Aysel Sabuncu Brain Research Center (BAM)

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https://hdl.handle.net/11693/53507

Interdisciplinary Program in Neuroscience (NEUROSCIENCE)

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Open Access
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
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.
Open Access
3 boyutlu kartezyen olmayan paralel görüntülemede değişken görüntü alanına dayalı geriçatım
(IEEE, 2018) Şenel, Celal Furkan; Çukur, Tolga
MRG’de yaygın olarak kullanılan geriçatım yöntemleri değişken yoğunluklu Kartezyen olmayan taramalara da uygulanabilmektedir; fakat bu durumda bu yöntemlerin genellikle yüksek hesaplama karmaşıklığı içeren çok sayıda yinelemeye ihtiyaç duyması özellikle 3 boyutlu geriçatımlara uygulanabilirliklerini sınırlamaktadır. 2 boyutlu Kartezyen olmayan veri için daha hızlı geriçatım almak amacıyla, PILS’e dayalı, değişken görüntü alanlarını kullanan bir teknik yakın zamanda teklif edilmiştir. Bu çalışmada bu teknik 3 boyutlu değişken yoğunluklu veriye uygulanmış, ek olarak elde edilen görüntüler dalgacık regülarizasyonu kullanılarak kalan artifaktlardan temizlenmiştir. Önce regülarizasyon için farklı parametrelerin başarımları karşılaştırılmış, sonra regülarizasyon da dâhil olmak üzere değişken görüntü alanı yönteminin, karelerin toplanması, PILS ve ESPIRiT geriçatımları ile başarımları karşılaştırılmıştır. Elde edilen sonuçlar teklif edilen yöntemin başarısının karşılaştırılan diğer geriçatımlardan üstün olduğunu göstermektedir.
Open Access
4,8 T/m manyetik parçacık görüntüleme tarayıcı tasarımı ve yapımı
(IEEE, 2018) Ütkür, Mustafa; Muslu, Yavuz; Sarıtaş, Emine Ülkü
Manyetik Parçacık Görüntüleme (MPG), ilk yayımlandığı 2005 yılından bu yana hızla gelişerek anjiyografi, kök hücre takibi ve kanser görüntüleme gibi uygulama alanlarında ciddi ilerlemeler kaydetmiştir. İyonlaştırıcı ışıma kullanmaması ve kullandığı izleyici maddelerin sağlığa zararlı olmayan demir oksit nanoparçacıkları olması sayesinde güvenli bir görüntüleme yöntemi olarak umut vaad etmektedir. Henüz insan boyutunda bir MPG tarayıcı yapılmamıs¸ olsa da yapılan preklinik araştırmalar MPG’nin milimetre altı çözünürlüğe sahip olduğunu göstermektedir. Bu çalışmada Bilkent Ulusal Manyetik Rezonans Araştırma Merkezi (UMRAM) bünyesinde geliştirdiğimiz ilk MPG tarayıcının tasarım ve yapım aşamaları sunulmaktadır. Bu MPG tarayıcı x-yönünde 4,8 T/m seçme alanı gradyanına sahiptir, ve 9,7 kHz eksitasyon alan frekansı kullanmaktadır.
Open Access
A dictionary-based algorithm for MNP signal prediction at unmeasured drive field frequencies
(Infinite Science Publishing, 2023-03-19) Alpman, Aslı; Utkur, Mustafa; Sarıtaş, Emine Ülkü
The signal in MPI depends on magnetic nanoparticle (MNP) parameters and environmental conditions, as wellas drive field (DF) settings and measurement system response. In this study, we propose a dictionary-basedalgorithm using a coupled Brown-Néel rotation model to simultaneously estimate the MNP parameters togetherwith system transfer function. We then propose an empirical method that enables signal prediction at unmeasuredDF frequencies, where measurement data is not available.
Open Access
A large video set of natural human actions for visual and cognitive neuroscience studies and its validation with fMRI
(MDPI, 2022-12-29) Ürgen, Burcu Ayşen; Nizamoğlu, Hilal; Eroğlu, Aslı; Orban, G. A.
The investigation of the perception of others’ actions and underlying neural mechanisms has been hampered by the lack of a comprehensive stimulus set covering the human behavioral repertoire. To fill this void, we present a video set showing 100 human actions recorded in natural settings, covering the human repertoire except for emotion-driven (e.g., sexual) actions and those involving implements (e.g., tools). We validated the set using fMRI and showed that observation of the 100 actions activated the well-established action observation network. We also quantified the videos’ low-level visual features (luminance, optic flow, and edges). Thus, this comprehensive video set is a valuable resource for perceptual and neuronal studies.
Open Access
A naturalistic setup for presenting real people and live actions in experimental psychology and cognitive neuroscience studies
(Journal of Visualized Experiments, 2023-08-04) Pekçetin, Tuğçe Nur; Evsen, Şeyda; Pekçetin, Serkan; Acarturk, Cengiz; Ürgen, Burcu A.
Perception of others' actions is crucial for survival, interaction, and communication. Despite decades of cognitive neuroscience research dedicated to understanding the perception of actions, we are still far away from developing a neurally inspired computer vision system that approaches human action perception. A major challenge is that actions in the real world consist of temporally unfolding events in space that happen "here and now" and are actable. In contrast, visual perception and cognitive neuroscience research to date have largely studied action perception through 2D displays (e.g., images or videos) that lack the presence of actors in space and time, hence these displays are limited in affording actability. Despite the growing body of knowledge in the field, these challenges must be overcome for a better understanding of the fundamental mechanisms of the perception of others' actions in the real world. The aim of this study is to introduce a novel setup to conduct naturalistic laboratory experiments with live actors in scenarios that approximate real-world settings. The core element of the setup used in this study is a transparent organic light-emitting diode (OLED) screen through which participants can watch the live actions of a physically present actor while the timing of their presentation is precisely controlled. In this work, this setup was tested in a behavioral experiment. We believe that the setup will help researchers reveal fundamental and previously inaccessible cognitive and neural mechanisms of action perception and will be a foundation for future studies investigating social perception and cognition in naturalistic settings.
Open Access
Abnormal subcortical activity in congenital mirror movement disorder with RAD51 mutation
(Turkish Society of Radiology, 2018) Demirayak, Pınar; Onat, Onur Emre; Gevrekci, A. Ö.; Gülsüner, S.; Uysal, H.; Bilgen, R.; Doerschner, Katja; Özçelik, Tayfun; Boyacı, Hüseyin
PURPOSE Congenital mirror movement disorder (CMMD) is characterized by unintended, nonsuppressible, homologous mirroring activity contralateral to the movement on the intended side of the body. In healthy controls, unilateral movements are accompanied with predominantly contralateral cortical activity, whereas in CMMD, in line with the abnormal behavior, bilateral cortical activity is observed for unilateral motor tasks. However, task-related activities in subcortical structures, which are known to play critical roles in motor actions, have not been investigated in CMMD previously. METHODS We investigated the functional activation patterns of the motor components in CMMD patients. By using linkage analysis and exome sequencing, common mutations were revealed in seven affected individuals from the same family. Next, using functional magnetic resonance imaging (fMRI) we investigated cortical and subcortical activity during manual motor actions in two right-handed affected brothers and sex, age, education, and socioeconomically matched healthy individuals. RESULTS Genetic analyses revealed heterozygous RAD51 c.401C>T mutation which cosegregated with the phenotype in two affected members of the family. Consistent with previous literature, our fMRI results on these two affected individuals showed that mirror movements were closely related to abnormal cortical activity in M1 and SMA during unimanual movements. Furthermore, we have found previously unknown abnormal task-related activity in subcortical structures. Specifically, we have found increased and bilateral activity during unimanual movements in thalamus, striatum, and globus pallidus in CMMD patients. CONCLUSION These findings reveal further neural correlates of CMMD, and may guide our understanding of the critical roles of subcortical structures for unimanual movements in healthy individuals.
Open Access
Adaptation to average duration
(Springer New York LLC, 2021) Corbett, Jennifer E.; Aydın, Berfin; Munneke, Jaap
There has been a recent surge of research examining how the visual system compresses information by representing the average properties of sets of similar objects to circumvent strict capacity limitations. Efficient representation by perceptual averaging helps to maintain the balance between the needs to perceive salient events in the surrounding environment and sustain the illusion of stable and complete perception. Whereas there have been many demonstrations that the visual system encodes spatial average properties, such as average orientation, average size, and average numerosity along single dimensions, there has been no investigation of whether the fundamental nature of average representations extends to the temporal domain. Here, we used an adaptation paradigm to demonstrate that the average duration of a set of sequentially presented stimuli negatively biases the perceived duration of subsequently presented information. This negative adaptation aftereffect is indicative of a fundamental visual property, providing the first evidence that average duration is encoded along a single visual dimension. Our results not only have important implications for how the visual system efficiently encodes redundant information to evaluate salient events as they unfold within the dynamic context of the surrounding environment, but also contribute to the long-standing debate regarding the neural underpinnings of temporal encoding.
Open Access
Advanced preclinical models for evaluation of drug-induced liver injury – consensus statement by the European Drug-Induced Liver Injury Network [PRO-EURO-DILI-NET]
(Elsevier, 2021-06-24) Fernandez-Checa, J. C.; Bagnaninchi, P.; Ye, H.; Sancho-Bru, P.; Falcon-Perez, J. M.; Royo, F.; Garcia-Ruiz, C.; Konu, Özlen; Miranda, J.; Lunov, O.; Dejneka, A.; Elfick, A.; McDonald, A.; Sullivan, G. J.; Aithal, G. P.; Lucena, M. I.; Andrade, R. J.; Fromenty, B.; Kranendonk, M.; Cubero, F. J.; Nelson, L. J.
Drug-induced liver injury (DILI) is a major cause of acute liver failure (ALF) and one of the leading indications for liver transplantation in Western societies. Given the wide use of both prescribed and over the counter drugs, DILI has become a major health issue for which there is a pressing need to find novel and effective therapies. Although significant progress has been made in understanding the molecular mechanisms underlying DILI, our incomplete knowledge of its pathogenesis and inability to predict DILI is largely due to both discordance between human and animal DILI in preclinical drug development and a lack of models that faithfully recapitulate complex pathophysiological features of human DILI. This is exemplified by the hepatotoxicity of acetaminophen (APAP) overdose, a major cause of ALF because of its extensive worldwide use as an analgesic. Despite intensive efforts utilising current animal and in vitro models, the mechanisms involved in the hepatotoxicity of APAP are still not fully understood. In this expert Consensus Statement, which is endorsed by the European Drug-Induced Liver Injury Network, we aim to facilitate and outline clinically impactful discoveries by detailing the requirements for more realistic human-based systems to assess hepatotoxicity and guide future drug safety testing. We present novel insights and discuss major players in APAP pathophysiology, and describe emerging in vitro and in vivo pre-clinical models, as well as advanced imaging and in silico technologies, which may improve prediction of clinical outcomes of DILI.
Open Access
Age-related synapse loss in hippocampal CA3 is not reversed by caloric restriction
(Pergamon Press, 2010) Adams, Michelle M.; Donohue, H. S.; Linville, M. C.; Iversen, E. A.; Newton, I. G.; Bechtold, J. K. B.
Caloric restriction (CR) is a reduction of total caloric intake without a decrease in micronutrients or a disproportionate reduction of any one dietary component. While CR attenuates age-related cognitive deficits in tasks of hippocampal-dependent memory, the cellular mechanisms by which CR improves this cognitive decline are poorly understood. Previously, we have reported age-related decreases in key synaptic proteins in the CA3 region of the hippocampus that are stabilized by lifelong CR. In the present study, we examined possible age-related changes in the functional microcircuitry of the synapses in the stratum lacunosum-moleculare (SL-M) of the CA3 region of the hippocampus, and whether lifelong CR might prevent these age-related alterations. We used serial electron microscopy to reconstruct and classify SL-M synapses and their postsynaptic spines. We analyzed synapse number and size as well as spine surface area and volume in young (10 months) and old (29 months) ad libitum fed rats and in old rats that were calorically restricted from 4 months of age. We limited our analysis to SL-M because previous work demonstrated age-related decreases in synaptophysin confined to this specific layer and region of the hippocampus. The results revealed an age-related decrease in macular axo-spinous synapses that was not reversed by CR that occurred in the absence of changes in the size of synapses or spines. Thus, the benefits of CR for CA3 function and synaptic plasticity may involve other biological effects including the stabilization of synaptic proteins levels in the face of age-related synapse loss. © 2010 IBRO.
Open Access
Aging alters the molecular dynamics of synapses in a sexually dimorphic pattern in zebrafish (Danio rerio)
(Elsevier, 2017-06) Karoglu, Elif Tugce; Halim, Dilara Ozge; Erkaya, Bahriye; Altaytas, Ferda; Arslan-Ergul, Ayca; Konu, Ozlen; Adams, Michelle M.
The zebrafish has become a popular model for studying normal brain aging due to its large fecundity, conserved genome, and available genetic tools; but little data exists about neurobiological age-related alterations. The current study tested the hypothesis of an association between brain aging and synaptic protein loss across males and females. Western blot analysis of synaptophysin (SYP), a presynaptic vesicle protein, and postsynaptic density-95 (PSD-95) and gephyrin (GEP), excitatory and inhibitory postsynaptic receptor-clustering proteins, respectively, was performed in young, middle-aged, and old male and female zebrafish (Danio rerio) brains. Univariate and multivariate analyses demonstrated that PSD-95 significantly increased in aged females and SYP significantly decreased in males, but GEP was stable. Thus, these key synaptic proteins vary across age in a sexually dimorphic manner, which has been observed in other species, and these consequences may represent selective vulnerabilities for aged males and females. These data expand our knowledge of normal aging in zebrafish, as well as further establish this model as an appropriate one for examining human brain aging.
Open Access
Alkaline phosphatase-mimicking peptide nanofibers for osteogenic differentiation
(American Chemical Society, 2015) Gülseren, Gülcihan; Yasa, I. Ceren; Ustahuseyin, Oya; Tekin, E. Deniz; Tekinay, Ayse B.; Güler, Mustafa O.
Recognition of molecules and regulation of extracellular matrix synthesis are some of the functions of enzymes in addition to their catalytic activity. While a diverse array of enzyme-like materials have been developed, these efforts have largely been confined to the imitation of the chemical structure and catalytic activity of the enzymes, and it is unclear whether enzyme-mimetic molecules can also be used to replicate the matrix-regulatory roles ordinarily performed by natural enzymes. Self-assembled peptide nanofibers can provide multifunctional enzyme-mimetic properties, as the active sequences of the target enzymes can be directly incorporated into the peptides. Here, we report enhanced bone regeneration efficiency through peptide nanofibers carrying both catalytic and matrix-regulatory functions of alkaline phosphatase, a versatile enzyme that plays a critical role in bone formation by regulating phosphate homeostasis and calcifiable bone matrix formation. Histidine presenting peptide nanostructures were developed to function as phosphatases. These molecules are able to catalyze phosphate hydrolysis and serve as bone-like nodule inducing scaffolds. Alkaline phosphatase-like peptide nanofibers enabled osteogenesis for both osteoblast-like and mesenchymal cell lines.
Open Access
Amyloid inspired self-assembled peptide nanofibers
(American Chemical Society, 2012) Çınar, Göksu; Ceylan, Hakan; Urel, Mustafa; Erkal, Turan S.; Tekin, E. Deniz; Tekinay, Ayse B.; Dâna, Aykutlu; Güler, Mustafa O.
Amyloid peptides are important components in many degenerative diseases as well as in maintaining cellular metabolism. Their unique stable structure provides new insights in developing new materials. Designing bioinspired self-assembling peptides is essential to generate new forms of hierarchical nanostructures. Here we present oppositely charged amyloid inspired peptides (AIPs), which rapidly self-assemble into nanofibers at pH 7 upon mixing in water caused by noncovalent interactions. Mechanical properties of the gels formed by self-assembled AIP nanofibers were analyzed with oscillatory rheology. AIP gels exhibited strong mechanical characteristics superior to gels formed by self-assembly of previously reported synthetic short peptides. Rheological studies of gels composed of oppositely charged mixed AIP molecules (AIP-1 + 2) revealed superior mechanical stability compared to individual peptide networks (AIP-1 and AIP-2) formed by neutralization of net charges through pH change. Adhesion and elasticity properties of AIP mixed nanofibers and charge neutralized AIP-1, AIP-2 nanofibers were analyzed by high resolution force-distance mapping using atomic force microscopy (AFM). Nanomechanical characterization of self-assembled AIP-1 + 2, AIP-1, and AIP-2 nanofibers also confirmed macroscopic rheology results, and mechanical stability of AIP mixed nanofibers was higher compared to individual AIP-1 and AIP-2 nanofibers self-assembled at acidic and basic pH, respectively. Experimental results were supported with molecular dynamics simulations by considering potential noncovalent interactions between the amino acid residues and possible aggregate forms. In addition, HUVEC cells were cultured on AIP mixed nanofibers at pH 7 and biocompatibility and collagen mimetic scaffold properties of the nanofibrous system were observed. Encapsulation of a zwitterionic dye (rhodamine B) within AIP nanofiber network was accomplished at physiological conditions to demonstrate that this network can be utilized for inclusion of soluble factors as a scaffold for cell culture studies. © 2012 American Chemical Society.
Open Access
Anatomical measurements correlate with individual magnetostimulation thresholds for kHz‐range homogeneous magnetic fields
(Wiley, 2020) Demirel, Ömer Burak; Kılıç, Toygan; Çukur, Tolga; Sarıtaş, Emine Ülkü
Purpose: Magnetostimulation, also known as peripheral nerve stimulation (PNS), is the dominant safety constraint in magnetic resonance imaging (MRI) for the gradient magnetic fields that operate around 0.1–1 kHz, and for the homogeneous drive field in magnetic particle imaging (MPI) that operates around 10–150 kHz. Previous studies did not report correlations between anatomical measures and magnetostimulation thresholds for the gradient magnetic fields in MRI. In contrast, a strong linear correlation was shown between the thresholds and the inverse of body part size in MPI. Yet, the effects of other anatomical measures on the thresholds for the drive field remain unexplored. Here, we investigate the effects of fat percentage on magnetostimulation thresholds for kHz‐range homogeneous magnetic fields such as the drive field in MPI, with the ultimate goal of predicting subject‐specific thresholds based on simple anatomical measures. Methods: Human subject experiments were performed on the upper arms of 10 healthy male subjects (age: 26 ± 2 yr) to determine magnetostimulation thresholds. Experiments were repeated three times for each subject, with brief resting periods between repetitions. Using a solenoidal magnetostimulation coil, a homogeneous magnetic field at 25 kHz with 100 ms pulse duration was applied at 4‐s intervals, while the subject reported stimulation via a mouse click. To determine the thresholds, individual subject responses were fitted to a cumulative distribution function modeled by a sigmoid curve. Next, anatomical images of the upper arms of the subjects were acquired on a 3 T MRI scanner. A two‐point Dixon method was used to obtain separate images of water and fat tissues, from which several anatomical measures were derived: the effective outer radius of the upper arm, the effective inner radius (i.e., the muscle radius), and fat percentage. Pearson’s correlation coefficient was used to assess the relationship between the threshold and anatomical measures. This statistical analysis was repeated after factoring out the expected effects of body part size. An updated model for threshold prediction is provided, where in addition to scaling in proportion with the inverse of the outer radius, the threshold has an affine dependence on fat percentage. Results: A strong linear correlation (r = 0.783, P < 0.008) was found between magnetostimulation threshold and fat percentage, and the correlation became stronger after factoring out the effects of outer radius (r = 0.839, P < 0.003). While considering body part size alone did not explain any significant variance in measured thresholds (P > 0.398), the updated model that also incorporates fat percentage yielded substantially improved threshold predictions with = 0.654 (P < 0.001). Conclusions: This work shows for the first time that fat percentage strongly correlates with magnetostimulation thresholds for kHz‐range homogenous magnetic fields such as the drive field in MPI, and that the correlations get even stronger after factoring out the effects of body part size. These results have important practical implications for predicting subject‐specific thresholds, which in turn can increase the performance of the drive field and improve image quality while remaining within the safety limits.
Open Access
Antigenic GM3 lactone mimetic molecule integrated mannosylated glycopeptide nanofibers for the activation and maturation of dendritic cells
(American Chemical Society, 2017) Gunay, Gokhan; Ekiz, Melis Sardan; Ferhati, X.; Richichi, B.; Nativi, C.; Tekinay, Ayse B.; Güler, Mustafa O.
The ability of dendritic cells to coordinate innate and adaptive immune responses makes them essential targets for vaccination strategies. Presentation of specific antigens by dendritic cells is required for the activation of the immune system against many pathogens and tumors, and nanoscale materials can be functionalized for active targeting of dendritic cells. In this work, we integrated an immunogenic, carbohydrate melanoma-associated antigen-mimetic GM3-lactone molecule into mannosylated peptide amphiphile nanofibers to target dendritic cells through DC-SIGN receptor. Based on morphological and functional analyses, when dendritic cells were treated with peptide nanofiber carriers, they showed significant increase in antigen internalization and a corresponding increase in the surface expression of the activation and maturation markers CD86, CD83 and HLA-DR, in addition to exhibiting a general morphology consistent with dendritic cell maturation. These results indicate that mannosylated peptide amphiphile nanofiber carriers are promising candidates to target dendritic cells for antigen delivery. © 2017 American Chemical Society.
Open Access
Aqueous paramagnetic solutions for MRI phantoms at 3 T: a detailed study on relaxivities
(Turkiye Klinikleri Journal of Medical Sciences, 2017) Thangavel, Kalaivani; Sarıtaş, Emine Ülkü
Phantoms with known T1 and T2 values that are prepared using solutions of easily accessible paramagnetic agents are commonly used in MRI imaging centers, especially with the goal of validating the accuracy of quantitative imaging protocols. The relaxivity parameters of several agents were comprehensively examined at lower B0 field strengths, but studies at 3 T remain limited. The main goal of this study is to measure r1 and r2 relaxivities of three common paramagnetic agents (CuSO4, MnCl2, and NiCl2) at room temperature at 3 T. Separate phantoms were prepared at various concentrations of 0.05-0.5 mM for MnCl2 and 1-6 mM for CuSO4 and NiCl2. For assessment of T1 relaxation times, inversion recovery turbo spin echo images were acquired at 15 inversion times ranging between 24 and 2500 ms. For assessment of T2 relaxation times, spin-echo images were acquired at 15 echo times ranging between 8.5 and 255 ms. Voxel-wise T1 and T2 relaxation times at each concentration were separately determined from the respective signal recovery curves (inversion recovery for T1 and spin echo decay for T2). Relaxivities r 1 and r2 for all three agents that were derived from these relaxation time measurements are reported: r1 = 0.602 mM-1 s-1 and r2 = 0.730 mM-1 s-1 for CuSO4, r1 = 6.397 mM-1 s-1 and r2 = 108.266 mM-1 s-1 for MnCl2, r1 = 0.620 mM-1 s-1 and r2 = 0.848 mM-1 s-1 for NiCl2. These results will serve as a practical reference to design phantoms of target T1 and T2 values at 3 T, in particular phantoms with relaxation times equivalent to specific human tissues.
Open Access
An arbitrary waveform MPI scanner
(Infinite Science Publishing, 2022) 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.
Open Access
Assessment of liliequist membrane by 3D-SPACE technique at 3 T
(Springer, 2016) Algın, Oktay; Kılın, M.; Ozmen, E.; Ocakoglu, G.
Introduction Liliequist membrane (LM) is the most important anatomic structure for the success of endoscopic third ventriculostomy (ETV). Identification of this membrane is difficult with conventional MRI techniques. The purpose of this retrospective study is to determine the impact of threedimensional sampling perfection with application-optimized contrasts using different flip-angle evolutions (3D-SPACE) sequence with variant flip-angle mode (VFAM) in the assessment of LM at 3-T MRI devices. Methods 3D-SPACE with VFAMimages were obtained in 445 patients. LM visibility and integrity were scored as 0 (good), 1 (moderate), and 2 (poor) on these images for each parts (sellar, diencephalic, and mesencephalic) and overall of the membrane. Results According to the LMoverall integrity scores, 11%(48 cases) of the patients had perforated membrane. According to subsegmental integrity scores, sellar part was completely intact in 63 % of patients, diencephalic segment was completely intact in 60 % of the patients, and mesencephalic segment was completely intact in 95 % of the patients. Visibility scores of the third ventricle inferior wall were significantly higher in the patients with intact LM (p = 0.001). There was not any statistically significant relationship between LM pattern and overall integrity (p = 0.352). LM attachment sites could be detected easier in the patients who had better visibility of third ventricle inferior wall or intact LM (p < 0.001 for both). Conclusion 3D-SPACE technique is a useful alternative for the evaluation of morphology, integrity, individual variations, topographic relationships, and visibility of LM since it has some advantages including lower SAR values, fewer artifacts, and high-resolution images.
Open Access
Assessment of third ventriculostomy patency with the 3D-SPACE technique: a preliminary multicenter research study
(American Association of Neurological Surgeons, 2015) Algın, Oktay; Uçar, M.; Ozmen, E.; Borcek, A.; Ozisik, P.; Ocakoglu, G.; Tali, E.
Object The goal of this study was to determine the value of the 3D sampling perfection with application-optimized contrasts using different flip-angle evolutions (3D-SPACE) technique in the evaluation of endoscopic third ventriculostomy (ETV) patency. Methods Twenty-six patients with ETV were examined using 3-T MRI units. Sagittal-plane 3D-SPACE with variant flip-angle mode, 3D T1-weighted (T1W), and 3D heavily T2-weighted (T2W) images were obtained with isotropic voxel sizes. Also, sagittal-axial plane phase-contrast cine (PC)-MR images were obtained. The following findings were evaluated: diameters of stoma and third ventricle, flow-void sign on 3D-SPACE and PC-MR images, integrity of the third ventricle on heavily T2W images, and quantitative PC-MRI parameters of the stoma. Obtained sequences were evaluated singly, in combination with one another, and all together. Results The mean area, flow, and velocity values measured at the level of stoma in patients with patent stoma were significantly higher than those measured in patients with closed stoma (p < 0.05). There was significant correlation among PC-MRI, 3D-SPACE, and 3D heavily T2W techniques regarding assessment of ETV patency (p < 0.001). The 3D-SPACE technique provided the lowest rate of ambiguous results. Conclusions The 3D-SPACE technique seems to be the most efficient one for determination of ETV patency. The authors suggest the use of 3D-SPACE as a stand-alone first-line sequence in addition to routine brain MRI protocols in assessing patients with ETV, thereby decreasing scan time and reserving the use of a combination of additional sequences such as PC-MRI and 3D heavily T2W images in suspicious or complex cases.
Open Access
Association of fine motor loss and allodynia in fibromyalgia: an fNIRS study
(Routledge, 2018) Eken, A.; Gökçay D.; Yılmaz, Cemre; Baskak, B.; Baltacı, A.; Kara, M.
Recent studies showed that fine motor control dysfunction was observed in fibromyalgia (FM) syndrome as well as allodynia. However, brain signatures of this association still remain unclear. In this study, finger tapping task (FTT) and median nerve stimulation (MNS) were applied to both hands of 15 FM patients and healthy controls (HC) to understand this relationship. Hemodynamic activity was measured simultaneously using functional near-infrared spectroscopy (fNIRS). Experiments were analyzed separately by using 2x2 repeated measures ANOVA. Results for the FTT experiment revealed that HC showed higher activity than FM patients in bilateral superior parietal gyrus (SPG), left supramarginal gyrus (SMG) and right somatosensory cortex (SI). Furthermore, right-hand FTT resulted in higher activity than left-hand FTT in left SPG, left SI and right motor cortex (MI). In the MNS experiment, FM patients showed higher activity than HC in bilateral SPG, right SMG, right SI and right middle frontal gyrus (MFG). Negative correlation was observed in left SPG between FTT and MNS activities. Besides, MNS activity in left SPG was negatively correlated with left-hand pain threshold.This study revealed that left SPG might be an important indicator to associate fine motor loss and allodynia in FM.