Scholarly Publications - BAM

Permanent URI for this collectionhttps://hdl.handle.net/11693/115580

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Open Access
Top-down modulation of visual action perception: distinct task effects in the action observation network
(Springer, 2025-11-10) Eroğlu, Aslı; Ürgen, Burcu Ayşen
Perceiving others’ actions is essential for survival and social interaction. Cognitive neuroscience research has identified a network of brain regions crucial to visual action perception, known as the Action Observation Network (AON), comprising the posterior superior temporal cortex (pSTS), posterior parietal cortex, and premotor cortex. Recent research highlights the importance of integrating top-down processes, such as attention, to gain a deeper understanding of action perception. This study investigates how attention modulates the AON during human action perception. We conducted a two-session fMRI experiment with 27 participants. They viewed eight videos of pushing actions, varying in actor (female vs. male), effector (hand vs. foot), and target (human vs. object). In the first session, participants focused on specific features of the videos (actor, effector, or target). In the second, they passively viewed the videos. From the passive viewing session data, we defined regions of interest (ROIs) in the pSTS, parietal, and premotor cortices for each hemisphere. We then performed model-based representational similarity analysis (RSA) and decoding analysis. RSA results showed that only the task model, among all tested models, exhibited a significant correlation with neural representational similarity matrices (RDMs) across all ROIs, indicating a specific alignment between AON nodes and the ongoing task. Decoding analysis further showed that different task types uniquely affected each AON node, indicating feature- and region-specific interactions. These findings underscore that top-down attentional processes significantly alter neural representations within the AON, highlighting the dynamic interplay between attention and action perception in the brain.
Embargo
Energy absorber inspired by spider webs
(Elsevier Ltd, 2025-08-15) Yavuz, Koray; Jahangirova, Seymur; Görgülüarslan, Recep M.
The spider orb web has evolved to efficiently absorb the energy of flying insects colliding with it. In this study, a novel three-dimensional lattice structure inspired by the specific structural characteristics of the spider orb web was designed and optimized to create a new lattice design. The design was optimized for energy absorption and energy absorption efficiency using a size optimization procedure with numerical modeling based on beam elements under quasi-static compression loading. This optimized lattice was additively manufactured and subjected to quasi-static compression testing. Numerical results for energy absorption and compression behavior showed good agreement with experimental findings. Additionally, numerical analysis of the optimized lattice was performed using solid elements to predict the energy absorption behavior more accurately, and the results showed even better agreement with experimental data. The resulting lattice also demonstrated improved energy absorption performance compared to existing lattice structures.
Open Access
Functional and structural plasticity induced by audiovisual associations and sensory experiences
(Springer Science and Business Media Deutschland GmbH, 2025-06-08) Yildirim-Keles, Fazilet Zeynep; Demirayak, Pinar; Kafalıgönül, Hacı Hulusi
Crossmodal associations and correspondences play important roles in shaping perception and guiding our actions. However, we still have a limited understanding of association-induced changes in the adult human brain. An important question to address is to what extent passive exposure to crossmodal associations leads to functional and structural changes in the brain. Utilizing an audiovisual association paradigm in which motion stimuli presented in the left visual field were paired with auditory tones, we investigated experience-dependent crossmodal plasticity by examining resting-state functional connectivity and cortical thickness. Following the association phase, we observed widespread increases in functional connectivity between the trained region (e.g., right V1, V2, and V3) and higher-order frontal, temporal, and occipital areas. In contrast, functional connectivity changes in the untrained region (e.g., left V1, V2, and V3) were markedly reduced, indicating that the observed plasticity was largely specific to the cortical representation of the stimulated visual field. Consistent with the functional results, cortical thickness analysis revealed a clear hemispheric asymmetry, with significant changes observed exclusively in the right hemisphere. Moreover, both the functional and structural assessments showed widespread changes in high-level association cortices, whereas changes in low-level sensory areas were less pronounced. The overlap between functional and structural measures suggests that enhanced connectivity aligns with structural changes due to crossmodal associations. These results illustrate that associations formed without explicit training or feedback can lead to functional and structural changes in the adult human brain, providing important implications for perception and neural plasticity in daily life situations.
Open Access
Higher-order visuospatial processing abilities in cerebral visual impairment: Behavioral assessment and neurophysiological mechanisms
(Annual Reviews Inc., 2025-06-09) Merabet, Lotfi B.; Manley, Claire E.; Pamir, Zahide
Cerebral visual impairment (CVI) is a brain-based visual disorder associated with early injury and maldevelopment of visual processing pathways and areas. The clinical profile of visual dysfunctions observed in CVI is broad and complex. In this review, we discuss how visuospatial processing deficits represent a core feature of this condition, focusing on evidence from behavioral studies investigating complex motion processing and visual search abilities. Results from functional and structural neuroimaging studies have also provided important insight into putative neurophysiological mechanisms associated with these functional visual impairments. We propose that higher-order visual processing dysfunctions in CVI result from an impaired interplay between bottom-up (stimulus-driven) and top-down (goal-driven) processing mechanisms that leads to characteristic challenges in interpreting and interacting with the surrounding visual environment.
Open Access
Predictive processing in biological motion perception: evidence from human behavior
(Sage Publications Ltd., 2025-07-15) Elmas, Hüseyin Orkun; Er, Sena; Rezaki, Ada Dilek; İzgi, Ayşesu; Urgen, Buse M.; Boyacı, Hüseyin; Ürgen, Burcu Ayşen
Biological motion perception plays a crucial role in understanding the actions of other animals, facilitating effective social interactions. Although traditionally viewed as a bottom-up driven process, recent research suggests that top-down mechanisms, including attention and expectation, significantly influence biological motion perception at all levels, particularly highlighted under complex or ambiguous conditions. In this study, we investigated the effect of expectation on biological motion perception using a cued individuation task with point-light display (PLD) stimuli. We conducted three experiments investigating how prior information regarding action, emotion, and gender of PLD stimuli modulates perceptual processing. We observed a statistically significant congruency effect when preceding cues informed about action of the upcoming biological motion stimulus; participants performed slower in incongruent trials compared to congruent trials. This effect seems to be mainly driven from the 75% congruency condition compared to the non-informative 50% (chance level) validity condition. The congruency effect that was observed in the action experiment was absent in the emotion and gender experiments. These findings highlight the nuanced role of prior information in biological motion perception, particularly emphasizing that action-related cues, when moderately reliable, can influence biological motion perception. Our results are in line with the predictive processing framework, suggesting that the integration of top-down and bottom-up processes is context-dependent and influenced by the nature of prior information. Our results also emphasize the need to develop more comprehensive frameworks that incorporate naturalistic, complex and dynamic, stimuli to build better models of biological motion perception.
Open Access
SSDiffusion: state-space diffusion model for medical image synthesis
(IEEE, 2025-08-15) Kabaş, Bilal; Nezhad, Valiyeh Ansarian; Atlı, Ömer Faruk; Arslan, Fuat; Çukur, Tolga
Medical image synthesis enables imputation of missing slices from acquired modalities, thereby reducing the need for repetitive and prolonged procedures in diagnostics. However, this is a non-trivial task due to the ill-posed and nonlinear characteristics of the problem. Generative adversarial networks (GANs) have shown promise in addressing these challenges. However, GANs can suffer from instability and mode collapse. Denoising diffusion models (DDMs) are recently demonstrated to be superior to GANs in terms of training stability and high fidelity. Yet, existing diffusion-based techniques rely on U-Net backbones, which are suboptimal for capturing contextual relationships between different tissue parts. Although transformers are adept at extracting the global context, their quadratic complexity makes them impractical for processing individual pixels rather than image patches. State-space models (SSMs) provide an efficient alternative with lower complexity, enabling the handling of extremely long sequences while effectively extracting contextual relationships. In this paper, we introduce SSDiffusion, a novel state-space diffusion model designed for multimodal medical image translation. By leveraging the strengths of state-space representations, our approach effectively captures contextual dependencies, improving the translation performance. We evaluate SSDiffusion on a variety of medical image translation tasks. Experiments indicate that SSDiffusion outperforms state-of-the-art GAN and diffusion methods.
Open Access
The ‘task’ of mind-wandering splits both multiple demand and default mode regions and ramps-up the deactivating regions
(Elsevier, 2025-09-09) Giray, İrem; Farooqui, Ausaf Ahmed
The activation of multiple demand (MD) regions to diverse tasks has been linked to the demands of making task-related cognitive control changes – keeping it focussed on task, controlling attention and working memory, organizing and maintaining a task model that will control the sequence and identity of what is to be done when, etc. Demanding tasks that require such control are also accompanied by a deliberative cognition whereby cognitive changes do not occur automatically and have to be made deliberately. We investigated whether the deliberativeness of cognition activates MD regions regardless of task-related demands. When not engaged in demanding tasks, the mind wanders. We asked participants to do the same during task periods, and to differentiate from rests, we asked them to deliberately and intensely wander their minds across random thoughts. We found that a set of MD regions – pre-supplementary motor area (preSMA), anterior insula, and posterior part of the middle frontal gyrus – activated during these periods, and another set – intraparietal sulcus, right anterior prefrontal cortex – deactivated. In fact, some of the activating regions (e.g., preSMA) activated more during this task than in response to robust working memory updating demands. Dissociations were also present in the Default Mode Network (DMN). Parts of the temporoparietal junction deactivated while posterior cingulate and medial prefrontal regions activated. Lastly, we found that the deactivating regions ramped-up their activity across the ‘task’ duration, showing that this ramp-up, previously linked to demands of sequentially organizing extended tasks, occurs during any construed task, including those without such demands.
Open Access
Dynamic reorganization of functional networks underlying audiovisual interactions
(Nature Research, 2025-11-12) Akdoğan, İrem; Aydin, Serap; Kafaligönül, Hulusi
Crossmodal interactions involve crosstalk between different cortical areas and dynamic recruitment of regions, which is crucial for integrating sensory information into a coherent percept. Despite their significance, the dynamic cortical networks underlying the crossmodal influence of auditory information on visual motion processing—particularly in terms of temporally resolved EEG connectivity—have yet to be comprehensively characterized. In the present study, we investigated frequency-specific networks underlying audiovisual interactions during motion and speed estimation. Functional networks were generated using directed transfer function (DTF) and adaptive DTF (ADTF) to estimate connectivity patterns of electroencephalogram (EEG) data. Network-based statistical analyses revealed frequency-specific networks in the theta and alpha bands, which supported long-range communication between occipital/parieto-occipital, parietal, and frontal regions during audiovisual interactions compared to unisensory visual motion processing. Graph theory analyses demonstrated a transition from localized and segregated processing to global integration, emphasizing cortical network reorganization according to the demands of sensory processing. Moreover, these analyses further revealed frequency-specific shifts in connectivity over time, with low-frequency oscillations exhibiting sustained connectivity increases, while high-frequency bands showed transient patterns, reflecting the temporal flexibility of neural networks. These findings illustrate how local and global network modulations reflect the brain’s dynamic reorganization, balancing integration and segregation during crossmodal influences.
Open Access
Effect of polygenic scores on the relationship between psychosis and cognition
(Nature Publishing Group, 2025-11-21) Varney, Lauren; Jedlovszky, Krisztina; Wang, Baihan; Murtough, Stephen; Cotic, Marius; Richards-Belle, Alvin; Saadullah Khani, Noushin; Lau, Robin; Abidoph, Rosemary; McQuillin, Andrew; Thygesen, Johan H.; Alizadeh, Behrooz Z.; Bender, Stephan; Crespo-Facorro, Benedicto; Hall, Jeremy; Iyegbe, Conrad; Kravariti, Eugenia; Lawrie, Stephen M.; Mata, Ignacio; McDonald, Colm; Murray, Robin M.; Prata, Diana; Toulopoulou, Timothea; van Haren, Neeltje EM; Bramon, Elvira
Cognitive impairment is an important but often under-researched symptom in psychosis. Both psychosis and cognition are highly heritable and there is evidence of a genetic effect on the relationship between them. Using samples of adults (N = 4 506) and children (N = 10 981), we investigated the effect of schizophrenia and bipolar disorder polygenic scores on cognitive performance, and intelligence and educational attainment polygenic scores on psychosis presentation. Schizophrenia polygenic score was negatively associated with visuospatial processing in adults (beta: −0.0569; 95% confidence interval [CI]: −0.0926, −0.0212) and working memory (beta: −0.0432; 95% CI: −0.0697, −0.0168), processing speed (beta: −0.0491; 95% CI: −0.0760, −0.0223), episodic memory (betas: −0.0581 to −0.0430; 95% CIs: −0.0847, −0.0162), executive functioning (beta: −0.0423; 95% CI: −0.0692, −0.0155), fluid intelligence (beta: −0.0583; 95% CI: −0.0847, −0.0320), and total intelligence (beta: −0.0458; 95% CI: −0.0709, −0.0206) in children. Bipolar disorder polygenic score was not associated with any cognitive domains studied. Lower polygenic scores for intelligence were associated with greater odds of psychosis in adults (odds ratio [OR]: 0.886; 95% CI: 0.811–0.968). In children, lower polygenic scores for both intelligence (OR: 0.829; 95% CI: 0.777–0.884) and educational attainment (OR: 0.771; 95% CI: 0.724–0.821) were associated with greater odds of psychotic-like experiences. Our findings suggest that polygenic scores for both cognitive phenotypes and psychosis phenotypes are implicated in the relationship between psychosis and cognitive performance. Further research is needed to determine the direction of this effect and the mechanisms by which it occurs.
Open Access
Replicating the unconscious working memory effect: a multisite Registered Report
(Oxford University Press, 2026-01-19) Franco Martínez, A.; Rey Sáez, R.; Adrián Ventura, J.; Amerio, P.; Baciero, A.; Bennis, A.; Bergström, F.; Cleeremans, A.; Contu, L.; Dell’Acqua, R.; Deng, X.; Dolu, Fatma Nur; Gambarota, F.; Gao, Y.; Garre Frutos, F.; Grubert, A.; Hernando, A.; Hinojosa, J. A.; Hoory, A.; Hou, Z.; Hung, S. M.; Ito, A.; Jimenez, M.; Kosachenko, A. I.; Kulaksız, M.; Lee, D. Y. H.; Malas, E. M.; Malejka, S.; Montoro, P. R.; Mudrik, L.; Pavlov Y. G.; Pesimena, G.; Prieto, A.; Rahnev, D.; Ringenberg L.; Sandoval Lentisco A.; Sarodo A.; Schreiber, M.; Sessa, P.; Solana, P.; Tarasov, D. A.; Tortajada, M.; Xue, K.; Xue, Z.; Zheng, Y.; Çinici, M.; Shanks, D. R.; Soto, D.; Vadillo, M. A.
Although in recent years some studies have found evidence suggesting that working memory (WM) may operate on unconscious perceptual contents, decisive demonstrations of the existence of unconscious WM are lacking. In the present Registered Report, we replicate the first study on this topic by Soto et al. (Working memory without consciousness. Curr Biol 2011;21:R912–3.): a visual discrimination task asking participants to report the direction in which a subliminal Gabor grating was rotated after a 2-s delay. We acquired a multisite sample from 19 laboratories, with a larger number of participants (N = 531) and trials (720 in two sessions) than those typically used in previous studies. As a result, a large-sample, international, and open-access dataset is now available for researchers and future analyses. Furthermore, some minimal baseline requirements were guaranteed for the experimental task (i.e. number of valid trials, motivation, and consistent labels for the Perceptual Awareness Scale). The results showed (1) above-chance WM performance in cue-present trials reported as unseen (.55 accuracy), (2) a significant positive correlation between WM performance and cue detection sensitivity (r = .228), and (3) a significant above-chance intercept in the regression of performance on sensitivity (β0 = .521). These findings suggest that WM can operate on unconscious representations, although it remains positively associated with perceptual sensitivity. Crucially, because measurement error could compromise the interpretation of these three results, we provide evidence for our measures’ excellent reliability and, more fundamentally, for their validity.
Open Access
Replicability of a resting-state functional connectivity study in profound early blindness
(Frontiers Research Foundation, 2025-04-28) Nadvar, Negin; Bauer, Corinna; Pamir, Zahide; Merabet, Lotfi B.; Koppelmans, Vincent; Weiland, James
It has been shown that the choice of preprocessing pipelines to remove contamination from functional magnetic resonance images can significantly impact the results, particularly in resting-state functional connectivity (rsFC) studies. This underscores the critical importance of replication studies with different preprocessing methodologies. In this study, we attempted to reproduce the rsFC results presented in an original study by Bauer et al. in 2017 on a group of sighted control (SC) and early blind (EB) subjects. By using the original dataset, we utilized another widely used software package to investigate how applying different implementations of the original pipeline (RMin model) or a more rigorous and extensive preprocessing stream (RExt model) can alter the whole-brain rsFC results. Our replication study was not able to fully reproduce the findings of the original paper. Overall, RExt shifted the distribution of rsFC values and reduced functional network density more drastically compared with RMin and the original pipeline. Remarkably, the largest rsFC effects appeared to primarily belong to certain connection pairs, irrespective of the pipeline used, likely demonstrating immunity of the larger effects and the true results against suboptimal processing. This may highlight the significance of results verification across different computational streams in pursuit of the true findings.
Open Access
Genetic contribution to idiosyncratic drug-induced liver injury: a systematic review and bioinformatic analysis
(Springer, 2025-06-10) Matilla-Cabello, Gonzalo; Sanabria-Cabrera, Judith; Remesal-Doblado, Angela; Çelebi-Çınar, Muazzez; Bodoque-Garcia, Ana; Metin-Yılmaz, Fatma Betül; de Los Santos-Fernandez, R. L.; Alvarez-Alvarez, Ismael; Karakayalı, Özlen Konu; Andrade, Raul J.; Cakan-Akdogan, Gulcin; Lucena, M. Isabel; Villanueva-Paz, Marina
Background: Individual genetics plays a crucial role in idiosyncratic drug-induced liver injury (DILI). This study performs a comprehensive systematic review and analysis of DILI and genetics literature, focused on elucidating relevant genes, drugs and functional enrichments. Methods: Using PRISMA 2020 Guidelines, we identified eligible literature published up to June 30th, 2023, in four databases with a refined search strategy for DILI and genetic-related terms. Original articles on human patients with at least one control group, that reported statistically significant variants between groups and indicated validated DILI biochemical criteria were included. Data extraction and bioinformatic analyses were performed using R v4.4.1. Functional enrichment analyses were conducted using KEGG database. Results: A total of 25,874 records were screened. Ultimately, 139 original articles were included: 124 studies involving variants associated to DILI susceptibility (DILI-Risk set), 36 involving variants associated to DILI protection (DILI-Protective set), and 21 for both. In DILI-Risk set 83 genes were included, being NAT2, HLA-B, HLA-DRB1, HLA-A and HLA-DQB1 the most frequent, whilst DILI-Protective set comprised 25 genes. The most common culprit drugs for both sets were antimycobacterials, antineoplastics and direct acting antivirals. Hierarchical analysis performed with KEGG enrichment analysis revealed major pathway clusters in DILI-Risk set corresponding to i) regulation of the adaptive immune response and cytotoxicity mediated by T and NK cells (HLA family); ii) general inflammatory response (TNF, NFKB1, and RELA); iii) porphyrin, ascorbate and aldarate metabolism (UGT family); iv) drug metabolism pathways (CYP450 and GST families) and v) biliary secretion and hepatic cellular transport (ABC family and SLCO1B1). Conclusion: This work highlights the major role of the immune system and oxidative stress response in DILI, providing a solid basis for further studies focused on most reported genes, as well as on more uncommon genes with strong functional significance in hepatotoxicity. Funding: PI21/01248; PID2022-140169OB-C21; HORIZON-STAYHLTH-101095679; PT23/00137; PI24/01205
Open Access
Predictive processing inbiological motion perceptionin audiovisual context
(Sage Publications Ltd., 2025-03-28) Uçkan, Cemre; Ürgen, Burcu Ayşen
Visual perception of biological motion (BM) is essential in comprehending our environment. Despitethe well-established contribution of cross-modal priming to our understanding of BM perception, theinﬂuence of expectations in audiovisual settings remains unexplored. The present study investigatesthe impact of congruent and incongruent auditory cues on detecting BMs presented in point-light dis-plays, exploring the impact of predictive processing on BM perception in the audiovisual context.Participants viewed either congruent auditory priors, which gave the correct information aboutthe BM, or incongruent priors. They were required to detect the BMs as fast and accurately as pos-sible. Our ﬁndings revealed shorter reaction times in congruent trials than incongruent ones althoughaccuracy remained unaffected by congruency. Overall, our results highlight that while prior informa-tion can facilitate faster detection of human motion, it does not necessarily enhance accuracy.
Open Access
Uncovering atypical gaze patterns in cerebral visual impairment: New insights from an exploratory gaze-based analysis
(Association for Research in Vision and Ophthalmology, 2026-01) Sağlam, Nilsu; Merabet, Lotfi B.; Pamir, Zahide
Individuals with cerebral visual impairment (CVI) often struggle with visuospatial processing, particularly in highly cluttered or complex environments. These challenges are commonly assessed through visual search tasks, using global measures such as reaction time (RT), accuracy, and search area. Accordingly, impaired search performance in CVI manifests as longer RTs, lower accuracy, and broader search areas. However, rather than elucidating the underlying mechanism of the impaired search process, these measures decode its outcome. In the present study, we utilized eye-tracking data to compute detailed measures of fixation count and duration, aiming to characterize gaze pattern sequences and determine whether prolonged RTs in CVI stem from slower visual scanning or increased fixation counts. Our reanalysis of two previously published datasets reveals that longer RTs in CVI arise from elevated fixation counts, specifically on distractors, rather than from slower visual scanning. Our findings indicate recurrent disruptions in maintaining gaze on the target, likely reflecting difficulties in sustaining attention on the target, suppressing distractors, and preventing inhibition of return. Together, these findings highlight an inefficient search pattern that is more biased toward distractors than focused on targets. By revealing these underlying mechanisms, gaze-based measures offer a deeper understanding of visuospatial processing deficits in CVI.
Open Access
Multimodal prediction of psychotic-like experiences using elastic net modeling: external validation in a clinical sample
(Cambridge University Press, 2025-11-14) Arslan, Seda; Kaşıkçı, Merve; Dağ, Osman; Şahin-Çevik, Didenur; Çakmak, Işık Batuhan; Vassos, Evangelos; Van Den Heuvel, Martijn; Toulopoulou, Timothea
Background Psychotic-like experiences (PLEs) are considered a subclinical component of psychosis continuum. Studies indicate that PLEs arise from multimodal factors, yet research comprehensively examining these factors together remains scarce. Using a large youth sample, we present the first model that simultaneously examines multimodal factors related to PLEs. As a secondary aim, we evaluate the model’s ability to explain psychosis in an external validation cohort that included individuals experiencing psychosis. Methods After applying variable selection including generalized estimating equations, correlation filtering, Least Absolute Shrinkage and Selection Operator model to 741 variables (i.e., environmental factors, cognitive appraisals, clinical variables, cognitive functioning, and structural brain connectome measures), obtained PLEs predictors (N = 27) and covariates (i.e., age, sex, IQ) were included in the classification model based on Elastic Net algorithm for predicting high/low PLEs in 396 healthy participants aged 14–24 (Mage = 19.72 ± 2.5). We externally validated PLE-related predictors in a clinical sample comprising first-episode psychosis patients (n = 19), their siblings (n = 20), and healthy controls (n = 19). Results Eleven factors, including environmental and cognitive appraisals, along with 16 structural network properties spanning frontal, temporal, occipital, and parietal regions, were identified as important predictors of PLEs. The model’s performance was moderate in predicting low versus high PLEs (accuracy = 75%, AUC = 0.750). Specificity was high (84.2%) in distinguishing siblings from patients. Conclusions Multimodal features, including environmental burden, cognitive schemas, and brain network alterations, predict PLEs and partially generalize to clinical psychosis. These variables may reflect intermediate phenotypes across the psychosis spectrum, offering insights into both vulnerability and resilience.
Open Access
Visual appearance and sensitivity are mediated by distinct mechanisms
(Elsevier Ltd, 2025-10-08) Karatok, Zahide Pamir; Boyacı, Hüseyin
Identifying a visual stimulus and sensitivity to changes in its features have different requirements. Thus, it is possible that different mechanisms underlie appearance and sensitivity judgments of visual stimuli. Here, we tested this possibility using a complex scene where two patches with physically identical luminances appeared to have different lightness. Human participants first judged the perceived contrast of incremental and decremental gratings superimposed on the patches. Next, we measured detection thresholds. Finally, fMRI activity was recorded in response to gratings on these patches. We found that incremental, but not the decremental gratings, appeared to have higher contrast when superimposed on the perceptually lighter patch compared to the darker. However, the thresholds were lower for both types of gratings superimposed on the lighter patch compared to the darker. Finally, using fMRI, we found that the activity in the primary visual cortex (V1) aligns well with the results of the detection task. These results suggest that partly distinct mechanisms underlie sensitivity and appearance and, further, that V1 plays an important role in sensitivity judgments.
Open Access
Randomization based evaluation of distinct topological and cancer expression characteristics of mutually acting gene pairs
(Oxford University Press, 2025-04-21) Dalgıç, Ertuğrul; Çelebi-Çınar, Muazzez; Vural-Özdeniz, Merve; Konu, Özlen
Small scale molecular network patterns and motifs are crucial for systems level understanding of cellular information transduction. Using randomizations, we statistically explored, previously overlooked basic patterns of mutually acting pairs, i.e. mutually positive (PP) or negative (NN) and positive-negative (PN) pairs, in two comprehensive and distinct large-scale molecular networks from literature; the human protein signaling network (PSN) and the human gene regulatory network (GRN). Only the positive and negative signs of all interacting pairs were randomized, while the gene pairs and the number of positive and negative signs in the original network were kept constant. While the numbers of NN and PN pairs were significantly higher, the number of PP pairs was significantly lower than randomly expected values. Genes participating in mutual pairs were more connected than other genes. NN genes were more connected than PP and PN in GRN for all types of degree values, including in, out, positive or negative connections, but less connected for in-degree and more connected for out-degree values in PSN. They also had significantly high number of intersections with each other and PN pairs than randomly expected values, indicating potential cooperative mechanisms. The three mutual interaction designs we examined had distinct RNA and protein expression correlation characteristics. NN protein pairs were uniquely over-represented across normal tissue samples, whose negative correlations were lost across cancer tissue samples. PP and PN pairs showed non-random positive RNA or protein expression correlation across normal or cancer tissue samples. Moreover, we developed an online tool, i.e. MGPNet, for further user specific analysis of mutual gene pairs. We identified SNCA with significantly enriched negatively correlated NN pairs. Unique non-random characteristics of mutual gene pairs identified in two different comprehensive molecular networks could provide valuable information for a better comparative understanding of molecular design principles between normal and cancer states. Insight Box/Paragraph Statement: This study provides a systems-level perspective on cellular information transduction by analyzing mutually acting pairs of genes. By examining mutually positive (PP), mutually negative (NN), and positive-negative (PN) pairs in the human protein signaling network (PSN) and the human gene regulatory network (GRN), we uncover significant variations in their connectivity and expression correlation. Our findings highlight the unique features of NN pairs across normal and cancer tissues and offer insights into molecular design principles. The development of the MGPNet tool further enhances user-specific analyses, enabling a deeper understanding of gene pair mechanisms and their potential cooperative roles in cellular processes.
Open Access
Self-consistent recursive diffusion bridge for medical image translation
(Elsevier BV, 2025-12) Arslan, Fuat; Kabas, Bilal; Dalmaz, Onat; Özbey, Muzaffer; Çukur, Tolga
Denoising diffusion models (DDM) have gained recent traction in medical image translation given their high training stability and image fidelity. DDMs learn a multi-step denoising transformation that progressively maps random Gaussian-noise images provided as input onto target-modality images as output, while receiving indirect guidance from source-modality images via a separate static channel. This denoising transformation diverges significantly from the task-relevant source-to-target modality transformation, as source images are governed by a non-noise distribution. In turn, DDMs can suffer from suboptimal source-modality guidance and performance losses in medical image translation. Here, we propose a novel self-consistent recursive diffusion bridge (SelfRDB) that leverages direct source-modality guidance within its diffusion process for improved performance in medical image translation. Unlike DDMs, SelfRDB devises a novel forward process with the start-point taken as the target image, and the end-point defined based on the source image. Intermediate image samples across the process are expressed via a normal distribution whose mean is taken as a convex combination of start-end points, and whose variance is controlled by additive noise. Unlike regular diffusion bridges that prescribe zero noise variance at start-end points and high noise variance at mid-point of the process, we propose a novel noise scheduling with monotonically increasing variance towards the end-point in order to facilitate information transfer between the two modalities and boost robustness against measurement noise. To further enhance sampling accuracy in each reverse step, we propose a novel sampling procedure where the network recursively generates a transient-estimate of the target image until convergence onto a self-consistent solution. Comprehensive experiments in multi-contrast MRI and MRI-CT translation indicate that SelfRDB achieves state-of-the-art results in terms of image quality.
Open Access
HR-ACT (human–robot action) database: communicative and noncommunicative action videos featuring a human and a humanoid robot
(Springer, 2026-01-12) Pekçetin, Tuǧçe Nur; Aşkın, Gaye; Evsen, Şeyda; Karaduman, Tuvana Dila; Barinal, Badel; Tunç, Jana; Acartürk, Cengiz; Ürgen, Burcu Ayşen
We present the HR-ACT (Human–Robot Action) Database, a comprehensive collection of 80 standardized videos featuring matched communicative and noncommunicative actions performed by both a humanoid robot (Pepper) and a human actor. We describe the creation of 40 action exemplars per agent, with actions executed in a similar manner, timing, and number of repetitions. The database includes detailed normative data collected from 438 participants, providing metrics on action identification, confidence ratings, communicativeness ratings, meaning clusters, and H values (an entropy-based measure reflecting response homogeneity). We provide researchers with controlled yet naturalistic stimuli in multiple formats: videos, image frames, and raw animation files (.qanim). These materials support diverse research applications in human–robot interaction, cognitive psychology, and neuroscience. The database enables systematic investigation of action perception across human and robotic agents, while the inclusion of raw animation files allows researchers using Pepper robots to implement these actions for real-time experiments. The full set of stimuli, along with comprehensive normative data and documentation, is publicly available at https://osf.io/8vsxq/.
Embargo
The interplay of prior information and motion cues in resolving visual ambiguity in agent perception
(Elsevier Ltd, 2025-10-10) Er, Sena; Elmas, Hüseyin Orkun; Saygın, Ayşe Pınar; Ürgen, Burcu Ayşen
Agent perception is essential for social interaction, allowing individuals to interpret and respond to the actions of others within dynamic environments. In this study, we examined whether and if so how prior information and motion information influence the temporal dynamics of perceiving agents. We presented short videos and images of three agents (a human, a robot, and an android) performing various actions while recording EEG. Using temporal representational similarity analysis (RSA) on EEG recordings, we analyzed the representation of agent identities under varying conditions: Still versus Moving stimuli and Prior versus Naive contexts. Our findings revealed that prior information and motion information interact to produce distinct temporal patterns of neural representation of agent identity. In the Naive condition (when no prior knowledge is available), agent processing was prolonged during still presentations compared to moving ones. These results demonstrate how the interplay between prior information and motion information shapes the temporal dynamics of agent perception.