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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 half-hour gap after examinations that involve humans, and animals (there is no need to leave a gap after studies that involve only phantom or console usage). ● 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 half-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 14 days? 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 half-hour gap after an animal study. There may be more than 1 animal subject during an animal examination session.

Cognitive Computational Neuroscience Lab (Ürgen Lab) students Hüseyin Orkun Elmas and Sena Er were awarded a TÜBİTAK BIDEB scholarship. Congratulations!   For more information ; https://tubitak.gov.tr/tr/duyuru/bideb-egitim-burs-programlari-2020-yili-2-donem-basvuru-sonuclari-aciklandi 

Zipfian regularities are important empirical laws in computational linguistics and natural language processing as well as several other areas of science. Zipf’s law of meaning distribution, one of the most important Zipfian laws, points out a power relation between frequencies of words and number of meanings that words have. In particular, frequent words have more meanings than less frequent words as a result of the Principle of Least Effort. In other words, word frequencies are indicators for polysemy characteristics of words. In their paper, KocLab showed that there exists another Zipfian regularity in semantics. It is shown that the generality and specificity of words display a Zipfian regularity when polysemy is neutralized. To measure the specificity levels of words, we utilize variance values of Gaussian embeddings, which is a non-point word representation. By neutralizing the polysemy from the corpus, we obtain Gaussian embeddings of different senses of words and demonstrate the Zipfian pattern in the variance values of words with respect to word frequency ranks. This regularity indicates that “frequent words tend to be more generic, while infrequent words tend to be more specific.” The paper can be accessed [here].   Abstract: Being one of the most common empirical regularities, the Zipf’s law for word frequencies is a power law relation between word frequencies and frequency ranks of words. We quantitatively study semantic uncertainty of words through non-point distribution-based word embeddings and reveal the Zipfian regularities. Uncertainty of a word can increase due to polysemy, the word having “broad” meaning (such as the relation between broader emotion and narrower exasperation) or a combination of both. Variances of Gaussian embeddings are utilized to quantify the extent a word can be used in different senses or contexts. By using the variance information embedded in the non-point Gaussian embeddings, we quantitatively show that semantic breadth of words also exhibits Zipfian patterns, when polysemy is controlled. This outcome is complementary to Zipf’s law of meaning distribution and the related meaning-frequency law by indicating the existence of Zipfian patterns: more frequent words tend to be generic while less frequent ones tend to be specific. Results for two languages, English and Turkish that belong to different language families, are also provided. Such regularities provide valuable information to extract and understand relationships between semantic properties of words and word frequencies. In various applications, performance improvements can be obtained by employing these regularities. We also propose a method that leverages the Zipfian regularity to improve the performance of baseline textual entailment detection algorithms. To the best of our knowledge, our approach is the first quantitative study that uses Gaussian embeddings to examine the relationships between word frequencies and semantic breadth.  

Discrete signal scaling is a basic operation of central importance that poses several challenges, which are usually addressed as an interpolation problem. Our approach, which does not involve interpolation in the conventional sense, provides a novel and unique perspective to this problem, and may be useful in a wide variety of theoretical and practical contexts. We also believe that the introduction of hyperdifferential operator theory to the problem of defining a discrete operation might also open up new research directions for other operations that are important for signal analysis and processing.   Paper link: https://www.sciencedirect.com/science/article/abs/pii/S1051200420302499   Abstract: Signal scaling is a fundamental operation of practical importance in which a signal is made wider or narrower along the coordinate direction(s). Scaling, also referred to as magnification or zooming, is complicated for signals of a discrete variable since it cannot be accomplished simply by moving the signal values to new coordinate points. Most practical approaches to discrete scaling involve interpolation. We propose a new approach based on hyperdifferential operator theory that does not involve conventional interpolation. This approach provides a self-consistent and pure definition of discrete scaling that is fully consistent with discrete Fourier transform theory. It can potentially be applied to other problems in signal theory and analysis such as transform designs. Apart from its theoretical elegance, it also provides a basis for numerical implementation.

Using dynamic dot displays, Schimid et al. show that a large network of brain regions respond to material motion. The dynamic dot displays are similar to those in biological motion studies, and they allow researchers to isolate motion cues from all other cues to material properties (e.g. surface reflectance). Interestingly, the areas that are found to respond to material motion in this study constitute a superset of those found to respond to biological motion in previous studies.

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Prior knowledge and expectations play a substantial role in recognition and decision-making processes by governing the interpretation of the sensory stimulus and allowing us to make fast and accurate decisions. Whether and how early sensory processes are affected by expectations, however, has remained a controversial issue. Using a behavioral experiment and a recursive Bayesian model, Urgen & Boyaci (2021) investigated the effect of expectations on perceptual thresholds and unveiled the possible mechanisms that underlie the observed effects. Specifically, they showed that unlike what is suggested for higher-level mechanisms, valid expectations do not facilitate perceptual processes, instead, unmet expectations delay them. Their modeling findings revealed that the mechanism that underlies this delay is the need for further processing required by the system to complete the sensory process. Urgen & Boyaci (2021) also discussed possible neural mechanisms that can explain their findings within the predictive processing framework.  

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One of our former PhD student Koray Ertan, has received 2020 Serhat Ozyar Young Scientist Award. ”Design of Z-Gradient Array and Applications in Magnetic Resonance Imaging” Koray Ertan completed his continuing doctoral thesis on “Design of Z-Gradient Array and Applications in Magnetic Resonance Imaging” in 2019 under the thesis advisory of Prof Dr Ergin Atalar in Bilkent University Electrical and Electronics Engineering Department. In Magnetic Resonance Imaging (MRI), it is important to reduce the warming caused by the radio frequency (RF) energy applied to the patient. Heating problem due to RF area is also an important safety problem in patients with pacemakers and similar implants and in interventional applications using MRI. The time (exposure time) that the patient stays in the device during imaging should be shortened. It has been observed that with the innovative hardware, software and techniques developed within the scope of Dr. Ertan’s thesis, the radio frequency energy applied to the patients during the shooting is reduced and the shooting time can be shortened. In addition, thanks to the proposed z-gradient array, gradient areas more compatible with nerve stimulation limits can be created, and their performance is increased by creating gradient areas only in the target organ or region. Dr. Ertan has designed unique windings to create regional gradient areas, manufactured prototypes, tested them with experimental studies and completed performance analyzes. Within the scope of the thesis, 3 articles were published in leading scientific journals in the field, 13 international and 3 national papers were presented. He is the first author in all peer-reviewed journal publications, eight international papers and two national papers. There are a total of 35 citations according to Google Scholar. In addition, five international patent applications were filed within the scope of the thesis, three from the USA and two for PCT.

Emine Ülkü Sarıtaş, faculty member at UMRAM, has received 2020 IEEE Turkey Research Incentive Award. Following its mission to encourage and support scientists, IEEE Turkey has launched an annual awards program in 2017. IEEE Turkey Research Incentive Award is awarded to scientists with outstanding research activity in IEEE related disciplines, who completed their doctorate in the last decade, performed a significant part of their postdoctoral research in Turkey, and currently reside in Turkey. 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.

Parlar foundation gives Honorary, Science, Service, Research and Technology Incentive Awards every year in order to evaluate the research studies and services carried out in science and industry and to encourage the growing generations. Emine Ülkü Sarıtaş, faculty member at UMRAM, has received 2020 Parlar Research Incentive Award. 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.

UMRAM faculty member Dr. Hulusi Kafalıgönül has received this year’s Outstanding Young Scientist Award from the Turkish Academy of Sciences (TÜBA). Dr. Kafalıgönül has been recognized for his work in the field of Cognitive Neuroscience, in particular on the dynamics of sensory and perceptual processing and alterations in perception due to adaptation and aging. TÜBA introduced the Program to Award Young Scientists (GEBİP) in 2001 to recognize and support outstanding young researchers working in the natural and social sciences, engineering, and medicine.

The 18th National Neuroscience Congress (Ulusal Sinirbilim Kongresi) was hosted by Bilkent University between 6-9 November 2020. The congress was held virtually on Zoom due to the ongoing pandemic. The scientific program included 10 keynotes by national and international scientists, 15 panels by 65 speakers from various universities, 63 oral presentations and 94 poster presentations as well as 5 educational courses. Key members of the organizing committee include Tolga Çukur (EE/Neuroscience), Hüseyin Boyacı (Psychology/Neuroscience), Burcu Ayşen Ürgen (Psychology/Neuroscience), Hulusi Kafalıgönül (Neuroscience) and Dicle Dövencioğlu (METU). Other Bilkent faculty members supporting the event were UMRAM director and EE faculty member Ergin Atalar and Aysel Sabuncu Brain Research Center director and chair of the Psychology department Michelle Adams (Psychology/Neuroscience). A team of graduate students in the Neuroscience, Psychology and EE programs provided technical support for the online sessions over Zoom. Successfully hosting over 600 attendees, the congress constitutes a remarkable example for upcoming online meetings. The scientific program and abstract book are available at http://bad.org.tr/usk18/

Dr. Huseyin Boyaci has been promoted to Professor rank. Dr. Boyaci is currently the vice-director of the National Magnetic Resonance Research Center (UMRAM). His primary affiliation is with the Department of Psychology of Bilkent. Dr. Boyaci received his Ph.D. degree from the Physics Department of Bilkent University. He was a postdoctoral fellow at New York University and the University of Minnesota. In 2008 he joined the Department of Psychology, Bilkent University. He and his wife, Katja Doerschner, became the first faculty members of UMRAM. Almost immediately after becoming an Associate Professor, Dr. Boyaci took one year of sabbatical leave in 2014 that he spent in University of California, San Diego. He became a guest professor at JL Giessen University in Germany during the summers of 2016-2019. His research area is visual perception and its neuronal underpinnings. His research team uses behavioral experimentation, neuroimaging (fMRI), and computational modeling to find answers to vision science problems. Congratulations on the well-deserved promotion.