contributes to advancing research in this domain for future research to transition from conceptualization to practical clinical application of miniature soft growing robots.Article Citation - WoS: 0Citation - Scopus: 0Reflective Thinking Predicts Disbelief in God Across 19 Countries(Springer, 2025) Yılmaz, Onurcan; Yilmaz, Onurcan; Isler, Ozan; Terry, Jenny; Ross, Robert M.; PsychologyIn the present study, we tested three hypotheses about relationships between reflective thinking, intuitive thinking (both measured using the Cognitive Reflection Test; CRT), and belief in God or gods (BiG) in university students across 19 culturally and geographically diverse countries (n = 7,771). In support of our first hypothesis, we found a negative relationship between reflective thinking and BiG; and in support of our second hypothesis, we found a positive relationship between intuitive thinking and BiG. Contrary to our third hypothesis, we found no evidence that measuring CRT prior to measuring BiG decreased BiG. Given that this is the first large cross-cultural test of these hypotheses to have a preregistered analysis plan, the first to hold education constant across countries, and the first to use both Bayesian and frequentist methods, these results considerably bolster the evidence in support of the first two hypotheses and against the third hypothesis.Article Citation - WoS: 0Can Reflection Mitigate Covid-19 Vaccine Conspiracy Beliefs and Hesitancy(Taylor & Francis Ltd, 2025) Yılmaz, Onurcan; Sarıbay, Selahattin Adil; Ozman, Nagihan; Yilmaz, Onurcan; Isler, Ozan; Saribay, S. Adil; PsychologyObjective design:Periods of social turmoil, such as the COVID-19 pandemic, tend to amplify conspiracy beliefs, evidenced by increased vaccine hesitancy. Despite this trend, effective interventions targeting vaccine-related conspiracy beliefs remain scarce, partly due to underexplored cognitive processes. Three competing theoretical accounts offer differing predictions about the role of reflective thinking in supporting conspiracy beliefs: the Motivated Reasoning Account suggests reflection strengthens commitment to pre-existing attitudes; the Reflective Reasoning Account posits that reflection enhances belief accuracy; and the Reflective Doubt Account proposes reflection fosters general scepticism. Main outcome measures:Utilising open science practices and a validated technique to activate reflection, we conducted an experimental investigation with a diverse sample (N = 1483) segmented by vaccine attitudes. We investigated the impact of reflection on specific and generic COVID-19 conspiracy beliefs and vaccine-support behaviours across pro-vaccine, neutral, and vaccine-hesitant groups, while examining the moderating effects of scientific literacy, intellectual humility, and actively open-minded thinking. Results:The confirmatory analysis provided no direct support for the theoretical predictions. However, findings indicated that intellectual humility significantly moderated the effect of reflection, enhancing vaccine-support behaviour among participants with high intellectual humility, highlighting the complex interplay of cognitive style and prior attitudes in shaping responses to conspiracy beliefs and vaccine-support actions. Conclusion:The study highlights that while reflective thinking alone did not directly influence vaccine support behavior, its positive effect emerged among individuals with higher intellectual humility, emphasizing the importance of individual differences in shaping belief-related outcomes.Article Citation - WoS: 0Citation - Scopus: 0Investigation of the Potential Effect of Complement 5 on Transplantation Outcome by Bioinformatics Tools(Iranian Soc Nephrolgy, 2025) Oguz, Suleyman Rustu; Kivanc, Demet; Ozdilli, Kursat; Karadeniz, Sedat; Kluge, Ekin Ece Gurer; Ciftci, Hayriye SenturkIntroduction. Activation of the complement system following transplantation may result in allograft rejection. Our study aimed to evaluate the potential relationship between factors affecting kidney transplant success and complement 5 (C5) using bioinformatic tools. Methods. GenCards and Genemania were used to provide the genetic functional information belonging to the C5 gene, and genomic browsers of STRING, UCSC, KEGG were used to reveal interactions with other genes and various pathways. MiRDB was used to specify the miRNAs that were associated with the C5 gene. The UniProt database was used to determine the tissues that expressed the C5 gene using protein-protein interactions. Results. In the bioinformatic analyses performed, high levels of C5 gene expression were found in the naiive kidney. Twenty-five genes were found to be strongly associated with C5. Fifty-four miRNAs targeting the C5 gene were specified. The C5 gene was found to be involved in biologic processes such as complement activation (FDR = 6.46e-22), complement binding (FDR = 2.20e-06), cytolysis (FDR = 4.82e-14), regulation of complement activation (FDR = 4.08e24), positive regulation of vascular endothelial growth factor production (FDR = 0.0430), regulation of macrophage chemotaxis (FDR = 0.0447), activation of the immune response (FDR = 1.26e13), leukocyte-mediated immunity (FDR = 1.41e-09), innate immune response (FDR = 3.05e-09), allograft rejection (FDR = 2.40e-12), oxidative injury response (FDR = 0.00016), and trigerring of the beginning of the complement cascade (FDR = 0.0244). Conclusions. The data obtained in this study will be used to guide future experimental investigations in the field of transplantation, and these data will give physicians with insight into allograft status following transplantation.Article Citation - WoS: 0Citation - Scopus: 0Decision Making, Emotion Recognition and Childhood Traumatic Experiences in Murder Convicts Imprisoned With Aggravated Life Sentence: a Prison Study(Turkish Neuropsychiatry Assoc-Turk Noropsikiyatri Derneği, 2025) Cikrikcili, Ugur; Yildirim, Elif; Buker, Seda; Ger, Can; Erozden, Ozan; Gurvit, Hakan; Saydam, BilginIntroduction: Decision-making and emotion recognition are two fundamental themes in social cognition. Disorders in these areas can lead to interpersonal, psychosocial, and legal problems for the individual and society. The likelihood of consequent aggression and crime makes them foci of forensic psychiatry over time. In this study, two developmental disorders that have a clear relationship with crime, that are antisocial personality disorder (ASPD), and psychopathy are investigated for their relationship with these social cognitive deficits. Methods: The present study involved 23 male prison inmates who were diagnosed with both antisocial personality disorder and psychopathy, as well as 23 control participants who were matched for age, gender, and level of education. Following the psychiatric interview, Reading the Mind in the Eyes Test (RMET), the Iowa Gambling Test (IGT), Toronto Alexithymia Scale (TAS), Defense Styles Questionnaire (DSQ), Childhood Psychic Trauma Scale (CTQ), Hare Psychopathy Checklist (PCL-R) were administered to all participants. Results: The results of the study showed that ASPD group performed statistically worse than healthy controls in TAS, CTQ, all items of DSQ, PCL-R Factor 1 and 2, and all the IGT scores (p<0.05). There were no statistically significant difference between in the RMETtest performances Conclusion: These results suggest that ASPD and psychopathy lead to impaired decision-making behaviors due to the inability to recognize one's own emotions and impulsivity, and that these characteristics play a critical role in the criminal behavior of individuals. In addition, contrary to expectations, the results of affective theory of mind assessed with the RMET showed similar characteristics in homicide convicts and healthy controls. These data indicate the need for further research in the field of forensic psychiatry.Article Citation - WoS: 0Citation - Scopus: 0Structural Descriptors for Subunit Interface Regions in Homodimers: Effect of Lipid Membrane and Secondary Structure Type(American Chemical Society, 2025) Yüksek, A.; Yıkınç, B.; Nayır, I.; Alnıgeniş, D.; Fidan, V.G.; Topuz, T.; Akten, E.D.A total of 1311 homodimers were collected and analyzed in three different categories to highlight the impact of lipid environment and secondary structure type: 422 cytoplasmic α-helix, 411 cytoplasmic β-strand, and 478 membrane complexes. Structural features of the interface connecting two monomers were investigated and compared to those of the non-interface surface. Every residue on the surface of each monomer was explored based on four attributes: solvent-accessible surface area (SASA), protrusion index (Cx), surface planarity, and surface roughness. SASA and Cx distribution profiles clearly distinguished the interface from the surface in all categories, where the rim of the interface displayed higher SASA and Cx values than the rest of the surface. Surface residues in membrane complexes protruded less than cytoplasmic ones due to the hydrophobic environment, and consequently, the difference between surface and interface residues became less noticeable in that category. Cytoplasmic β-strand complexes displayed markedly lower SASA at the interface core than at the surface. The major distinction between the surface and interface was achieved through surface roughness, which displayed significantly higher values for the interface than the surface, especially in cytoplasmic complexes. Clearly, a surface which is relatively rugged favors the association of two monomers through multiple van der Waals interactions and hydrogen-bond formations. Another structural descriptor with strong distinguishing ability was surface planarity, which was higher at the interface than at the non-interface surface. Surface flatness would eventually facilitate the interconnectedness of an interface with a network of residue pairs bridging two complementary surfaces. Analysis of contact pairs revealed that hydrophobic pairs have the highest frequency of occurrence in the lipid environment of membrane complexes. However, despite the scarcity of polar residues at the interface, the likelihood of observing a contact between polar residues was markedly higher than that of hydrophobic ones. © 2025 The Authors. Published by American Chemical Society.Article Citation - WoS: 1Citation - Scopus: 1Behavioral but Not Psychological Control Predicts Self-Regulation, Adjustment Problems and Academic Self-Efficacy Among Early Adolescents(Routledge Journals, Taylor & Francis Ltd, 2025) Harma, Mehmet; Aktas, Busra; Sumer, Nebi; PsychologyPrior work has documented that parental psychological and behavioral control have varying impacts on self-regulation skills and social-academic outcomes in early adolescence, with effects differing across cultures. The present study explores the role of psychological and behavioral control in predicting adjustment difficulties and academic self-confidence through self-regulatory skills among early adolescents in Turkiye using data from mothers and their children (N = 295, Ngirls=145, Mage=12.14 years). The results yielded that parental behavioral control, but not psychological control, predicts self-regulation of adolescents, which, in turn, predicts adjustment and academic self-efficacy. Our results underscore the pivotal role of parental knowledge and monitoring, mainly through behavioral control strategies, in fostering psychological adjustment and academic self-efficacy in the Turkish cultural context. The discussion delves into the potential culture-specific effects of psychological control and the universal influence of behavioral control during early adolescence.Article Citation - WoS: 0Citation - Scopus: 0Quantum Models of Consciousness From a Quantum Information Science Perspective(Mdpi, 2025) Pusuluk, Onur; Pusuluk, Onur; Cattaneo, Marco; Muestecaplioglu, Ozgur E.; Core ProgramThis perspective explores various quantum models of consciousness from the viewpoint of quantum information science, offering potential ideas and insights. The models under consideration can be categorized into three distinct groups based on the level at which quantum mechanics might operate within the brain: those suggesting that consciousness arises from electron delocalization within microtubules inside neurons, those proposing it emerges from the electromagnetic field surrounding the entire neural network, and those positing it originates from the interactions between individual neurons governed by neurotransmitter molecules. Our focus is particularly on the Posner model of cognition, for which we provide preliminary calculations on the preservation of entanglement of phosphate molecules within the geometric structure of Posner clusters. These findings provide valuable insights into how quantum information theory can enhance our understanding of brain functions.Article Citation - WoS: 1Citation - Scopus: 1Hydrogels From Protein-Polymer Conjugates: a Pathway To Next-Generation Biomaterials(Mdpi, 2025) Pekcan, Mehmet Önder; Poyraz, Yagmur; Hassan, Gana; Gul, Sumeyye Berfin; Calhan, Nergiz; Mert Sahin, Naz Mina; Pekcan, Onder; Molecular Biology and GeneticsHybrid hydrogels from protein-polymer conjugates are biomaterials formed via the chemical bonding of a protein molecule with a polymer molecule. Protein-polymer conjugates offer a variety of biological properties by combining the mechanical strength of polymers and the bioactive functionality of proteins. These properties allow these conjugates to be used as biocompatible components in biomedical applications. Protein-polymer conjugation is a vital bioengineering strategy in many fields, such as drug delivery, tissue engineering, and cancer therapy. Protein-polymer conjugations aim to create materials with new and unique properties by combining the properties of different molecular components. There are various ways of creating protein-polymer conjugates. PEGylation is one of the most common conjugation techniques where a protein is conjugated with Polyethylene Glycol. However, some limitations of PEGylation (like polydispersity and low biodegradability) have prompted researchers to devise novel synthesis techniques like PEGylation, where synthetic polypeptides are used as the polymer component. This review will illustrate the properties of protein-polymer conjugates, their synthesis methods, and their various biomedical applications.Article Citation - WoS: 1Citation - Scopus: 1Deviation From the Balanced Time Perspective and Depression and Anxiety Symptoms: the Mediating Roles of Cognitive-Behavioral Emotion Regulation in a Cross-Cultural Model(Frontiers Media Sa, 2025) Ranjbar, Hamed Abdollahpour; Altan-Atalay, Ayse; Asgarabad, Mojtaba Habibi; Turan, Bulent; Eskin, MehmetBackground Time perspective (TP) influences how individuals perceive and classify their past, present, and future, impacting their cognition, behavior, and psychological outcomes. Deviation from the balanced time perspective (DBTP) is associated with mental health problems (e.g., depression and anxiety). Emotion regulation (ER) encompasses cognitive and behavioral processes to regulate emotions, with maladaptive strategies like rumination and withdrawal linked to depression and anxiety. Despite extensive research on TP and ER, their joint impact, particularly in the context of depression and anxiety, and cultural differences remain underexplored.Method Participants (N = 513 Iranian, N = 470 Turkish) completed self-report questionnaires on time perspective, cognitive and behavioral ER, anxiety, and depression symptoms. A moderated mediation model was assessed, incorporating the exogenous variable of DBTP, with ER strategies as mediators, and endogenous variables of depressive and anxiety symptoms. The model accounted for cultural variations in the paths as a moderator.Results Significant associations were found between DBTP, ER strategies, depression, and anxiety symptoms. Mediation analyses revealed that both cognitive and behavioral ER strategies (except for adaptive behavioral ER strategies) significantly mediated the associations between DBTP and depression and anxiety. Additionally, multigroup analyses suggested that these mediating effects were consistent across Iranian and Turkish samples, with exceptions in adaptive cognitive ER strategies.Conclusion The study highlights the crucial role of TPs and ER strategies in predicting anxiety and depression symptoms, with notable cultural nuances. Specifically, maladaptive strategies exacerbate symptoms, while adaptive strategies mitigate them primarily in Iranian contexts. Cultural subtleties are discussed in detail.Article Citation - WoS: 0Citation - Scopus: 0From 'Safe Haven' To 'zone of Precarity': Locating Istanbul Through the Perceptions and Everyday Urban Practices of Skilled Migrants(Springernature, 2025) Tuncer, Ezgi; ArchitectureThis article seeks to position Istanbul through the practices of everyday life of middle-class, skilled migrants from both the Global North and South and their perceptions of urban safety and precarity. It examines individuals' processes of migration to Turkey, revealing their initial impressions of Istanbul as a safe city of opportunities, and then analyses their everyday urban lives, highlighting hidden forms of precarity and discrimination. Through in-depth interviews with 45 women and 34 men-more than half of whom are North American and European-and participant observation in people's living environments and at various social events, I argue that Istanbul, while perceived as a 'safe haven' at first, becomes a 'zone of precarity' where most of the participants have experienced intersectional forms of precarity, latent patterns of discrimination, and insecurities that belie the common perception that skilled migrants are privileged. To substantiate this argument, this ethno-spatial study presents an analysis of qualitative data as well as an online subjective mapping of Istanbul, where perceptions of urban safety and spatial precarity are displayed through socio-spatial experiences encountered in neighbourhoods, workplaces, and public spaces.Article Citation - WoS: 0Citation - Scopus: 0Differentiating Functional Connectivity Patterns in Adhd and Autism Among the Young People: a Machine Learning Solution(Sage Publications inc, 2025) Ballı, Tuğçe; Balli, Tugce; Roeyers, Herbert; Wiersema, Jan R.; Camkerten, Sami; Ozturk, Ozan Cem; Sonuga-Barke, Edmund; Management Information SystemsObjective: ADHD and autism are complex and frequently co-occurring neurodevelopmental conditions with shared etiological and pathophysiological elements. In this paper, we attempt to differentiate these conditions among the young people in terms of intrinsic patterns of brain connectivity revealed during resting state using machine learning approaches. We had two key objectives: (a) to determine the extent to which ADHD and autism could be effectively distinguished via machine learning from one another on this basis and (b) to identify the brain networks differentially implicated in the two conditions.Method: Data from two publicly available resting-state functional magnetic resonance imaging (fMRI) resources-Autism Brain Imaging Data Exchange (ABIDE) and the ADHD-200 Consortium-were analyzed. A total of 330 participants (65 females and 265 males; mean age = 11.6 years), comprising equal subgroups of 110 participants each for ADHD, autism, and healthy controls (HC), were selected from the data sets ensuring data quality and the exclusion of comorbidities. We identified region-to-region connectivity values, which were subsequently employed as inputs to the linear discriminant analysis algorithm.Results: Machine learning models provided strong differentiation between connectivity patterns in participants with ADHD and autism-with the highest accuracy of 85%. Predominantly frontoparietal network alterations in connectivity discriminate ADHD individuals from autism and neurotypical group. Networks contributing to discrimination of autistic individuals from neurotypical group were more heterogeneous. These included language, salience, and frontoparietal networks.Conclusion: These results contribute to our understanding of the distinct neural signatures underlying ADHD and autism in terms of intrinsic patterns of brain connectivity. The high level of discriminability between ADHD and autism, highlights the potential role of brain based metrics in supporting differential diagnostics.Article Citation - WoS: 0Citation - Scopus: 0Economic Uncertainty and Climate Change Exposure(Academic Press Ltd- Elsevier Science Ltd, 2025) Öztürk Danışman, Gamze; Erdoğan, Seda; Demir, Ender; International Trade and FinanceThis paper explores how economic uncertainty affects firms' climate change exposure. We use an extensive sample from 24 countries from 2002 to 2021. Employing a novel measure of firm-level climate change exposure developed by Sautner et al. (2023b), we empirically demonstrate that prior to the Paris Agreement in 2015, economic uncertainty leads to a decrease in climate change disclosures. However, after the Paris Agreement, our findings reveal a positive association between economic uncertainty and climate change exposure. The positive disclosure effect is primarily driven by higher climate-related opportunities and regulatory exposures. Our findings are robust when we employ alternative definitions for economic uncertainty, alternative samples, additional firm-level and country-level control variables, and alternative methodologies. We find that institutional and foreign ownership positively moderates the association between economic uncertainty and climate change exposure after the Paris Agreement. Further analysis investigates the moderating impact of country-level environmental performance indicators. We present novel empirical evidence suggesting that firms operating in countries with less climate vulnerability, higher readiness, more stringent environmental policies, superior climate protection performance, and higher environmental litigation risk tend to have higher climate change exposure in uncertain times.Article Citation - WoS: 3Citation - Scopus: 3Cultural Context Shapes the Selection and Adaptiveness of Interpersonal Emotion Regulation Strategies(Amer Psychological Assoc, 2024) Pruessner, Luise; Altan-Atalay, AyseIn everyday life, we commonly experience, express, and regulate our emotions in interpersonal contexts. However, much of the existing research on utilizing others for modulating one's emotions has focused on Western, individualistic cultures, leaving a significant gap in understanding how the selection and adaptiveness of interpersonal emotion regulation (IER) strategies vary across cultural contexts. This cross-national comparison study aims to bridge this gap by examining intrinsic IER in 1,187 participants from Turkey and Germany, which are characterized by different cultural norms, values, and socialization practices regarding emotional experience and expression. All participants completed measures of intrinsic IER strategies alongside measures of adaptive outcomes, including depression, anxiety, negative affect, and positive affect. The results revealed cross-national differences between Turkish and German individuals in terms of the intrinsic IER strategies most frequently selected and their associations with depression, anxiety, negative affect, and positive affect. These findings emphasize the significance of cultural context in intrinsic IER and offer insights into the conditions under which these strategies are linked to adaptive outcomes. By recognizing the cultural nuances in how people navigate their emotions via social interactions, clinicians and researchers can develop more culturally sensitive interventions tailored to the specific needs of individuals in diverse cultural contexts.Article Citation - WoS: 0Citation - Scopus: 1Maternal Underestimations and Overestimations of Their Infants' Word Comprehension: Effects on Mothers' Verbal Input and Infants' Receptive Vocabulary(Cambridge Univ Press, 2024) Ertas, Sura; Kuntay, Aylin C.; Aktan-Erciyes, AsliInfants' language is often measured indirectly via parent reports, but mothers may underestimate or overestimate their infants' word comprehension. The current study examined estimations of mothers from diverse educational backgrounds regarding their infants' word comprehension and how these estimations are associated with their verbal input and infants' receptive vocabulary at 14 months. We compared 34 infants' looking-while- listening (LWL) performances with the mothers' Turkish Communicative Development Inventory (TCDI) reports to calculate the mothers' overestimation and underestimation. During free-play sessions, we assessed the mothers' number of words, number of clauses, lexical diversity, and linguistic complexity. We found that mothers have overestimations and underestimations regardless of their educational background. Crucially, mothers' only overestimations were positively associated with their number of words and lexical diversity. Mothers' verbal input was not related to infants' receptive vocabulary scores. The findings suggest that mothers' input might be aligned with their estimations of their infants' language capabilities, which might not reflect the infants' true performance.Article Citation - WoS: 0Citation - Scopus: 0Regime Switching in Coupled Nonlinear Systems: Sources, Prediction, and Control-Minireview and Perspective on the Focus Issue(Aip Publishing, 2024) Eroğlu, Deniz; Eydam, Sebastian; Eroglu, Deniz; Molecular Biology and GeneticsRegime switching, the process where complex systems undergo transitions between qualitatively different dynamical states due to changes in their conditions, is a widespread phenomenon, from climate and ocean circulation, to ecosystems, power grids, and the brain. Capturing the mechanisms that give rise to isolated or sequential switching dynamics, as well as developing generic and robust methods for forecasting, detecting, and controlling them is essential for maintaining optimal performance and preventing dysfunctions or even collapses in complex systems. This Focus Issue provides new insights into regime switching, covering the recent advances in theoretical analysis harnessing the reduction approaches, as well as data-driven detection methods and non-feedback control strategies. Some of the key challenges addressed include the development of reduction techniques for coupled stochastic and adaptive systems, the influence of multiple timescale dynamics on chaotic structures and cyclic patterns in forced systems, and the role of chaotic saddles and heteroclinic cycles in pattern switching in coupled oscillators. The contributions further highlight deep learning applications for predicting power grid failures, the use of blinking networks to enhance synchronization, creating adaptive strategies to control epidemic spreading, and non-feedback control strategies to suppress epileptic seizures. These developments are intended to catalyze further dialog between the different branches of complexity.Article Citation - WoS: 0Citation - Scopus: 0Investigation and Development of Novel Synthetic Approaches for Synthesis of Euxanthone and Derived Dyes(Royal Soc Chemistry, 2024) Cetin, M. MustafaThe historical dye Indian yellow, derived from euxanthic acid formed from 1,7-dihydroxyxanthone (euxanthone) and methyl (tri-O-acetyl-alpha-d-glucopyranosyl bromide) uronate, has significantly influenced the art world due to its vibrant color and unique production process. Studying Indian yellow is important for its historical relevance and impact on various art forms, as well as the challenges in its synthetic production. Herein, this work investigates the synthesis of the two main components, a novel method for obtaining euxanthone, and attempts to produce euxanthic acid and Indian yellow. All key intermediates and desired compounds have successfully been synthesized with good to high isolated yields, and characterized using different analytical and spectroscopic techniques. A proposed mechanism for euxanthone synthesis via 2,6,2 ',5 '-tetramethoxybenzophenone formation is also offered. During this process, 2,7-dihydroxyxanthone has also been synthesized, revealing an equilibration reaction that produced three isomeric tetramethoxybenzophenones, confirmed by both GC/MS and NMR. Following the synthesis of euxanthone and clarification of the equilibration, the production of Indian yellow via euxanthic acid formation has further been explored.Article Citation - WoS: 0Citation - Scopus: 0Distinct Deregulation Trends of Transcriptional Protein Complexes in Aging Naive T Cells(Oxford University Press, 2025) Kökrek, E.; Kökrek, Emel; Pir, P.; Molecular Biology and GeneticsThe impact of aging on T cell subsets, specifically CD4+ and CD8+ T cells, leading to immune system dysfunction has been the focus of scientific investigation due to its potential to reverse age-associated deterioration. Transcriptomic and epigenomic studies have identified the primary regulators in T cell aging. However, comprehending the underlying dynamic mechanisms requires studying these proteins with their interactors. Here, we integrated single-cell RNA sequencing data of naive CD4+ and CD8+ T cells obtained from 3 different age groups with protein-protein and domain-domain interaction networks to predict and compare the transcriptional protein complexes and identify their capacity to explain age-associated variances. Our novel approach revealed significant effects of aging on the repertoire of complexes, which remains unchanged in naive CD4+ T cells, while in naive CD8+ T cells, it diminishes. In both cell types, there was major deregulation of complexes with the same composition, involving a range of transcription factors. This aging-associated deregulation is characterized by a specific set of protein complexes in naive CD4+ T cells, but this pattern is not observed in naive CD8+ T cells. SMAD3 and BCL11A complexes emerge as key markers in defining a trajectory in aging naive CD4+ T cells. These complexes can accurately distinguish between 3 different age groups, indicating their potential as targets. The direct link between SMAD3 and FOS complexes whose regulatory role has been previously implicated in aging and MBD3 as the novel key link between SMAD3 and BCL11A complexes implicates a coordinated mechanism in age-associated deregulation. © The Author(s) 2024. Published by Oxford University Press on behalf of Society for Leukocyte Biology.Article Citation - WoS: 0Citation - Scopus: 0Effective Drug Design Screening in Bacterial Glycolytic Enzymes Via Targeting Alternative Allosteric Sites(Elsevier Science inc, 2024) Akdoğan, Ebru Demet; Kurtulus, Gamze; Sesal, Cenk; Kurkcuoglu, Ozge; Ayyildiz, Merve; Celiker, Serkan; Akten, Ebru Demet; Molecular Biology and GeneticsThree glycolytic enzymes phosphofructokinase (PFK), glyceraldehyde-3-phosphate dehydrogenase (GADPH) and pyruvate kinase (PK) that belong to Staphylococcus aureus were used as targets for screening a dataset composed of 7229 compounds of which 1416 were FDA-approved. Instead of catalytic sites, evolutionarily less conserved allosteric sites were targeted to identify compounds that would selectively bind the bacteria's glycolytic enzymes instead of the human host. Seven different allosteric sites provided by three enzymes were used in independent screening experiments via docking. For each of the seven sites, a total of 723 compounds were selected as the top 10 % which displayed the highest binding affinities. All compounds were then united to yield the top 54 drug candidates shared by all seven sites. Next, 17 out of 54 were selected and subjected to in vitro experiments for testing their inhibition capability for antibacterial growth and enzymatic activity. Accordingly, four compounds displaying antibacterial growth inhibition above 40 % were determined as Candesartan cilexetil, Montelukast (sodium), Dronedarone (hydrochloride) and Thonzonium (bromide). In a second round of experiment, Candesartan cilexetil and Thonzonium displayed exceptionally high killing efficiencies on two bacterial strains of S. aureus (methicillin-sensitive and methicillin-resistant) with concentrations as low as 4 mu g/mL and 0.5 mu g/mL. Yet, their enzymatic assays were not in accordance with their killing effectiveness. Different inhibitory effects was observed for each compound in each enzymatic assay. A more effective target strategy would be to screen for drug compounds that woud inhibit a combination of glycolytic enzymes observed in the glycolytic pathway.Article Citation - WoS: 1Citation - Scopus: 1Composite Hydrogel of Polyacrylamide/Starch as a Novel Amoxicillin Delivery System(Mdpi, 2024) Özuğur Uysal, Bengü; Pekcan, Mehmet Önder; Hassan, Gana; Alayoubi, Oubadah; Uysal, Bengu Ozugur; Pekcan, Onder; Molecular Biology and GeneticsThis study investigates the development and characterization of a novel composite hydrogel composed of polyacrylamide (PAAm), starch, and gelatin for use as an amoxicillin delivery system. The optical properties, swelling behavior, and drug release profile of the composite hydrogel's were studied to evaluate its efficacy and potential applications. UV-visible spectroscopy was employed to determine the optical properties, revealing significant transparency in the visible range, which is essential for biomedical applications. The incorporation of starch and gelatin into the polyacrylamide matrix significantly enhanced the hydrogel's swelling capacity and biocompatibility. Studies on drug delivery demonstrated a sustained release profile of amoxicillin in simulated gastrointestinal fluids, which is essential for maintaining therapeutic levels for a prolonged amount of time. The results indicate that the composite hydrogel of PAAm/starch/gelatin has good swelling behavior, appealing optical characteristics, and a promising controlled drug release mechanism. These results point to this hydrogel's considerable potential as a drug delivery method, providing a viable path toward enhancing the medicinal effectiveness of amoxicillin and maybe other medications.
