PubMed İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12469/4466

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When Care Faces Violence: Anticipatory Grief, Chronic Vigilance, and Ambiguous Loss Among Street Dog Care-Givers in Istanbul
(MDPI, 2026) Yildirim, Mine
This article examines how Turkey's 2024 amendment to the Animal Protection Law reshapes volunteer caregiving for free-roaming dogs in Istanbul by reconfiguring the practical conditions under which care is sought, coordinated, and sustained. Drawing on 43 in-depth interviews and five months of fieldwork (1 July-30 November 2025), this study combines constructivist grounded theory with reflexive thematic analysis to trace how legal change is encountered through everyday governance interfaces and how these encounters reorganize caregivers' routines, capacities, and moral worlds. The analysis yields four interlocking findings. First, caregivers describe a temporality of living in pre-loss, in which anticipated removal, disappearance, and uncertain outcomes generate chronic vigilance, anticipatory grief, and ambiguous loss without closure. Second, caregiving is increasingly recalibrated as risk management: commitments persist, but intervention narrows through heightened exposure to complaints, reputational scrutiny, and fears that help-seeking may backfire. Third, institutional pathways-hotlines, shelter intake, and municipal responses-are experienced as discretionary and opaque, producing a fluctuating threshold between assistance and harm that conditions whether caregivers engage official systems at all. Fourth, this study identifies a recurring veterinary bottleneck at the street-clinic-recovery handover, where limited short-term holding capacity stalls treatment trajectories and displaces recovery labor into precarious domestic and informal spaces. Together, these findings argue that caregiver well-being is not ancillary to animal welfare governance but constitutive of it. It shapes the continuity of monitoring, the timeliness of intervention, and the everyday mediation through which coexistence is maintained under intensified legal and political pressure.
Robust HMM-Based Remaining Useful Life Estimation Using a Ridge-Regularized EM Algorithm
(MDPI, 2026) Kucukdag, Halime Beyza; Kirkil, Gokhan; Hekimoglu, Mustafa
Estimating the remaining useful life (RUL) of engineering systems is crucial for maintenance planning and the reliability of complex mechanical units. Accurate RUL predictions support timely interventions and help to prevent unexpected failures. This study proposes a statistically robust framework that models degradation signals up to the end of life using a hidden Markov model (HMM) with a simple-failure structure and an absorbing terminal state. The proposed method estimates state-dependent linear emission parameters and transition probabilities using a ridge-regularized expectation-maximization (EM) algorithm. The ridge penalty stabilizes slope estimates under limited data, while a robust Huber-based scale estimator reduces sensitivity to outliers in the sensor-derived health indicator. RUL is computed as a weighted expected time to absorption, combining transient-state survival characteristics with smoothed posterior-state probabilities obtained via the forward-backward algorithm. This yields a low-variance state-aware estimator that preserves the probabilistic structure of the HMM. Simulation studies show that the proposed ridge-regularized EM significantly reduces parameter variance and improves predictive accuracy compared with the baseline weighted least squares EM (WLS-EM). A real-data case analysis demonstrates further improvements in RUL estimation accuracy and smoother, more reliable prediction trajectories. Overall, the framework provides a robust and interpretable approach for practical prognostics applications.
Quantum Information Flow in Microtubule Tryptophan Networks
(MDPI, 2026) Craddock, Travis J. A.; Gassab, Lea; Pusuluk, Onur
Networks of aromatic amino acid residues within microtubules, particularly those formed by tryptophan, may serve as pathways for optical information flow. Ultraviolet excitation dynamics in these networks are typically modeled with effective non-Hermitian Hamiltonians. By extending this approach to a Lindblad master equation that incorporates explicit site geometries and dipole orientations, we track how correlations are generated, routed, and dissipated, while capturing both energy dissipation and information propagation among coupled chromophores. We compare localized injections, fully delocalized preparations, and eigenmode-based initial states. To quantify the emerging quantum-informational structure, we evaluate the L1 norm of coherence, the correlated coherence, and the logarithmic negativity within and between selected chromophore sub-networks. The results reveal a strong dependence of both the direction and persistence of information flow on the type of initial preparation. Superradiant components drive the rapid export of correlations to the environment, whereas subradiant components retain them and slow their leakage. Embedding single tubulin units into larger dimers and spirals reshapes pairwise correlation maps and enables site-selective routing. Scaling to larger ordered lattices strengthens both export and retention channels, whereas static energetic and structural disorder suppresses long-range transport and reduces overall correlation transfer. These findings provide a Lindbladian picture of information flow in cytoskeletal chromophore networks and identify structural and dynamical conditions that transiently preserve nonclassical correlations in microtubules.
pH-Driven β2AR Dynamics Reveal Loop-Mediated Allosteric Communication
(Amer Chemical Soc, 2026) Sogunmez Erdogan, Nuray; Akten, E. Demet
Membrane protein structure and dynamics are highly sensitive to environmental conditions, including changes in pH that can alter the protonation states of ionizable residues and, in turn, influence local electrostatics and stability. Constant-pH molecular dynamics (CpHMD) provides a framework to explore such effects by allowing dynamic proton exchange during simulations. Here, we applied CpHMD at pH:6.5, 7.0, and 8.0, alongside conventional MD, to examine how pH variations may influence the local conformational behaviors of the beta 2-adrenergic receptor (beta 2AR). During the 1.2-mu s-long total simulation, loop regions rich in titratable residues, particularly ICL3 and ECL2, showed the strongest responses to protonation changes. CpHMD trajectories suggested a pH-dependent redistribution of loop flexibility and hydrogen-bonding patterns, producing a see-saw-like effect, while fixed-protonation Control runs showed more constrained behavior. Across all simulations, the key GPCR microswitches, such as the ionic lock, the Y-Y gate, the NPxxY and PIF motifs, and the Trp286-Phe290 toggle pair, stayed within the ranges expected for an inactive receptor. This suggests that pH changes mainly influence local loop motions in the inactive receptor without pushing it toward activation-like states. Finally, mutual information analysis on both C alpha atoms and dihedral angles revealed altered communication between the extracellular and intracellular loops under different pH environments. While limited in time scale, these results provide a computational perspective on how protonation dynamics can modulate the GPCR behavior and highlight the value of incorporating pH effects in molecular-level investigations.
Screen Media Exposure and Inhibitory Control: A Longitudinal Study from Infancy to Toddlerhood
(John Wiley and Sons Inc, 2026) Uzundag, B.A.; Güven, İ.N.; Sivis, Ö.; Başpınar, G.
Inhibitory control, a core executive function, supports children's ability to manage automatic and prepotent responses and regulate behavior. Screen media may disrupt its development by displacing activities supporting self-regulation or overstimulating the attention system. While findings in preschoolers are mixed, infancy and toddlerhood may represent particularly sensitive periods due to young children's strong reliance on social learning and their limited ability to process screen content. This longitudinal study examined associations between toddlers' inhibitory control and both the duration and context of screen media exposure, specifically, background television and parental use of media for emotion regulation. Data were collected from 75 infants and their mothers at Time 1 (infant age range = 9–16 months; M = 11.8, SD = 1.4) and again approximately 19 months later at Time 2 (infant age M = 31.1, SD = 1.8). Mothers reported on screen time and background television at both times and on media emotion regulation at Time 2. At Time 2, children completed two inhibitory control tasks (Prohibition and Reverse Categorization), and parents rated their children's inhibitory control. Greater background television exposure at Time 2 was linked to poorer performance on both behavioral tasks. Higher screen time at Time 2 predicted shorter delay of gratification in the Prohibition Task, after controlling for age, earlier screen time, and the time interval between assessments. Parental ratings of inhibitory control were not associated with screen media use. These findings point to a potential association between greater screen exposure, namely background television and overall duration, and lower inhibitory control skills during a sensitive period, independent of parental perception. © 2026 International Congress of Infant Studies.
Distinct Temporal Dynamics of Speech and Gesture Processing: Insights From Event-Related Potentials Across L1 and L2
(American Psychological Association, 2026) Ozer, Demet; Soyman, Efe; Badakul, Ayse Nur; Arslan, Burcu; Yilmaz, Fatma Sena; Goksun, Tilbe
This study examined the neural and behavioral processing of speech and iconic gestures across L1-Turkish and L2-English when participants attended the speech or gesture channel. We recorded electroencephalogram activity in Experiment 1 and reaction times in Experiment 2 (24 participants in each) during a mismatch task where concurrent speech and gesture expressed either matching or mismatching information in relation to a preceding action. Participants were asked to detect whether the gesture (gesture-focused task) or the speech (speech-focused task) was related to the preceding action. Speech was presented in Turkish or English in separate blocks. In Experiment 1, we focused on N400 and N2 components as indices of late semantic processing and early sequential matching, respectively. In the gesture-focused task, our results demonstrated a gesture mismatch effect, which was evident in more negative N400 amplitudes for mismatching than matching gestures only in the context of simultaneous matching speech. In the speech-focused task, we observed the N2 effect, which was apparent in more negative N2 amplitudes for mismatching than matching speech, regardless of the simultaneous gesture. These dynamics were largely reflected in reaction times in Experiment 2. These results point to potentially distinct neural and temporal dynamics in processing speech versus gestures and suggest that speech processing might be instantiated earlier, whereas gestures recruit later stages of processing. Notably, we observed some differential patterns across L1-Turkish and L2-English, suggesting that speech and gesture processing may operate differently across languages. Our findings highlight a complex interplay between modality, modality focus, language, and neural processing of multimodal information.
Personal and Collective Memories and Future Thoughts: A Laboratory Study of Episodic and Non-Episodic Detail
(Sage Publications Inc, 2026) Cheriet, Nawel; Oner, Sezin; Watson, Lynn; Cole, Scott
Self-based mental time travel - the ability to remember past events and imagine future events on a personal timeline - is well-characterized in cognitive science. A similar, but less-understood, ability is that of collective memory and collective future thinking, termed collective mental time travel (CMTT). To our knowledge, this is the first study to investigate the episodic richness of collective memory and future thoughts using an in-person laboratory paradigm. In two studies (UK and Turkey), we examined the effect of Event Type (collective, personal; between-groups) and Temporal Orientation (past, future; within-groups) on quantities of episodic and non-episodic details. Results show that personal events contained more episodic detail compared to collective events, and past events were associated with more episodic detail than future events. The distinction between personal and collective events was more pronounced in the UK than in Turkish sample, hinting at an influence of cross-cultural context on the episodicity of collective memories and future thoughts. Additionally, we observed a relationship between the episodicity of the past and the future exclusively in the UK population and for personal events, partially supporting the constructive episodic simulation hypothesis. These findings initiate a deeper understanding of the underlying cognitive processes that enable humans to engage in collective mental time travel.
Notum1a Inhibition Promotes Neurogenesis in the Adult Zebrafish Brain
(Nature Portfolio, 2025) Kocagoz, Yigit; Erdogan, Nuray Sogunmez; Ozdinc, Sevval; Ipekgil, Dogac; Katkat, Esra; Ozhan, Gunes
Notum is a carboxylesterase enzyme that modulates extracellular signaling by hydrolyzing palmitoleoyl residues from proteins, thereby influencing key pathways involved in cell differentiation, survival, and proliferation. While notum1 expression has been identified in the brain, its role in adult neurogenesis remains poorly understood. Using the adult zebrafish brain as a model system, we demonstrate that the notum1a homolog is broadly expressed across various brain cell types but is absent in undifferentiated radial glial cells. Pharmacological inhibition of Notum activity with the small molecule inhibitor ABC99 stimulates activation of radial glial cells, leading to increased neurogenesis. A BrdU pulse-chase assay confirms that ABC99-induced proliferation enhances the production of mature neurons. Despite Notum's established role in Wnt signaling, transcriptional analysis following ABC99 treatment reveals no sustained impact on Wnt pathway targets, suggesting that Notum may regulate neurogenesis through alternative mechanisms. Our findings highlight notum1a as a potential modulator of neural progenitor cell dynamics in the adult brain and suggest that targeting Notum could represent a novel therapeutic strategy for neurodegenerative conditions characterized by impaired neurogenesis.
Critical-Size Muscle Defect Regeneration Using an Injectable Cell-Laden Nanofibrous Matrix: An Ex Vivo Mouse Hindlimb Organ Culture Study
(MDPI, 2025) Jacho, Diego; Huynh, James; Crowe, Emily; Rabino, Agustin; Yildirim, Mine; Czernik, Piotr J.; Yildirim-Ayan, Eda
Musculoskeletal injuries involving volumetric muscle loss remain difficult to treat due to limited regenerative capacity and the lack of physiologically relevant experimental models. This study introduces a computer-controlled ex vivo mouse hindlimb culturing platform that applies dynamic mechanical loading to evaluate muscle regeneration in a critical-size tibialis anterior (TA) defect. The defect was treated with an injectable myoblast-laden nanofibrous scaffold composed of polycaprolactone nanofibers and collagen (PNCOL). The ex vivo mouse hindlimb culturing platform maintained tissue viability and transmitted physiological strain across bone and muscle without disrupting the unity of the bone-muscle structure. PNCOL treatment under mechanical loading enhanced muscle fiber organization, extracellular matrix regeneration, and anti-inflammatory responses (CD206) while upregulating paired box 7 (PAX7), myogenic factor 5 (MYF5), myogenic regulatory factor 4 (MRF4), and transforming growth factor beta1 (TGF beta 1) expression. Cytokine profiling revealed an anabolic shift involving wingless/integrated (WNT) and insulin-like growth factor-1 (IGF-1) signaling, indicating a pro-regenerative microenvironment. Overall, the combination of mechanical stimulation and biomaterial-based therapy significantly improved muscle regeneration within a controlled ex vivo model. This multidimensional approach provides a reproducible and ethical platform that advances musculoskeletal regenerative research while reducing animal use.
Does Your Love Lift Me Higher? A Direct Replication of the Energising Role of Secure Relationships
(John Wiley & Sons Ltd, 2025) Lagap, Adar Cem; Harma, Mehmet
Previous work has revealed that priming people with significant others increases feelings of security and energy, and in turn, boosts exploration motivations. In this preregistered study, we directly replicated Luke et al.'s (2012) Study 2 (N = 281). We found similar results as the replicated study regarding increased security feelings and exploration motivations on the self-report measures after the priming. However, we did not find any support for the increased energy feelings after the attachment security priming. In addition, contrary to Luke et al.'s (2012) results, energy feelings did not mediate the relationship between security priming and exploration motivations. A discussion of null findings, along with the limitations of self-reports and potential misinterpretation of the mediational analyses, follows. We also discuss possible future implications of the current findings.
Better Reflective Functioning in Mothers Linked to Longer Joint Attention with Infants
(Elsevier Science Inc, 2026) Koc, Nursena; Unlu, Huseyin; Uzundag, Berna A.
Joint attention is a foundational precursor to later developmental outcomes such as vocabulary, intelligence, and theory of mind. Previous research has shown that maternal sensitivity, depressive symptoms, and parent-child attachment security are associated with attention-sharing behaviors between mothers and their infants. The present study examined the relationship between mothers' reflective functioning (the ability to recognize and interpret one's own and one's child's mental states, as well as the behaviors motivated by those mental states) and joint attention. Data were collected from 72 infants aged 10-16 months and their mothers. Results indicated that mothers who reported greater difficulty in understanding and distinguishing between their own and their child's mental states (i.e., higher prementalization) tended to engage in joint attention episodes that were shorter and more frequent, and they were also more likely to terminate these interactions. In contrast, mothers expressing greater interest and curiosity about their infants' mental states spent longer periods in joint attention, initiated these episodes less often, and were less inclined to terminate them. Additionally, mothers who felt more certain about their infants' mental states were less likely to end joint attention episodes. After controlling for infant age and socioeconomic status, higher levels of interest and certainty continued to predict lower maternal termination, while prementalization was still linked to a higher number of joint attention episodes. These findings suggest that mothers' perceptions of their infants' mental states shape how they engage in shared attention during everyday play interactions.
A Polish Adaptation of the Autobiographical Recollection Test (ART): Toward a Reliable and Valid Measure of Individual Differences in Autobiographical Memory
(Routledge Journals, Taylor & Francis Ltd, 2025) Barzykowski, Krystian; Ilczuk, Ewa; Oner, Sezin; Chwilka, Paulina; Wereszczynski, Michal; Chwiłka, Paulina
Although previous research has extensively examined the characteristics of specific autobiographical memories, few tools have been available to assess how individuals recall their personal past in general. To address this gap, we adapted into Polish the Autobiographical Recollection Test (ART), a self-report instrument originally designed to capture general autobiographical remembering across seven components: vividness, narrative coherence, reliving, rehearsal, scene construction, visual imagery, and life story relevance. Confirmatory factor analysis supported the factorial validity of the Polish version, demonstrating adequate psychometric properties. The Polish adaptation also showed expected correlations with another self-report measure of autobiographical memory ability (Survey of Autobiographical Memory, SAM), supporting its convergent validity. Furthermore, both the full and brief versions of ART showed significant associations with scores on the Involuntary Autobiographical Memory Inventory (IAMI). These findings provide robust support for the Polish adaptation of ART as a reliable tool for assessing the subjective qualities of autobiographical memory, with potential applications in research on diverse populations.
Reshaping Globular Dynamics of S. Aureus Pyruvate Kinase via Bond Restraints to Allosteric Sites
(Springer, 2025) Fidan, Vahap Gazi; Aydin, Dilvin; Yazgi, Irem; Akten, E. Demet
The global dynamics of pyruvate kinase were examined using molecular dynamics (MD) simulations to investigate the effects of allosteric inhibition through bond restraints applied at two key allosteric sites. The study employed the experimentally resolved structure of the enzyme complexed with the allosteric inhibitor IS-130 at the small C-C interface, serving as a reference for analyzing an additional, computationally predicted allosteric site at the large A-A interface. Simulations identified the B and CT domains as the most mobile regions, with bond restraints at either interface significantly reducing CT domain flexibility up to 9 & Aring; across all chains. Restraints at the C-C interface limited minimal global conformational sampling, whereas restraints at the A-A interface altered the dynamic profile without narrowing the sampled conformational space, suggesting distinct regulatory roles for each interface. Distance fluctuation analyses revealed enhanced interchain communication and reduced mobility near restrained sites, suggesting that these restraints reinforce allosteric inhibition by stabilizing otherwise flexible domains. Cross-correlation analysis showed a marked reduction in long-range residue-residue correspondence, especially under C-C restraints, indicating disrupted dynamic coordination essential for catalytic activity. Mutual information analysis, capturing both linear and non-linear dependencies, further supported these findings by showing a widespread loss of dynamic correspondence in positional fluctuations across the receptor upon restraint application. Notably, although the C-C interface has been experimentally linked to inhibition, these results suggest that the computationally predicted large A-A interface may also contribute to allosteric regulation. Together, these findings highlight the distributed and cooperative nature of allosteric control in pyruvate kinase.
Citation - WoS: 1
Citation - Scopus: 1
Infants' Background Television Exposure and Maternal Language Input: A Home Observation Study
(Cambridge Univ Press, 2025) Kessafoglu, Dilara; Yildiz, Ezgi; Kuntay, Aylin C.; Uzundag, Berna A.
Parental reports and experimental studies indicate that parents speak less to their children in the presence of background television. However, there is a lack of home observations examining the relations between infants' background TV exposure and maternal infant-directed speech. In the current study, 32 infants and their mothers were observed for 60 minutes in their homes at 8, 10, and 18 months of age. Results revealed that the number of words, the number of different words, and the number of questions in infant-directed speech were consistently lower in households with background TV. Furthermore, these aspects of maternal language input were negatively related to the duration of background TV, controlling for families' socioeconomic background. These findings suggest that television may have a negative impact on young children's language development via disrupted parent-child interactions in the presence of background TV in the home environment. Ebeveynlerden al & imath;nan bildirimler ve deneysel & ccedil;al & imath;& scedil;malar, arka planda televizyon a & ccedil;& imath;kken ebeveynlerin & ccedil;ocuklar & imath;yla daha az konu & scedil;tuklar & imath;n & imath; g & ouml;stermektedir. Ancak, arka plan televizyon ile ebeveynlerin bebeklerine y & ouml;nelttikleri dil aras & imath;ndaki ili & scedil;kiyi inceleyen ev g & ouml;zlemlerine ihtiya & ccedil; duyulmaktad & imath;r. Bu & ccedil;al & imath;& scedil;mada, 32 bebek ve anneleri, bebekler 8, 10 ve 18 ayl & imath;kken evlerinde her ziyarette 60'ar dakika boyunca g & ouml;zlemlenmi & scedil;tir. Bulgular, arka planda televizyonun a & ccedil;& imath;k oldu & gbreve;u evlerde bebeklere y & ouml;neltilen dildeki toplam kelime say & imath;s & imath;n & imath;n, farkl & imath; kelime say & imath;s & imath;n & imath;n ve soru say & imath;s & imath;n & imath;n tutarl & imath; bi & ccedil;imde daha d & uuml;& scedil;& uuml;k oldu & gbreve;unu g & ouml;stermi & scedil;tir. Ayr & imath;ca, bu dil girdisi & ouml;l & ccedil;& uuml;tleri, ailelerin sosyoekonomik d & uuml;zeyi kontrol edildi & gbreve;inde, arka plan televizyon s & uuml;resiyle olumsuz y & ouml;nde ili & scedil;kili bulunmu & scedil;tur. Bu bulgular, televizyonun aktif olarak izlenmiyor olsa bile ebeveyn-& ccedil;ocuk etkile & scedil;imini s & imath;n & imath;rlayarak k & uuml;& ccedil;& uuml;k & ccedil;ocuklar & imath;n dil geli & scedil;imini olumsuz y & ouml;nde etkileyebilece & gbreve;ini d & uuml;& scedil;& uuml;nd & uuml;rmektedir.
Exploring Children's Causal Language Production: The Role of Mothers and Fathers Across Different Tasks in Dyadic Interactions
(Cambridge Univ Press, 2025) Kandemir, Songul; Aktan-Erciyes, Asli
Causal language is essential for children's language development, helping them understand and explain the reasons behind events. This study focuses on children's causal language production and the role of parental input, aiming to (1) investigate differences in maternal and paternal language use, (2) analyse children's causal language production across tasks and communication partners, and (3) examine the relationship between parental input and children's causal language skills. Sixty children aged 4-5 and their parents participated in dyadic sessions, which included free play, guided play, and storytelling tasks. Results showed that fathers used more causal language than mothers during free play, and children also produced more causal language with their fathers in this context compared to storytelling. Overall, both maternal and paternal causal language inputs were linked to children's causal language production, highlighting the significant influence of parental input on language development. Nedensel dil, & ccedil;ocuklar & imath;n dil geli & scedil;imi i & ccedil;in temel & ouml;neme sahiptir ve onlar & imath;n olaylar & imath;n ard & imath;ndaki nedenleri anlamalar & imath;na ve a & ccedil;& imath;klamalar & imath;na yard & imath;mc & imath; olur. Bu & ccedil;al & imath;& scedil;ma, & ccedil;ocuklar & imath;n nedensel dil & uuml;retimine ve ebeveyn girdisinin rol & uuml;ne odaklanarak (1) anne ve baba dil kullan & imath;mlar & imath; aras & imath;ndaki farkl & imath;l & imath;klar & imath; incelemeyi, (2) & ccedil;ocuklar & imath;n farkl & imath; g & ouml;revler ve ileti & scedil;im partnerleri ba & gbreve;lam & imath;nda nedensel dil & uuml;retimini analiz etmeyi ve (3) ebeveyn girdisi ile & ccedil;ocuklar & imath;n nedensel dil becerileri aras & imath;ndaki ili & scedil;kiyi ara & scedil;t & imath;rmay & imath; ama & ccedil;lamaktad & imath;r. D & ouml;rt-be & scedil; ya & scedil; aral & imath;& gbreve;& imath;nda 60 & ccedil;ocuk ve ebeveynleri, serbest oyun, y & ouml;nlendirilmi & scedil; oyun ve hikaye anlat & imath;m & imath; g & ouml;revlerini i & ccedil;eren ikili etkile & scedil;im oturumlar & imath;na kat & imath;lm & imath;& scedil;t & imath;r. Bulgular, babalar & imath;n serbest oyun s & imath;ras & imath;nda annelere k & imath;yasla daha fazla nedensel dil kulland & imath;& gbreve;& imath;n & imath; ve & ccedil;ocuklar & imath;n da bu ba & gbreve;lamda babalar & imath;yla etkile & scedil;imde hikaye anlat & imath;m & imath;na k & imath;yasla daha fazla nedensel dil & uuml;retti & gbreve;ini g & ouml;stermi & scedil;tir. Genel olarak, hem anne hem de baba nedensel dil girdileri, & ccedil;ocuklar & imath;n nedensel dil & uuml;retimiyle ili & scedil;kili bulunmu & scedil; ve ebeveyn girdisinin dil geli & scedil;imi & uuml;zerindeki belirgin etkisini ortaya koymu & scedil;tur.
Hands-On Docking With Molegro Virtual Docker
(Humana Press Inc., 2026) Dere, D.; Pehlivan, S.N.; da Silva, A.D.; de Azevedo Junior, W.F.; de Azevedo, Walter Filgueira
Molegro Virtual Docker (MVD) integrates state-of-the-art search algorithms and scoring functions dedicated to protein-ligand docking simulations. It implements differential evolution as a search engine and MolDock and Plants scores to calculate binding affinity. In this work, we describe a workflow focused on how to build regression models to predict the inhibition of cyclin-dependent kinase 2 (CDK2). We employ available structural and binding data to construct machine learning models to calculate CDK2 inhibition based on the atomic coordinates obtained through docking simulations performed with MVD. We present a hands-on approach to show how to integrate docking results and machine learning methods available at Scikit-Learn to build targeted scoring functions. Our regression models show superior predictive performance compared with classical scoring functions. All CDK2 datasets and Jupyter Notebooks discussed in this work are available at GitHub: https://github.com/azevedolab/docking#readme. We made the source code of the program SAnDReS 2.0 available at https://github.com/azevedolab/sandres. © 2025 Elsevier B.V., All rights reserved.
Haptic-Assisted Soldering Training Protocol in Virtual Reality: The Impact of Scaffolded Guidance
(Institute of Electrical and Electronics Engineers Inc., 2025) Yilmaz, M.; Batmaz, A.U.; Sarac, M.
In this paper, we present a virtual training platform for soldering based on immersive visual feedback (i.e., a Virtual Reality (VR) headset) and scaffolded guidance (i.e., disappearing throughout the training) provided through a haptic device (Phantom Omni). We conducted a between-subject user study experiment with four conditions (2D monitor with no guidance, VR with no guidance, VR with constant, active guidance, and VR with scaffolded guidance) to evaluate their performance in terms of procedural memory, motor skills in VR, and skill transfer to real life. Our results showed that the scaffolded guidance offers the most effective transitioning from the virtual training to the real-life task — even though the VR with no guidance group has the best performance during the virtual training. These findings are critical for the industry and academy looking for safer and more effective training techniques, leading to better learning outcomes in real-life implementations. Furthermore, this work offers new insights into further haptic research in skill transfer and learning approaches while offering information on the possibilities of haptic-assisted VR training for complex skills, such as welding and medical stitching. © 2025 Elsevier B.V., All rights reserved.
Citation - WoS: 1
Citation - Scopus: 1
Engineering of Geobacillus Kaustophilus Lipase for Enhanced Catalytic Efficiency and Methanol Tolerance in Biodiesel Production from Sunflower Oil
(Elsevier, 2025) Tulek, Ahmet; Poyraz, Yagmur; Sukur, Gozde; Pacal, Nurettin; Ozdemir, F. Inci; Yildirim, Deniz; Essiz, Sebnem
Lipase-mediated biodiesel production offers a sustainable and environmentally friendly alternative to conventional chemical methods. However, enzyme limitations such as low activity, poor thermal stability, and limited solvent tolerance remain challenges. In this study, a lipase from Geobacillus kaustophilus (Gklip) was engineered for improved biodiesel production using molecular docking, molecular dynamics (MD) simulations, and molecular mechanics/generalized born surface area (MM/GBSA) free energy calculations. Five mutants (Y29S, Q114T, F289D, Q184M, and Q114F) were generated via site-directed mutagenesis and expressed in Escherichia coli. Biochemical characterization revealed that all mutants retained the wild-type's optimal temperature (50 degrees C) and pH (8.0), while showing varying pH ranges, with the broadest observed in Q184M. Thermal stability increased significantly in Q184M (32.86-fold) and Q114F (5.93-fold). Catalytic efficiencies improved by 2.07-, 2.05-, and 2.63-fold in Q184M, F289D, and Y29S, respectively, compared to the wild-type (0.57). In the presence of 60 % methanol, the wild-type retained only 30.4 % activity, while Q184M maintained 67.5 %, highlighting superior solvent tolerance. Biodiesel conversion assays using sunflower oil showed no product formation by the wild-type, whereas Q184M, Q114F, and F289D achieved yields of 58.7 %, 56.3 %, and 49.2 %, respectively. These findings identify Q184M and Q114F as promising enzyme candidates for enzymatic biodiesel production.
Citation - WoS: 1
Steady-State Entanglement Generation Via Casimir-Polder Interactions
(Nature Portfolio, 2025) Izadyari, Mohsen; Pusuluk, Onur; Sinha, Kanu; Mustecaplioglu, Ozgur E.
We investigate the generation of steady-state entanglement between two atoms resulting from the fluctuation-mediated Casimir-Polder (CP) interactions near a surface. Starting with an initially separable state of the atoms, we analyze the atom-atom entanglement dynamics for atoms placed at distances in the range of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sim 25$$\end{document} nm away from a planar medium, examining the effect of medium properties and geometrical configuration of the atomic dipoles. We show that perfectly conducting and superconducting surfaces yield an optimal steady-state concurrence value of approximately 0.5. Furthermore, although the generated entanglement decreases with medium losses for a metal surface, we identify an optimal distance from the metal surface that assists in entanglement generation by the surface. While fluctuation-mediated interactions are typically considered detrimental to the coherence of quantum systems at nanoscales, our results demonstrate a mechanism for leveraging such interactions for entanglement generation.
Citation - WoS: 2
Citation - Scopus: 2
Measuring the Semantic Priming Effect Across Many Languages
(Nature Portfolio, 2025) Buchanan, Erin M.; Cuccolo, Kelly; Heyman, Tom; van Berkel, Niels; Coles, Nicholas A.; Iyer, Aishwarya; Lewis, Savannah C.
Semantic priming has been studied for nearly 50 years across various experimental manipulations and theoretical frameworks. Although previous studies provide insight into the cognitive underpinnings of semantic representations, they have suffered from small sample sizes and a lack of linguistic and cultural diversity. In this Registered Report, we measured the size and the variability of the semantic priming effect across 19 languages (n = 25,163 participants analysed) by creating the largest available database of semantic priming values using an adaptive sampling procedure. We found evidence for semantic priming in terms of differences in response latencies between related word-pair conditions and unrelated word-pair conditions. Model comparisons showed that the inclusion of a random intercept for language improved model fit, providing support for variability in semantic priming across languages. This study highlights the robustness and variability of semantic priming across languages and provides a rich, linguistically diverse dataset for further analysis. The Stage 1 protocol for this Registered Report was accepted in principle on 15 July 2022. The protocol, as accepted by the journal, can be found at https://osf.io/u5bp6 (registration) or https://osf.io/q4fjy (preprint version 6, 31 May 2022).

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