News

Our faculty member Burcu Ayşen Ürgen published a new paper titled “A parietal region processing numerosity of observed actions: An fMRI study”  in European Journal of Neuroscience. The other authors of the paper are Hiromasa Sawamura from University of Tokyo (Japan), Guy A. Orban from University of Parma (Italy), and Daniele Corbo from University of Brescia (Italy). The study examined numerosity specific brain regions during action observation using functional magnetic resonance imaging in humans.    ABSTRACT When observing others’ behavior, it is important to perceive not only the identity of the observed actions, but also the number of times they were performed. Given the mounting evidence implicating posterior parietal cortex in action observation, and in particular that of manipulative actions, the aim of this study was to identify the parietal region, if any, that contributes to the processing of observed‐manipulative‐action numerosity, using the functional magnetic resonance imaging technique. Twenty‐one right‐handed healthy volunteers performed two discrimination tasks while in the scanner, responding to video stimuli in which an actor performed manipulative actions on colored target balls that appeared four times consecutively. The subjects discriminated between two small numerosities of either observed manipulative actions (“Action” condition) or colors of balls (“Ball” condition). A significant difference between the “Action” and “Ball” conditions was observed in occipito‐temporal cortex and the putative human anterior intraparietal sulcus (phAIP) area as well as the third topographic map of numerosity‐selective neurons at the post‐central sulcus (NPC3) of the left parietal cortex. A further ROI analysis of the group‐average data showed that at the single voxel level the latter area, more than any other parietal or occipito‐temporal numerosity map, favored numerosity of observed actions. These results suggest that phAIP processes the identity of observed manipulative actions, while neighboring NPC3 likely processes the numerosity of the identified observed actions.

A work from UMRAM focused on the fast methods for designing RF transmit array coils resulted in a manuscript entitled “Accelerating the co-simulation method for the design of transmit array coils for MRI.” In this study, the co-simulation method is considerably accelerated for the design of tramsnit array coils. As a proof of concept, an eight-channel degenerate birdcage coil is designed and constructed in a fast and accurate manner. Now, UMRAM facilities are aequiped with this coil, which can be used for head imaging at 3 T. The first author of the paper is Alireza Sadeghi‐Tarakameh who is a PhD student of Ergin Atalar.  The other authors of the paper are Ehsan Kazemivalipour, Umut Gündoğdu and Serhat Erdoğan of UMRAM.   Abstract Objective Accelerating the co-simulation method for the design of transmit array (TxArray) coils is studied using equivalent circuit models. Materials and methods Although the co-simulation method dramatically reduces the complexity of the design of TxArray coils, finding the optimum solution is not trivial since there exist many local minima in the optimization problem. We propose to utilize an equivalent circuit model of the TxArray coil to obtain a proper initial guess for the optimization process of the co-simulation method. To prove the concept, six different TxArray coils (i.e., three degenerate birdcage coils (DBC), two dual-row head coils, and one elliptical body TxArray coil) with two different loading strategies (cylindrical phantom and human head/body model) at 3 T field strength are investigated theoretically; as an example study, an eight-channel head-DBC is constructed using the obtained values. Results This approach accelerates the design process more than 20-fold for the coils that are investigated in this manuscript. Conclusion A fast and accurate method for tuning and decoupling of a TxArray coil can be achieved using its equivalent circuit model combined with the co-simulation method.  

Görkem Er, Zahide Pamir and Hüseyin Boyaci have published an article titled ”Distinct patterns of surround modulation in V1 and hMT+” in NeuroImage. Using fMRI and a well-studied motion paradigm, in which sensitivity to direction of motion increases (decreases) for a low (high) contrast stimulus as its size gets bigger, Er et al. show that patterns of center-surround interaction are different in primary visual cortex (V1) and middle temporal complex (hMT+). Furthermore, the authors show that the divisive normalization model can successfully predict the responses in V1 and hMT+, and link the behavioral and fMRI data.  

Abstract

Mehdi Shafiei Aporvari, Mustafa Utkur, and Emine Ulku Saritas have published an article titled “Anisotropic Dynamics of a Self-assembled Colloidal Chain in an Active Bath” in Soft Matter. This paper was a collaborative work with Giovanni Volpe (previously with the Department of Physics in Bilkent, now with University of Gothenburg) and Joakim Stenhammar (with Lund University). This paper presents an experimental investigation of the dynamics of isolated self-assembled chains moving at an interface between a suspension of swimming bacteria and air, finding an anomalous, non-monotonic size dependence in the anisotropic center-of-mass diffusivity.  

Anisotropic macromolecules exposed to non-equilibrium (active) noise are very common in biological systems, and an accurate understanding of their anisotropic dynamics is therefore crucial. Here, we experimentally investigate the dynamics of isolated chains assembled from magnetic microparticles at a liquid-air interface and moving in an active bath consisting of motile E. coli bacteria. We investigate both the internal chain dynamics and the anisotropic center-of-mass dynamics through particle tracking. We find that both the internal and center-of-mass dynamics are greatly enhanced compared to the passive case, i.e., a system without bacteria, and that the center-of-mass diffusion coefficient D features a non- monotonic dependence as a function of the chain length. Furthermore, our results show that the relationship between the components of D parallel and perpendicular with respect to the direction of the applied magnetic field is preserved in the active bath compared to the passive case, with a higher diffusion in the parallel direction, in contrast to previous findings in the literature. We argue that this qualitative difference is due to subtle differences in the experimental geometry and conditions and the relative roles played by long-range hydrodynamic interactions and short-range collisions.

Emine Ülkü Sarıtaş, faculty member at UMRAM and Department of Electrical and Electronics Engineering (EEE) of Bilkent, has been promoted to Associate Professor level. Prior to joining Bilkent as a faculty member in 2013, she was a postdoctoral fellow at the Department of Bioengineering at University of California, Berkeley from 2010-2013. She received her Ph.D. degree in 2009 and M.S. degree in 2004 from the Department of Electrical Engineering at Stanford University, and her B.S. degree in 2002 from Bikent EEE. She was the recipient of the Lucent Technologies Stanford Graduate Fellowship during her PhD studies and Siebel Stem Cell Institute Postdoctoral Fellowship during her postdoctoral studies. She is the recipient of the 2015 “Young Scientist Outstanding Achievement Award” (GEBIP) given by the Turkish Academy of Sciences (TÜBA), the 2016 “Young Scientist Award” (BAGEP) given by the Science Academy Turkey (Bilim Akademisi), the 2017 “Scientist of the Year Award” given by Science Heroes Association (Bilim Kahramanlari Dernegi), and the 2019 “Incentive Award” given by the Scientific and Technological Research Council of Turkey (TÜBİTAK). She has also received the Distinguished Teaching Award of Bilkent University in 2018. In her research, Assoc. Prof. Sarıtaş focuses on novel magnetic resonance imaging (MRI) and magnetic particle imaging (MPI) systems, and their diagnostic and scientific applications. She has developed innovative technologies to advance technical and clinical capabilities of these imaging modalities. Her leading contributions include imaging techniques that enable high-resolution diffusion-weighted MRI in targeted body areas, comprehensive evaluation of human safety limits of magnetic imaging systems, and novel contrast mechanisms for MPI. Her research has been published in leading journals including IEEE Transactions on Medical Imaging (TMI), Magnetic Resonance in Medicine, Applied Physics Letters, and Advanced Materials. Her academic work has resulted in 45 journal publications, 110 conference proceedings, 1 book chapter, and 1 US patent, and has received over 2200 citations. Assoc. Prof. Sarıtaş is currently serving as an Associate Director for National Magnetic Resonance Research Lab (UMRAM), as an Associate Editor for IEEE TMI, and as an Editorial Board Member for the International Journal on Magnetic Particle Imaging (IJMPI). She has previously served as an Editorial Board Member for Nature Scientific Reports, and was the chair of IEEE Turkey Section Women in Engineering.

Dear 3T users, We would like to kindly ask all investigators to provide us the ethical and/or institutional approvals of their studies. Such an approval is required for all human and animal studies. You can hand in a hard copy or send a soft copy to the UMRAM administration. Furthermore, please put the study-specific approval number in the “Description” part of your reservations on the 3T Calendar. Please let us know if you have any questions.

Alireza Sadeghi-Tarakameh, who is a PhD student of Ergin Atalar, published the results of a collaborative work between CMRR and UMRAM in a paper entitled “Improving radiofrequency power and specific absorption rate management with bumped transmit elements in ultra‐high field MRI.” The main goal of this study is to facilitate prostate imaging and assure patient safety at ultra-high field MRI. The senior author of the article, Yiğitcan Eryaman, is an assistant professor at CMRR and received his PhD degree from Bilkent University. Other authors of this article, Gregor Adriany, Gregory J. Metzger, Russell L. Lagore, Steve Jungst, Lance DelaBarre, Pierre-Francois Van de Moortele, and Kamil Ugurbil, are from the University of Minnesota.  

Abstract

Purpose

In this study, we investigate a strategy to reduce the local specific absorption rate (SAR) while keeping B₁⁺ constant inside the region-of-interest (ROI) at the ultra-high field (B₀ ≥ 7 T) MRI.

Methods Locally raising the resonance structure under the discontinuity (i.e., creating a bump) increases the distance between the accumulated charges and the tissue. As a result, it reduces the electric field and local SAR generated by these charges inside the tissue. The B₁⁺ at a point that is sufficiently far from the coil however is not affected by this modification. In this study, three different resonant elements (i.e., loop coil, snake antenna, and fractionated dipole (FD)) are investigated. For experimental validation, a bumped FD is further investigated at 10.5 T. After the validation, the transmit performances of eight-channel arrays of each element are compared through EM simulations. Results Introducing a bump reduced the peak 10g-averaged SAR by 21, 26, 23% for the loop and snake antenna at 7 T, and FD at 10.5 T, respectively. In addition, eight-channel bumped FD array at 10.5 T had a 27% lower peak 10g-averaged SAR in a realistic human body simulation (i.e., prostate imaging) compared to an eight-channel FD array. Conclusion In this study, we investigated a simple design strategy based on adding bumps to a resonant element to reduce the local SAR while maintaining B₁⁺ inside an ROI.  As an example, we modified an FD and performed EM simulations and phantom experiments with a 10.5T scanner. Results show that the peak 10g-averaged SAR can be reduced more than 25%.

The following hygiene procedures have been prepared for the safety of examiners, human participants and patients, our animal friends, and everyone working in UMRAM. Everyone MUST follow these rules strictly. Examiners, who do not follow these rules, will be BANNED from using the scanner. These rules are effective immediately and valid until further notice. Note that these are hygiene procedures, all other regular procedures MUST still be followed, such as checking for metals and MR-incompatible implants, and obtaining written informed consent forms. The following hygiene procedures have been prepared for the safety of examiners, human participants and patients, our animal friends, and everyone working in UMRAM. Everyone MUST follow these rules strictly. Examiners, who do not follow these rules, will be BANNED from using the scanner. These rules are effective immediately and valid until further notice. Note that these are hygiene procedures, all other regular procedures MUST still be followed, such as checking for metals and MR-incompatible implants, and obtaining written informed consent forms. General procedures: In the rest of the document, MUST means an absolute requirement, SHOULD means a strong recommendation. “Scanner room” refers to the room where the scanner is located. “Scanner site” refers to the combination of the scanner room and the control room. ● The nature of examination (phantom, human, or animal) MUST be noted on the calendar when making a reservation. ● There MUST be at least a 3-hour gap between examinations that involve humans or animals. ● The morning appointment MUST end latest at 14:00. This includes the subsequent obligatory gap. For example, if it is a human exam, the actual exam MUST end at 11:00. ● The afternoon appointment MUST start after 14:00. If possible please start the exam as early as possible after 14:00, this would give a reasonable amount of time for a third session at night. ● There MUST be at least a 1-hour gap after examinations involving only phantoms. ● Users will not be charged for the extra gap time. However, users MUST separately reserve those extra gap times on the calendar with the following note: “DO NOT USE SCANNER”. ● The gap time MUST not be used for any additional examination, analysis or a study of any other nature in the scanner site. Examiners MUST complete their examination and leave the scanner site by the end of their regular appointment. ● Examiners MUST NOT have any flu-like symptoms. A sample checklist is provided below. With a positive answer to ANY of the questions, the study MUST be postponed. ● Examiners MUST wear mouth and nose protection masks at all times. ● Examiners MUST wash and dry their hands before entering the scanner site. ● Upon entering the scanner site examiners MUST immediately disinfect their hands and MUST wear gloves. They MUST NOT touch any personal belongings afterward. ● Masks and gloves will be provided by UMRAM. ● All objects and surfaces that are used, touched, breathed on or otherwise interacted with MUST be disinfected at the end of the examination. Disinfecting agents will be provided by UMRAM. If you need help, our technical personnel will guide you for applying the disinfectants, so please ask them. ● All waste MUST be disposed of in the medical trash bin placed outside of the scanner site. Our technical personnel will help you locate the bin. ● Masks and gloves MUST NOT be reused and they MUST be renewed if removed. ● Gloves MUST be taken off in a way such that the outer surface of the glove does not touch the skin; turn the inner surface outwards so that one glove wraps the other. ● Personal belongings MUST NOT be placed on the console desk and chairs. They should be properly stored in cabinets or placed on the new desk placed in the scanner site. ● There MUST NOT be any eating or drinking, including water. Human participants or patients may be allowed to take their exam-related medicine if necessary. Disposable cups and/or containers MUST be used for this. ● There SHOULD NOT be more than two examiners at the scanner site unless the nature of the examination requires more than two examiners. ● Examiners SHOULD preserve a distance of 1.5m between them. ● Examiners SHOULD wear long clothing. ● All surfaces, e.g. the bed, head cushions, that the human participants, patients, or animals will contact MUST be appropriately covered. ● Examiners, who need to wash and disinfect their hands frequently, are advised to use skincare products. Human participant and patient (HPP) procedures: ● HPPs MUST be contacted beforehand and it MUST be ensured that they do not have any flu-like symptoms. A sample checklist is provided below. With a positive answer to ANY of the questions the examination MUST be postponed. ● There MUST be at least a 3-hour gap between the examinations of two HPPs, even if they are related to the same study. ● External HPPs MUST be met outside the building. ● HPPs’ body temperature MUST be measured before allowing them inside the building. A measurement device will be provided by UMRAM. ● HPPs MUST wear a mask before entering the building. If the HPP will wear a mask during examination, and if the mask has a metal part, it can create artifacts in MRI images. If this is a concern, ask the HPP to remove the metal part of their mask before entering the building. ● HPPs MUST be accompanied into the bathroom to wash and dry their hands. ● HPPs MUST be accompanied to the scanner site. ● Only one HPP at a time MUST be admitted into the scanner site. ● HPPs MUST remove all belongings and safely store them once inside the scanner site. ● HPPs MUST wear a medical gown. These gowns will be provided by UMRAM. The gown can be worn over HPPs’ clothes. ● HPPs MUST be guided to disinfect their hands and advised not to touch anything after disinfection. ● HPPs SHOULD bring their signed consent form if possible. If this is not possible HPPs SHOULD be provided with the form in the scanner site. The form SHOULD be signed on the new desk placed in the scanner site. HPPs SHOULD use their own pen to sign the papers. If they do not have a pen they SHOULD be provided with a disinfected pen. ● If needed, an accompanying person may accompany the HPP into the scanner site. Other visitors MUST remain in the waiting lounge and follow the rules of social distance ● Maximum possible distance between the examiner and HPP MUST be preserved at all times, including while positioning the HPP on the bed and attaching the coils. Only one examiner SHOULD prepare the HPP and send inside the scanner bore. ● HPPs SHOULD not be allowed to enter the part of the scanner site where the console desk is located. This part SHOULD be reserved for the examiners only. ● HPPs SHOULD keep their masks on during the examination. If this is not possible, for example, to avoid artifacts or head movements, HPPs’ masks may be removed just before positioning them on the bed. ● HPPs MUST put on earplugs themselves. ● In case the HPP cannot wear a mask due to the nature of the study, the examiners SHOULD exercise extra caution and are advised to wear a full-face protective transparent screen. Those screens will be provided by UMRAM. Flu-symptom checklist: 1. Have you had a fever in the past 14 days? Yes/No 2. Have you had a dry cough in the past 14 days? Yes/No 3. Have you had any acute muscle problems/limb pain in the past 14 days? Yes/No 4. Have you had an acute headache in the past 14 days? (If you frequently experience headaches, answer “No” if the headache felt as usual) Yes/No 5. Have you had any sudden changes in taste, flavor or olfactory sensation in the past 14days? Yes/No 6. Have you had acute diarrhea in the past 14 days? Yes/No 7. Have you been in contact with other suspected cases in the past 14 days? Yes/No 8. Have you been abroad in the last 14 days? Yes/No Animal Examination Procedures: ● Animals SHOULD be admitted to the scanner room through the side door. ● There MUST be a 3-hour gap after an animal study. There may be more than 1 animal subject during an animal examination session.