Aysel Sabuncu Brain Research Center (BAM)

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Interdisciplinary Program in Neuroscience (NEUROSCIENCE)


Recent Submissions

Now showing 1 - 20 of 249
  • ItemOpen Access
    An Exploratory Analysis of the Neural Correlates of Human-Robot Interactions With Functional Near Infrared Spectroscopy
    (Frontiers Media S.A., 2022-07-18) Yorgancigil, Emre; Yildirim, Funda; Ürgen, Burcu Ayşen; Ürgen, Burcu Ayşen
    Functional near infrared spectroscopy (fNIRS) has been gaining increasing interest as a practical mobile functional brain imaging technology for understanding the neural correlates of social cognition and emotional processing in the human prefrontal cortex (PFC). Considering the cognitive complexity of human-robot interactions, the aim of this study was to explore the neural correlates of emotional processing of congruent and incongruent pairs of human and robot audio-visual stimuli in the human PFC with fNIRS methodology. Hemodynamic responses from the PFC region of 29 subjects were recorded with fNIRS during an experimental paradigm which consisted of auditory and visual presentation of human and robot stimuli. Distinct neural responses to human and robot stimuli were detected at the dorsolateral prefrontal cortex (DLPFC) and orbitofrontal cortex (OFC) regions. Presentation of robot voice elicited significantly less hemodynamic response than presentation of human voice in a left OFC channel. Meanwhile, processing of human faces elicited significantly higher hemodynamic activity when compared to processing of robot faces in two left DLPFC channels and a left OFC channel. Significant correlation between the hemodynamic and behavioral responses for the face-voice mismatch effect was found in the left OFC. Our results highlight the potential of fNIRS for unraveling the neural processing of human and robot audio-visual stimuli, which might enable optimization of social robot designs and contribute to elucidation of the neural processing of human and robot stimuli in the PFC in naturalistic conditions. Copyright © 2022 Yorgancigil, Yildirim, Urgen and Erdogan.
  • ItemOpen Access
    MNP characterization and signal prediction using a model-based dictionary
    (Infinite Science Publishing, 2022-03-21) Alpman, Asli; Utkur, Mustafa; Saritas, Emine Ulku; Alpman, Asli; Utkur, Mustafa; Saritas, Emine Ulku
    Magnetic Particle Imaging (MPI) utilizes the nonlinear magnetic response of magnetic nanoparticles (MNPs) for signal localization. Accurate modeling of the magnetization behavior of MNPs is crucial for understanding their MPI signal responses. In this work, we propose a model-based dictionary approach using a coupled Brown-Néel rotation model. With experimental results on a Magnetic Particle Spectrometer (MPS), we show that this approach can successfully characterize MNPs and predict their signal responses.
  • ItemOpen Access
    Suppression of aquaporin-4 by antisense oligonucleotides reduces brain edema in experimental traumatic brain injury
    (Turkish Neurosurgical Society, 2022-03-08) Hekimoğlu, Mehdi; Lule, Sevda; Özer, Hıdır; Çakır-Aktas, Canan; Mut, Melike; Karlı Oğuz, Hatice Kader
    AIM: To investigate the suppression of aquaporin-4 (AQP4) synthesis through intracerebroventricular (i.c.v.) injection of antisense oligonucleotide after focal cortical contusion injury in mice. MATERIAL and METHODS: This study used 12-week-old female Swiss albino mice (weight, 20–25 g) to create a focal cortical contusion model by the weight-drop method (35 g blunt weight, 70 cm height) onto the parietal cortex after craniectomy. The sham group underwent craniectomy without trauma. In the control group, weight was dropped onto the parietal cortex immediately after i.c.v. injection of Dulbecco’s Modified Eagle Medium after craniectomy. In addition, 1 nM of aquaporin-4 (AQP4) antisense oligonucleotide (ASO) was injected via the i.c.v. route immediately after trauma (0 hour) and 4 hours after trauma. All animals underwent magnetic resonance (MR) imaging and were sacrificed at 24 hours. The brain–water content was determined using the wet/dry weight method. RESULTS: In the sham group, the average percentage of the brain–water content was 77.75% compared with the control group with 79.87%, and the difference was significant (p=0.017). The average was 78.81% and significantly reduced in the therapy group compared with the control group (p=0.026) at 0 hour. In the 4-hour treatment group, the average of 79.11% was not significant (p=0.39). MR imaging findings also showed a substantial reduction in brain edema in the 0-h treatment group. However, the 4-h treatment results, when compared with the control trauma group, did not show a significant difference. CONCLUSION: This study demonstrated that AQP4-ASO therapy, when administered early after diffuse traumatic brain injury, leads to a significant reduction in brain edema. © 2022, The Korean Society of Clothing and Textiles. All rights reserved.
  • ItemOpen Access
    Attentional modulations of audiovisual interactions in apparent motion: Temporal ventriloquism effects on perceived visual speed
    (Springer New York LLC, 2022-08-22) Duyar, Aysun; Pavan, Andrea; Duyar, Aysun
    The timing of brief stationary sounds has been shown to alter different aspects of visual motion, such as speed estimation. These effects of auditory timing have been explained by temporal ventriloquism and auditory dominance over visual information in the temporal domain. Although previous studies provide unprecedented evidence for the multisensory nature of speed estimation, how attention is involved in these audiovisual interactions remains unclear. Here, we aimed to understand the effects of spatial attention on these audiovisual interactions in time. We utilized a set of audiovisual stimuli that elicit temporal ventriloquism in visual apparent motion and asked participants to perform a speed comparison task. We manipulated attention either in the visual or auditory domain and systematically changed the number of moving objects in the visual field. When attention was diverted to a stationary object in the visual field via a secondary task, the temporal ventriloquism effects on perceived speed decreased. On the other hand, focusing attention on the auditory stimuli facilitated these effects consistently across different difficulty levels of secondary auditory task. Moreover, the effects of auditory timing on perceived speed did not change with the number of moving objects and existed in all the experimental conditions. Taken together, our findings revealed differential effects of allocating attentional resources in the visual and auditory domains. These behavioral results also demonstrate that reliable temporal ventriloquism effects on visual motion can be induced even in the presence of multiple moving objects in the visual field and under different perceptual load conditions.
  • ItemOpen Access
    edaGAN: Encoder-Decoder Attention Generative Adversarial Networks for multi-contrast MR image synthesis
    (Institute of Electrical and Electronics Engineers, 2022-05-16) Dalmaz, Onat; Sağlam, Baturay; Gönç, Kaan; Çukur, Tolga; Dalmaz, Onat; Sağlam, Baturay; Gönç, Kaan; Çukur, Tolga
    Magnetic resonance imaging (MRI) is the preferred modality among radiologists in the clinic due to its superior depiction of tissue contrast. Its ability to capture different contrasts within an exam session allows it to collect additional diagnostic information. However, such multi-contrast MRI exams take a long time to scan, resulting in acquiring just a portion of the required contrasts. Consequently, synthetic multi-contrast MRI can improve subsequent radiological observations and image analysis tasks like segmentation and detection. Because of this significant potential, multi-contrast MRI synthesis approaches are gaining popularity. Recently, generative adversarial networks (GAN) have become the de facto choice for synthesis tasks in medical imaging due to their sensitivity to realism and high-frequency structures. In this study, we present a novel generative adversarial approach for multi-contrast MRI synthesis that combines the learning of deep residual convolutional networks and spatial modulation introduced by an attention gating mechanism to synthesize high-quality MR images. We show the superiority of the proposed approach against various synthesis models on multi-contrast MRI datasets.
  • ItemOpen Access
    Predicting personality traits with semantic structures and LSTM-based neural networks
    (Elsevier, 2022-10) Kosan, Muhammed Ali; Karacan, Hacer; Ürgen, Burcu Ayşen; Ürgen, Burcu Ayşen
    There is a need to obtain more information about target audiences in many areas such as law enforcement agencies, institutions, human resources, and advertising agencies. In this context, in addition to the information provided by individuals, their personal characteristics are also important. In particular, the predictability of personality traits of individuals is seen as a major parameter in making decisions about individuals. Textual and media data in social media, where people produce the most data, can provide clues about people's personal lives, characteristics, and personalities. Each social media environment may contain different assets and structures. Therefore, it is important to make a structural analysis according to the social media platform. There is also a need for a labelled dataset to develop a model that can predict personality traits from social media data. In this study, first, a personality dataset was created which was retrieved from Twitter and labelled with IBM Personality Insight. Then the unstructured data were transformed into meaningful and processable data, LSTM-based prediction models were created with the structural analysis, and evaluations were made on both our dataset and PAN-2015-EN. © 2022 THE AUTHORS
  • ItemOpen Access
    Effects of psychosis-associated genetic markers on brain volumetry: A systematic review of replicated findings and an independent validation
    (Cambridge University Press, 2022-09-28) Ribeiro, Nuno Vouga; Tavares, Vânia; Bramon, Elvira; Toulopoulou, Timothea; Valli, Isabel; Shergill, Sukhi; Murray, Robin; Prata, Diana; Toulopoulou, Timothea
    Background. Given psychotic illnesses’ high heritability and associations with brain structure, numerous neuroimaging-genetics findings have been reported in the last two decades. However, few findings have been replicated. In the present independent sample we aimed to replicate any psychosis-implicated SNPs (single nucleotide polymorphisms), which had previously shown at least two main effects on brain volume. Methods. A systematic review for SNPs showing a replicated effect on brain volume yielded 25 studies implicating seven SNPs in five genes. Their effect was then tested in 113 subjects with either schizophrenia, bipolar disorder, ‘at risk mental state’ or healthy state, for whole-brain and region-of-interest (ROI) associations with grey and white matter volume changes, using voxel-based morphometry. Results. We found FWER-corrected (Family-wise error rate) (i.e. statistically significant) associations of: (1) CACNA1C-rs769087-A with larger bilateral hippocampus and thalamus white matter, across the whole brain; and (2) CACNA1C-rs769087-A with larger superior frontal gyrus, as ROI. Higher replication concordance with existing literature was found, in decreasing order, for: (1) CACNA1C-rs769087-A, with larger dorsolateral-prefrontal/superior frontal gyrus and hippocampi (both with anatomical and directional concordance); (2) ZNF804Ars11681373-A, with smaller angular gyrus grey matter and rectus gyri white matter (both with anatomical and directional concordance); and (3) BDNF-rs6265-T with superior frontal and middle cingulate gyri volume change (with anatomical and allelic concordance). Conclusions. Most literature findings were not herein replicated. Nevertheless, high degree/ likelihood of replication was found for two genome-wide association studies- and one candidate-implicated SNPs, supporting their involvement in psychosis and brain structure. © The Author(s), 2022. Published by Cambridge University Press.
  • ItemOpen Access
    A comparison of equivalent noise methods in investigating local and global form and motion integration
    (Springer New York LLC, 2022-11-15) Pavan, A.; Contillo, A.; Koç, Şeyma; Kafalıgönül, Hulusi; Donato, R.; O’Hare, L.; Koç, Şeyma; Kafalıgönül, Hulusi
    Static and dynamic cues within certain spatiotemporal proximity are used to evoke respective global percepts of form and motion. The limiting factors in this process are, first, internal noise, which indexes local orientation/direction detection, and, second, sampling efficiency, which relates to the processing and the representation of global orientation/direction. These parameters are quantified using the equivalent noise (EN) paradigm. EN has been implemented with just two levels: high and low noise. However, when using this simplified version, one must assume the shape of the overall noise dependence, as the intermediate points are missing. Here, we investigated whether two distinct EN methods, the 8-point and the simplified 2-point version, reveal comparable parameter estimates. This was performed for three different types of stimuli: random dot kinematograms, and static and dynamic translational Glass patterns, to investigate how constant internal noise estimates are, and how sampling efficiency might vary over tasks. The results indicated substantial compatibility between estimates over a wide range of external noise levels sampled with eight data points, and a simplified version producing two highly informative data points. Our findings support the use of a simplified procedure to estimate essential form-motion integration parameters, paving the way for rapid and critical applications to populations that cannot tolerate protracted measurements.
  • ItemOpen Access
    An arbitrary waveform MPI scanner
    (Infinite Science Publishing, 2022) Alyuz, Beril; Alyuz, Beril
    In magnetic particle imaging (MPI) systems, impedance matching or tuning circuitry has to be employed at a particular operating frequency to handle the reactive power. In this work, we propose a drive coil design with a Rutherford cable winding comprised of 12 Litz wires twisted together to enable arbitrary waveform (AW) characteristics in an MPI scanner. The AW drive coil achieves a 144-fold reduction in inductance and 12-fold reduction in voltage to generate a given drive field amplitude, compared to a standard drive coil with regular Litz wire windings. With imaging experiments, we show that the proposed design can enable imaging in a wide bandwidth, providing flexibility for different functional imaging applications of MPI.
  • ItemOpen Access
    Rapid TAURUS for real-time color MPI: A feasibility study
    (Infinite Science Publishing, 2022) Arslan, Musa Tunç; Saritas, Emine Ulku; Arslan, Musa Tunç; Saritas, Emine Ulku
    Recent developments in color magnetic particle imaging (MPI) provided additional functionalities to MPI, such as distinguishing magnetic nanoparticles (MNPs) by type or by their environmental conditions. In this work, we propose rapid TAURUS (TAU estimation via Recovery of Underlying mirror Symmetry) to achieve relaxation-based real-time color MPI. The method can successfully map the effective relaxation time constants in a relatively wide field-of-view (FOV) at frame rates exceeding 5 frames-per-second (FPS). We present the first simulation results demonstrating that rapid TAURUS is capable of generating high fidelity and high FPS color MPI images in real time.
  • ItemOpen Access
    Vicinity effects of field free point on the relaxation behavior of MNPs
    (Infinite Science Publishing, 2022-03-21) Topcu, Atakan; Topcu, Atakan
    In Magnetic Particle Imaging (MPI), the distribution of magnetic nanoparticles (MNPs) is imaged by moving a field free point (FFP) in space. All MNPs in close vicinity of the FFP contribute to the signal induced on the receive coil. The relaxation behavior of these MNPs are subject to a DC field due to the selection field (SF). In this work, we investigate the effects of the DC field on the relaxation behavior of the MNPs, with the goal of understanding the differences between the measured relaxations in Magnetic Particle Spectrometer (MPS) setups vs. MPI scanners.
  • ItemOpen Access
    PNS limits for Human Head-Size MPI systems: Preliminary results
    (Infinite Science Publishing, 2022) Ozaslan, Ali Alper; Utkur, Mustafa; Canpolat, Ugur; Tuncer, Meryem Asli; Oguz, Kader Karli; Saritas, Emine Ulku; Ozaslan, Ali Alper; Utkur, Mustafa; Oguz, Kader Karli; Saritas, Emine Ulku
    Magnetic Particle Imaging (MPI) utilizes kHz-range sinusoidal drive fields to excite magnetic nanoparticles. These time-varying magnetic fields induce electric fields within the human body, which in turn can induce peripheral nerve stimulation (PNS), also known as magnetostimulation. In this work, we report the preliminary results of human subject experiments for human head-size MPI systems. These experiments were performed on a solenoidal head coil that achieved an order of magnitude reduction in the voltages needed to generate the targeted magnetic fields.
  • ItemOpen Access
    Increasing the spatial extent of attention strengthens surround suppression
    (Elsevier Ltd, 2022-10) Kınıklıoğlu, Merve; Boyacı, Hüseyin; Kınıklıoğlu, Merve; Boyacı, Hüseyin
    Here we investigate how the extent of spatial attention affects center-surround interaction in visual motion processing. To do so, we measured motion direction discrimination thresholds in humans using drifting gratings and two attention conditions. Participants were instructed to limit their attention to the central part of the stimulus under the narrow attention condition, and to both central and surround parts under the wide attention condition. We found stronger surround suppression under the wide attention condition. The magnitude of the attention effect increased with the size of the surround when the stimulus had low contrast, but did not change when it had high contrast. Results also showed that attention had a weaker effect when the center and surround gratings drifted in opposite directions. Next, to establish a link between the behavioral results and the neuronal response characteristics, we performed computer simulations using the divisive normalization model. Our simulations showed that using smaller versus larger multiplicative attentional gain and parameters derived from the medial temporal (MT) area of the cortex, the model can successfully predict the observed behavioral results. These findings reveal the critical role of spatial attention on surround suppression and establish a link between neuronal activity and behavior. Further, these results also suggest that the reduced surround suppression found in certain clinical disorders (e.g., schizophrenia and autism spectrum disorder) may be caused by abnormal attention mechanisms.
  • ItemOpen Access
    Feasibility of freehand CT and 3-T MR guided brain aspiration biopsies with 18/20-gauge coaxial needles
    (Springer, 2022-07) Algın, Oktay; Ayberk, G.; Algın, Oktay
    Background and purpose: An accurate histopathological examination with minimal neuronal damage is essential for optimizing treatment strategies of central nervous system lesions. We investigated the feasibility and safety of CT and 3-tesla (3 T) MR-guided freehand brain aspiration biopsies with 18/20-gauge coaxial needles in performing a single imaging unit. Materials and methods: We reviewed CT and 3 T-MR guided freehand aspiration biopsies with 18/20-gauge coaxial needles of 33 patients (11-female and 22-male, mean and median ages: 53 years, min–max 21–79 years) in our tertiary hospital within an 8-year-period were included in this retrospective study. Lesion sizes, diagnostic yield, morbidity, and mortality rates of these biopsies without a scalp incision, surgical burr-hole, or stereotactic-instrumentation/neuro-navigation guidance were assessed. All biopsies were performed with local anesthesia and sedation within a single imaging unit of our radiology department. All free-hand biopsies were done as in-patient procedures and the patients were closely observed after the biopsies. Results: The mean diameter of the lesions was 27 mm (median 25; range 15–46 mm). The diagnostic yield of all free-hand brain biopsies was 88% [one inconclusive result (90%) for 3 T-MR; three inconclusive results (87%) for CT]. There was no major hemorrhage or hematoma, no clinical deterioration, or no infection in our patients on early- and late-phase examinations. Postprocedural minor hemorrhage with a ≤ 2 cm diameter was observed in two patients. The morbidity rate of the study population is 6%. There was no procedure-related infection or mortality in the post-procedural 3 weeks. Conclusions: Freehand CT or 3 T-MR guided aspiration biopsy was a safe and feasible method for pathological diagnosis of intracranial lesions. Biopsy workflow was simplified with this technique. It could be considered a valuable alternative for stereotaxic biopsies, especially for centers that do not have stereotaxic equipment or experience. © 2022, The Author(s) under exclusive licence to Japan Radiological Society.
  • ItemOpen Access
    Motion processing impaired by transient spatial attention: Potential implications for the magnocellular pathway
    (Elsevier Ltd, 2022-06-21) Pavan, Andrea; Yılmaz, Şeyma Koç; Kafalığonul, Hulusi; Battaglini, L.; Blurton, S. P.; Yılmaz, Şeyma Koç; Kafalığonul, Hulusi
    Spatial cues presented prior to the presentation of a static stimulus usually improve its perception. However, previous research has also shown that transient exogenous cues to direct spatial attention to the location of a forthcoming stimulus can lead to reduced performance. In the present study, we investigated the effects of transient exogenous cues on the perception of briefly presented drifting Gabor patches. The spatial and temporal frequencies of the drifting Gabors were chosen to mainly engage the magnocellular pathway. We found better performance in the motion direction discrimination task when neutral cues were presented before the drifting target compared to a valid spatial cue. The behavioral results support the hypothesis that transient attention prolongs the internal response to the attended stimulus, thus reducing the temporal segregation of visual events. These results were complemented by applying a recently developed model for perceptual decisions to rule out a speed-accuracy trade-off and to further assess cueing effects on visual performance. In a model-based assessment, we found that valid cues initially enhanced processing but overall resulted in less efficient processing compared to neutral cues, possibly caused by reduced temporal segregation of visual events.
  • ItemOpen Access
    Behavioral and ERP evidence that object-based attention utilizes fine-grained spatial mechanisms
    (2022-06) Catak, Esra N.; Özkan, M.; Kafaligonul, Hulusi; Stoner, G. R.; Catak, Esra N.; Kafaligonul, Hulusi
    Valdes-Sosa, Cobo, and Pinilla (1998) introduced a transparent-motion design that provided evidence of object-based attention whereby attention embraces all features of an attentionally cued perceptual object including new unpredictable features such as a brief translation. Subsequent studies using variants of that design appeared to provide further behavioral, electrophysiological, and brain imaging evidence of object-based attention. Stoner and Blanc (2010) observed, however, that these previous results could potentially be explained by feature-based competition/normalization models of attention. To distinguish between the object-based and feature-based accounts, they introduced “feature swaps” into a delayed-onset variant of the transparent-motion design (Reynolds, Alborzian, & Stoner, 2003). Whereas the object-based attention account predicted that the effect of cueing would survive these feature swaps, the motion-competition account predicted that the effect of cueing would be reversed by these feature swaps. The behavioral results of Stoner and Blanc (2010) supported the object-based account, and in doing so, provided evidence that the attentional advantage in this design is spatially selective at the scale of the intermixed texture elements (i.e., dots) of the overlapping and moving dot fields. In the present study, we used the design of Stoner and Blanc (2010) to investigate both psychophysical performance and evoked activities under different cueing and feature swapping conditions. We confirmed that the behavioral effects of attentional cueing survived feature swaps and found event-related potential (ERP) correlates of those effects in the N1 component range over occipital and parieto-occipital scalp sites. These modulations of the neural activity were, moreover, significantly associated with variation in behavioral performance values across the different conditions. Our findings thus provide the first evidence of the role of the N1 component in object-based attention in this transparent-motion design under conditions that rule out feature-based mechanisms and that reveal selective processing at a fine spatial scale.
  • ItemOpen Access
    Phronêsis and Kalokagathia in Eudemian Ethics VIII.3
    (Johns Hopkins Univ Press, 2022-01) Wolt, Daniel; Wolt, Daniel
    In Eudemian Ethics VIII.3, Aristotle treats a virtue that he calls kalokagathia, "nobility-and-goodness." This virtue appears to be quite important, and he even identifies it with "perfect virtue" (EEVIII.3, 1249a17). This makes it puzzling that the Nicomachean Ethics, a text that largely parallels the Eudemian Ethics, does not discuss kalokagathia at all. I argue that the reason for this difference has to do with the role that the intellectual virtue practical wisdom (phronesis) plays in these treatises. The Nicomachean Ethics, I argue, makes use of a more expansive conception of phronesis than does the Eudemian Ethics. Hence, the work that is done by kalokagathia in the Eudemian Ethics-crucially, accounting for the unity of the virtues-is done in the Nicomachean Ethics by phronesis.
  • ItemEmbargo
    2D RF pulse design for optimized reduced field-of-view imaging at 1.5T and 3T
    (Elsevier Inc., 2021-10-22) Eren, Orhun Caner; Barlas, Bahadır Alp; Sarıtaş, Emine Ülkü; Eren, Orhun Caner; Barlas, Bahadır Alp; Sarıtaş, Emine Ülkü
    Two-dimensional spatially selective radiofrequency (2DRF) excitation pulses are widely used for reduced field-of-view (FOV) targeted high-resolution diffusion weighted imaging (DWI), especially for anatomically small regions such as the spinal cord and prostate. The reduction in FOV achieved by 2DRF pulses significantly improve the in-plane off-resonance artifacts in single-shot echo planar imaging (ss-EPI). However, long durations of 2DRF pulses create a sensitivity to through-plane off-resonance effects, especially at 3 T where the off-resonance field doubles with respect to 1.5 T. This work proposes a parameter-based optimization approach to design 2DRF pulses with blips along the slice-select axis, with the goal of maximizing slab sharpness while minimizing off-resonance effects on 1.5 T and 3 T MRI scanners, separately. Extensive Bloch simulations are performed to evaluate the off-resonance robustness of 2DRF pulses. Three different metrics are proposed to quantify the similarity between the actual and ideal 2D excitation profiles, based on the signals within and outside the targeted reduced-FOV region. In addition, simulations on a digital brain phantom are performed for visual comparison purposes. The results show that maintaining a sharp profile is the primary design requirement at 1.5 T, necessitating the usage of relatively high slab sharpness with a time-bandwidth product (TBW) around 8–10. In contrast, off-resonance robustness is the primary design requirement at 3 T, requiring the usage of a moderate slap sharpness with TBW around 5–7.
  • ItemOpen Access
    Improving image synthesis quality in multi-contrast MRI using transfer learning via autoencoders
    (IEEE, 2022-08-29) Selçuk, Şahan Yoruç; Dalmaz, Onat; Ul Hassan Dar, Salman; Çukur, Tolga; Selçuk, Şahan Yoruç; Dalmaz, Onat; Ul Hassan Dar, Salman; Çukur, Tolga
    The capacity of magnetic resonance imaging (MRI) to capture several contrasts within a session enables it to obtain increased diagnostic information. However, such multi-contrast MRI tests take a long time to scan, resulting in acquiring just a part of the essential contrasts. Synthetic multi-contrast MRI has the potential to improve radiological observations and consequent image analysis activities. Because of its ability to generate realistic results, generative adversarial networks (GAN) have recently been the most popular choice for medical imaging synthesis. This paper proposes a novel generative adversarial framework to improve the image synthesis quality in multi-contrast MRI. Our method uses transfer learning to adapt pre-trained autoencoder networks to the synthesis task and enhances the image synthesis quality by initializing the training process with more optimal network parameters. We demonstrate that the proposed method outperforms competing synthesis models by 0.95 dB on average on a well-known multi-contrast MRI dataset.
  • ItemOpen Access
    Engineered bacteria with genetic circuits accumulating nanomagnets as MRI contrast agents
    (Wiley, 2022-01-25) Yavuz, Merve; Ütkür, Mustafa; Kehribar, Ebru Şahin; Yağız, Ecrin; Sarıtaş, Emine Ülkü; Şeker, Urartu Özgür Şafak; Yavuz, Merve; Ütkür, Mustafa; Kehribar, Ebru Şahin; Yağız, Ecrin; Sarıtaş, Emine Ülkü; Şeker, Urartu Özgür Şafak
    The demand for highly efficient cancer diagnostic tools increases alongside the high cancer incidence nowadays. Moreover, there is an imperative need for novel cancer treatment therapies that lack the side effects of conventional treatment options. Developments in this aspect employ magnetic nanoparticles (MNPs) for biomedical applications due to their stability, biocompatibility, and magnetic properties. Certain organisms, including many bacteria, can synthesize magnetic nanocrystals, which help their spatial orientation and survival by sensing the earth's geomagnetic field. This work aims to convert Escherichia coli to accumulate magnetite, which can further be coupled with drug delivery modules. The authors design magnetite accumulating bacterial machines using genetic circuitries hiring Mms6 with iron-binding activity and essential in magnetite crystal formation. The work demonstrates that the combinatorial effect of Mms6 with ferroxidase, iron transporter protein, and material binding peptide enhances the paramagnetic behavior of the cells in magnetic resonance imaging (MRI) measurements. Cellular machines are also engineered to display Mms6 peptide on the cell surface via an autotransporter protein that shows augmented MRI performance. The findings are promising for endowing a probiotic bacterium, able to accumulate magnetite intracellularly or extracellularly, serving as a theranostics agent for cancer diagnostics via MRI scanning and hyperthermia treatment. © 2022 Wiley-VCH GmbH.