Bio+and+Brain+Engineering
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A Single Biological Factor Predicts Distinct Cortical Organizations across Mammalian Species
-A KAIST team’s mathematical sampling model shows that retino-cortical mapping is a prime determinant in the topography of cortical organization.-
Researchers have explained how visual cortexes develop uniquely across the brains of different mammalian species. A KAIST research team led by Professor Se-Bum Paik from the Department of Bio and Brain Engineering has identified a single biological factor, the retino-cortical mapping ratio, that predicts distinct cortical organizations across mammalian species.
This new finding has resolved a long-standing puzzle in understanding visual neuroscience regarding the origin of functional architectures in the visual cortex. The study published in Cell Reports on March 10 demonstrates that the evolutionary variation of biological parameters may induce the development of distinct functional circuits in the visual cortex, even without species-specific developmental mechanisms.
In the primary visual cortex (V1) of mammals, neural tuning to visual stimulus orientation is organized into one of two distinct topographic patterns across species. While primates have columnar orientation maps, a salt-and-pepper type organization is observed in rodents.
For decades, this sharp contrast between cortical organizations has spawned fundamental questions about the origin of functional architectures in the V1. However, it remained unknown whether these patterns reflect disparate developmental mechanisms across mammalian taxa, or simply originate from variations in biological parameters under a universal development process.
To identify a determinant predicting distinct cortical organizations, Professor Paik and his researchers Jaeson Jang and Min Song examined the exact condition that generates columnar and salt-and-pepper organizations, respectively. Next, they applied a mathematical model to investigate how the topographic information of the underlying retinal mosaics pattern could be differently mapped onto a cortical space, depending on the mapping condition.
The research team proved that the retino-cortical feedforwarding mapping ratio appeared to be correlated to the cortical organization of each species. In the model simulations, the team found that distinct cortical circuitries can arise from different V1 areas and retinal ganglion cell (RGC) mosaic sizes. The team’s mathematical sampling model shows that retino-cortical mapping is a prime determinant in the topography of cortical organization, and this prediction was confirmed by neural parameter analysis of the data from eight phylogenetically distinct mammalian species.
Furthermore, the researchers proved that the Nyquist sampling theorem explains this parametric division of cortical organization with high accuracy. They showed that a mathematical model predicts that the organization of cortical orientation tuning makes a sharp transition around the Nyquist sampling frequency, explaining why cortical organizations can be observed in either columnar or salt-and-pepper organizations, but not in intermediates between these two stages.
Professor Paik said, “Our findings make a significant impact for understanding the origin of functional architectures in the visual cortex of the brain, and will provide a broad conceptual advancement as well as advanced insights into the mechanism underlying neural development in evolutionarily divergent species.”
He continued, “We believe that our findings will be of great interest to scientists working in a wide range of fields such as neuroscience, vision science, and developmental biology.”
This work was supported by the National Research Foundation of Korea (NRF).
Image credit: Professor Se-Bum Paik, KAIST
Image usage restrictions: News organizations may use or redistribute this image, with proper attribution, as part of news coverage of this paper only.
Publication:
Jaeson Jang, Min Song, and Se-Bum Paik. (2020). Retino-cortical mapping ratio predicts columnar and salt-and-pepper organization in mammalian visual cortex. Cell Reports. Volume 30. Issue 10. pp. 3270-3279. Available online at https://doi.org/10.1016/j.celrep.2020.02.038
Profile:
Se-Bum Paik
Assistant Professor
sbpaik@kaist.ac.kr
http://vs.kaist.ac.kr/
VSNN Laboratory
Department of Bio and Brain Engineering
Program of Brain and Cognitive Engineering
http://kaist.ac.kr
Korea Advanced Institute of Science and Technology (KAIST)
Daejeon, Republic of Korea
Profile:
Jaeson Jang
Ph.D. Candidate
jaesonjang@kaist.ac.kr
Department of Bio and Brain Engineering, KAIST
Profile:
Min Song
Ph.D. Candidate
night@kaist.ac.kr
Program of Brain and Cognitive Engineering, KAIST
(END)
2020.03.11 View 11703 -
Professor Jong Chul Ye Appointed as Distinguished Lecturer of IEEE EMBS
Professor Jong Chul Ye from the Department of Bio and Brain Engineering was appointed as a distinguished lecturer by the International Association of Electrical and Electronic Engineers (IEEE) Engineering in Medicine and Biology Society (EMBS). Professor Ye was invited to deliver a lecture on his leading research on artificial intelligence (AI) technology in medical video restoration. He will serve a term of two years beginning in 2020.
IEEE EMBS's distinguished lecturer program is designed to educate researchers around the world on the latest trends and technology in biomedical engineering. Sponsored by IEEE, its members can attend lectures on the distinguished professor's research subject.
Professor Ye said, "We are at a time where the importance of AI in medical imaging is increasing.” He added, “I am proud to be appointed as a distinguished lecturer of the IEEE EMBS in recognition of my contributions to this field.”
(END)
2020.02.27 View 8240 -
Cancer cell reversion may offer a new approach to colorectal cancer treatment
A novel approach to reverse the progression of healthy cells to malignant ones may offer a more effective way to eradicate colorectal cancer cells with far fewer side effects, according to a team of researchers based in South Korea.
Colorectal cancer, or cancer of the colon, is the third most common cancer in men and the second most common in women worldwide. South Korea has the second highest incident rate of colorectal cancer in the world, topped only by Hungary, according to the World Cancer Research Fund.
Their results were published as a featured cover article on January 2 in Molecular Cancer Research, a journal of the American Association for Cancer Research.
Led by Kwang-Hyun Cho, a professor and associate vice president of research at KAIST , the researchers used a computational framework to analyze healthy colon cells and colorectal cancer cells. They found that some master regulator proteins involved in cellular replication helped healthy colon cells mature, or differentiate into their specific cell type, and remain healthy. One particular protein, called SETDB1, suppressed the helpful proteins, forcing new cells to remain in a state of immaturity with the potential to become cancerous.
“This suggests that differentiated cells have an inherent resistance mechanism against malignant transformation and indicates that cellular reprogramming is indispensable for malignancy,” said Cho. “We speculated that malignant properties might be eradicated if the tissue-specific gene expression is reinstated — if we repress SETDB1 and allow the colon cells to mature and differentiate as they would normally.”
Image credit: Kwang-Hyun Cho, KAIST
Image restriction: News organizations may use or redistribute this image, with proper attribution, as part of news coverage of this paper only.
Using human-derived cells, Cho and his team targeted the tissue-specific gene expression programs identified in their computational analysis. These are the blueprints for the proteins that eventually help immature cells differentiate into tissue-specific cell types, such as colon cells. When a person has a genetic mutation, or has exposure to certain environmental factors, this process can go awry, leading to an overexpression of unhelpful proteins, such as SEDTB1.
The researchers specifically reduced the amount of SEDTB1 in these tissue-specific gene expression programs, which allowed the cells to mature and fully differentiate into colon cells.
“Our experiment also shows that SETDB1 depletion combined with cytotoxic drugs might be potentially beneficial to anticancer treatment,” Cho said. Cytotoxic drugs are often used for cancer treatment because the type of medicine contains chemicals that are toxic to cancer cells which can prevent them from replicating or growing. He noted that this combination could be more effective in treating cancer by transforming the cancer cell state into a less malignant or resistant state. He eventually pursues a cancer reversion therapy alone instead of conventional cytotoxic drug therapy since the cancer reversion therapy can provide a much less painful experience for patients with cancer who often have severe side effects from treatments intended to kill off cancerous cells, such as chemotherapy.
The researchers plan to continue studying how to return cancer cells to healthier states, with the ultimate goal of translating their work to therapeutic treatment for patients with colorectal cancer.
“I think our study of cancer reversion would eventually change the current medical practice of treating cancer toward the direction of keeping the patient’s quality of life while minimizing the side effects of current anti-cancer therapies,” Cho said.
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This work was funded by KAIST and the National Research Foundation of Korea grants funded by the Korean government, the Ministry of Science and Information and Communication Technology.
Other authors include Soobeom Lee, Chae Young Hwang and Dongsan Kim, all of whom are affiliated with the Laboratory for Systems Biology and Bio-Inspired Engineering in the Department of Bio and Brain Engineering at KAIST; Chansu Lee and Sung Noh Hong, both with the Department of Medicine, and Seok-Hyung Kim of the Department of Pathology in the Samsung Medical Center at the Sungkyunkwan University School of Medicine.
-Profile
Professor Kwang-Hyun Cho
ckh@kaist.ac.kr
http://sbie.kaist.ac.kr/
Department of Bio and Brain Engineering
KAIST
https://www.kaist.ac.kr
2020.01.31 View 5858 -
New Insights into How the Human Brain Solves Complex Decision-Making Problems
A new study on meta reinforcement learning algorithms helps us understand how the human brain learns to adapt to complexity and uncertainty when learning and making decisions. A research team, led by Professor Sang Wan Lee at KAIST jointly with John O’Doherty at Caltech, succeeded in discovering both a computational and neural mechanism for human meta reinforcement learning, opening up the possibility of porting key elements of human intelligence into artificial intelligence algorithms. This study provides a glimpse into how it might ultimately use computational models to reverse engineer human reinforcement learning.
This work was published on Dec 16, 2019 in the journal Nature Communications. The title of the paper is “Task complexity interacts with state-space uncertainty in the arbitration between model-based and model-free learning.”
Human reinforcement learning is an inherently complex and dynamic process, involving goal setting, strategy choice, action selection, strategy modification, cognitive resource allocation etc. This a very challenging problem for humans to solve owing to the rapidly changing and multifaced environment in which humans have to operate. To make matters worse, humans often need to often rapidly make important decisions even before getting the opportunity to collect a lot of information, unlike the case when using deep learning methods to model learning and decision-making in artificial intelligence applications.
In order to solve this problem, the research team used a technique called 'reinforcement learning theory-based experiment design' to optimize the three variables of the two-stage Markov decision task - goal, task complexity, and task uncertainty. This experimental design technique allowed the team not only to control confounding factors, but also to create a situation similar to that which occurs in actual human problem solving.
Secondly, the team used a technique called ‘model-based neuroimaging analysis.’ Based on the acquired behavior and fMRI data, more than 100 different types of meta reinforcement learning algorithms were pitted against each other to find a computational model that can explain both behavioral and neural data. Thirdly, for the sake of a more rigorous verification, the team applied an analytical method called ‘parameter recovery analysis,’ which involves high-precision behavioral profiling of both human subjects and computational models.
In this way, the team was able to accurately identify a computational model of meta reinforcement learning, ensuring not only that the model’s apparent behavior is similar to that of humans, but also that the model solves the problem in the same way as humans do.
The team found that people tended to increase planning-based reinforcement learning (called model-based control), in response to increasing task complexity. However, they resorted to a simpler, more resource efficient strategy called model-free control, when both uncertainty and task complexity were high. This suggests that both the task uncertainty and the task complexity interact during the meta control of reinforcement learning. Computational fMRI analyses revealed that task complexity interacts with neural representations of the reliability of the learning strategies in the inferior prefrontal cortex.
These findings significantly advance understanding of the nature of the computations being implemented in the inferior prefrontal cortex during meta reinforcement learning as well as providing insight into the more general question of how the brain resolves uncertainty and complexity in a dynamically changing environment. Identifying the key computational variables that drive prefrontal meta reinforcement learning, can also inform understanding of how this process might be vulnerable to break down in certain psychiatric disorders such as depression and OCD. Furthermore, gaining a computational understanding of how this process can sometimes lead to increased model-free control, can provide insights into how under some situations task performance might break down under conditions of high cognitive load.
Professor Lee said, “This study will be of enormous interest to researchers in both the artificial intelligence and human/computer interaction fields since this holds significant potential for applying core insights gleaned into how human intelligence works with AI algorithms.”
This work was funded by the National Institute on Drug Abuse, the National Research Foundation of Korea, the Ministry of Science and ICT, Samsung Research Funding Center of Samsung Electronics.
Figure 1 (modified from the figures of the original paper doi:10.1038/s41467-019-13632-1). Computations implemented in the inferior prefrontal cortex during meta reinforcement learning. (A) Computational model of human prefrontal meta reinforcement learning (left) and the brain areas whose neural activity patterns are explained by the latent variables of the model. (B) Examples of behavioral profiles. Shown on the left is choice bias for different goal types and on the right is choice optimality for task complexity and uncertainty. (C) Parameter recoverability analysis. Compared are the effect of task uncertainty (left) and task complexity (right) on choice optimality.
-Profile
Professor Sang Wan Lee
sangwan@kaist.ac.kr
Department of Bio and Brain Engineering
Director, KAIST Center for Neuroscience-inspired AI
KAIST Institute for Artificial Intelligence (http://aibrain.kaist.ac.kr)
KAIST Institute for Health, Science, and Technology
KAIST (https://www.kaist.ac.kr)
2020.01.31 View 5252 -
New IEEE Fellow, Professor Jong Chul Ye
Professor Jong Chul Ye from the Department of Bio and Brain Engineering was named a new fellow of the Institute of Electrical and Electronics Engineers (IEEE). IEEE announced this on December 1 in recognition of Professor Ye’s contributions to the development of signal processing and artificial intelligence (AI) technology in the field of biomedical imaging.
As the world’s largest society in the electrical and electronics field, IEEE names the top 0.1% of their members as fellows based on their research achievements.Professor Ye has published more than 100 research papers in world-leading journals in the biomedical imaging field, including those affiliated with IEEE.
He also gave a keynote talk at the yearly conference of the International Society for Magnetic Resonance Imaging (ISMRM) on medical AI technology. In addition, Professor Ye has been appointed to serve as the next chair of the Computational Imaging Technical Committee of the IEEE Signal Processing Society, and the chair of the IEEE Symposium on Biomedical Imaging (ISBI) 2020 to be held in April in Iowa, USA.
Professor Ye said, “The importance of AI technology is developing in the biomedical imaging field. I feel proud that my contributions have been internationally recognized and allowed me to be named an IEEE fellow.”
2019.12.18 View 7860 -
Professor Je-Kyun Park, Awarded by The Korean BioChip Society
On November 9, Je-Kyun Park from the Department of Bio and Brain Engineering at KAIST received an award from the 2017 Fall Meeting of The Korean BioChip Society held in Paradise Hotel Busan, Korea. This year’s meeting recognized Professor Park for developing lab-on-a-chip and microfluidic analytical technologies.
The Korean BioChip Society is a corporation of biochip professional established in 2006 for the development of biochip technology. Every year, the Society selects a recipient based on the nominees’ academic achievements and contributions to bio-fusion industry.
Professor Park served on the international editorial boards of renowned international journals in related fields, including Biosensors and Bioelectronics and Lab on a Chip. He was also the Committee Chairman of MicroTas in 2015.
2017.11.22 View 6794 -
Dr. Hyundoo Hwang Receives a Tenured Position at Monterrey Institute of Technology and Higher Education
Hyundoo Hwang, a former graduate student in the Department of Bio & Brain Engineering at KAIST, has been granted a tenured position at the Monterrey Institute of Technology and Higher Education (ITSEM), Mexico.
Dr. Hwang received his bachelor’s, master’s, and doctoral degree at KAIST and started his professorship at Ulsan National Institute of Science & Technology (UNIST) in Korea. He continued his research in the United States as a professor at Georgia Institute of Technology. He has been acknowledged for the development of an advanced nanotechnology for the diagnosis of rare diseases and research in cell signals. He is one of the leading researchers in an international research project in microelectromechanical systems (MEMS) with participation by researchers from over ten countries. He has been active in commercializing biosensor technology in the U.S. and Mexico.
Since its establishment in 1943, ITSEM has grown to 33 campuses in 25 cities in Mexico. It is the largest university in Latin America with over 90,000 students (47% of its graduate students has oversea research experience). It recruits over 5,000 international students and professors every year.
Dr. Hwang will begin teaching at ITSEM as a professor in the Department of Biomedical Engineering (Ingeniería Biomédica) this fall. He will also conduct research in nano- and micro-technology as a member of Sensors and Devices research group.
Professor Gwang Hyun Cho, head of KAIST's Department of Bio and Brain Engineering said that Dr. Hwang’s tenure professorship at ITSEM demonstrated that the academic program at KAIST—from undergraduate to doctoral—was on par with the international standard. He hoped that more talents from the department would seek academic careers in internationally renowned universities around the world.
2015.08.13 View 5779 -
Professor Kwang-Hyun Cho Recognzied by "Scientist of the Month" Award
Professor Kwang-Hyun Cho of KAIST’s Department of Bio and Brain Engineering received the “Scientist of the Month” award in February 2015 from the Ministry of Science, ICT, and Future Planning of the Republic of Korea and the National Research Foundation of Korea. The award was in recognition of Professor Cho’s contribution to the advanced technique of controlling the death of cancer cells based on systems biology, a convergence research in information technology (IT) and biotechnology.
Professor Cho has published around 140 articles in international journals, including 34 papers in renowned science journals such as Nature, Science, and Cell in the past three years. His work also includes systems biology textbooks and many entries in international academic encyclopaedia.
His field, systems biology, is a new biological research paradigm that identifies and controls the fundamental principles of organisms on a systems level.
A well-known tumour suppressor protein, p53, is known to suppress abnormal cell growth and promote apoptosis of can cells, and thus was a focus of research by many scientists, but its effect has been insignificant and brought many side effects. This was due to the complex function of p53 that controls various positive and negative feedbacks. Therefore, there was a limit to understanding the protein with the existing biological approach.
However, Professor Cho found the kinetic change and function of p53 via a systems biology approach. By applying IT technology to complex biological networks, he also identified the response to stress and the survival and death signal transduction pathways of cardiomyocytes and developed new control methods for cancer cells.
Professor Cho said, “This award served as a momentum to turn over a new leaf.” He added, “I hope convergence research such as my field will bring more innovative ideas on the boundaries of academia.”
2015.02.09 View 11461 -
Newsweek: The Goosebump Sensor That Knows How You Feel
Newsweek covered the introduction of the goosebump sensor invented by Professor Young-Ho Cho of the Department of Bio and Brain Engineering at KAIST in an article dated July 27, 2014.
The article entitled “The Goosebump Sensor That Knows How You Feel” explains how the sensor works and reports on the current research and development trends in emotion-sensing technology.
Professor Cho’s research paper was originally published in the journal Applied Physics Letters on June 24, 2014, titled “A Flexible Skin Piloerection Monitoring Sensor."
Newsweek, July 27, 2014
“The Goosebump Sensor That Knows How You Feel”
http://www.newsweek.com/goosebump-sensor-knows-how-you-feel-260689
2014.07.28 View 7681 -
Hidden Mechanism for the Suppression of Colon Cancer Identified
Published in Cell Reports : cells at the risk of causing colorectal cancer due to genetic mutation are discharged outside the colon tissue
Korean researchers have successfully identified the cancer inhibitory mechanism of the colon tissue. The discovery of the inherent defense mechanism of the colon tissues is expected to provide understanding of the cause of colorectal cancer.
The research was led by Kwang-Hyun Cho, a professor of Bio and Brain Engineering at KAIST (corresponding author) and participated by Dr. Jehun Song (the first author), as well as Dr. Owen Sansom, David Huels, and Rachel Ridgway from the Beatson Institute for Cancer Research in the UK and Dr. Walter Kolch from Conway Institute in Ireland.
The research was funded by the Ministry of Science, ICT and Future Planning and the National Research Foundation of Korea, and its results were published in the 28th March online edition of Cell Reports under the title of “The APC network regulates the removal of mutated cells from colonic crypts.”
The organism can repair damaged tissues by itself, but genetic mutations, which may cause cancer, can occur in the process of cell division s for the repair. The rapid cell division s and toxic substances from the digestive process cause a problem especially in colon crypt that has a high probability for genetic mutation.
The research team was able to find out that the colon tissues prevent cancer by rapidly discharging carcinogenic cells with genetic mutations from the colon crypt durin ga frequent tissue repair process.
This defense mechanism, which inhibits abnormal cell division s by reducing the time mutated cells reside in the crypt, is inherent in the colon.
Extensive mathematical simulation results show that the mutated cells with enhanced Wnt signaling acquire increased adhesion in comparison to the normal cells, which therefore move rapidly toward the upper part of the crypt and are discharged more easily.
If beta-catenine, the key factor in Wnt signal transduction pathway, is not degraded due to genetic mutation, the accumulated beta-catenine activates cell proliferation and increases cell adhesion. The special environment of crypt tissue and the tendency of the cells with similar adhesion to aggregate will therefore discharge the mutated cell, hence maintaining the tissue homeostasis.
In vivo experiment with a mouse model confirms the simulation results that, in the case of abnormal crypt, the cells with high proliferation in fact move slower.
Professor Cho said, “This research has identified that multicellular organism is exquisitely designed to maintain the tissue homeostasis despite abnormal cell mutation. This also proves the systems biology research, which is a convergence of information technology and bio-technology , can discover hidden mechanisms behind complex biological phenomena.”
Crypt: Epithelium, consisting of approximately 2,000 cells, forms a colon surface in the shape of a cave.
Wnt Signaling: A signal transduction pathway involved in the proliferation and differentiation of cells that are particularly important for the embryonic development and management of adult tissue homeostasis.
2014.04.17 View 11217 -
A research paper by Professor Myung-Chul Choi reviewed in Science (February 28, 2014)
A research paper entitled “Transformation of taxol-stabilized microtubules into inverted tubulin tubules triggered by a tubulin conformation switch” was published in
Nature Materials
this year, dated January 19, 2014.
Professor Myung-Chul Choi and Dr. Chae-Yeon Song from the Department of Bio and Brain Engineering at KAIST co-authored the paper together with researchers from the University of California in Santa Barbara and the Hebrew University of Jerusalem.
Science,
dated February 28, 2014, has recently reviewed the paper in its section called "Perspectives."
2014.03.13 View 8193 -
Professor Yoon-Key Nam Received the 2013 Emerging Scholars Award
Professor Yoon-Key Nam, the Department of Bio and Brain Engineering at KAIST, received the 2013 Emerging Scholars Award from the Korean BioChip Society (KBCS), an organization consisted of professionals and researchers in the biochip field such as proteomics, functional genomics, Bio-MEMS, nanotechnology, biosensors, and bioinformatics, at the fall annual conference of KBCS held on November 13th, 2013 at Kangwon National University in Korea.
Professor Nam was recognized for his development of neuron-on-a-chip technology through the convergence research of neuroscience and biochip.
Since 2008, the KBCS has been giving an award to one or two scholars under 40 years of age who have made a great stride in biochip research.
2014.01.27 View 7420