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EPCO-38. TYPE B ULTRA LONG-RANGE interactionS IN PFAS (TULIPS) ARE RECURRENT EPIGENOMIC FEATURES OF PFA EPENDYMOMA

Neuro-Oncology 2022年第SUPPLEMENT_7期24卷 vii124–vii124页

作者： Johnston, Michael Lee, John J Y Hu, Bo Nikolic, Ana Baguette, Audrey Paik, Seungil Chen, Haifen Kumar, Sachin Chen, Carol Jessa, Selin Balin, Polina Fong, Vernon Zwaig, Melissa MichealRaj, Kulandaimanuvel Chen, Xun Zhang, Yanlin Varadharajan, Srinidhi Billon, Pierre Juretic, Nikoleta Daniels, Craig Giannini, Caterina Thompson, Eric Hauser, Peter Kim, Seung-Ki Wang, Kyu-Chang Lee, Ji Yeoun Grajkowska, Wieslawa Agnihotri, Sameer Mack, Stephen C Ellezam, Benjamin Weil, Alex Bourque, Guillaume Chan, Jennifer Lupien, Mathieu Ragoussis, Jiannis Kleinman, Claudia Majewski, Jacek Jabado, Nada Taylor, Michael Blanchette, Mathieu Gallo, Marco Arnie Charbonneau Cancer Institute Cumming School of Medicine University of Calgary Calgary AB Canada Calgary Alberta Canada The Arthur and Sonia Labatt Brain Tumor Research Center The Hospital for Sick Children Toronto Canada Department of Human Genetics McGill University Montreal Canada Quantitative Life Sciences McGill University Montreal Canada The Arthur and Sonia Labatt Brain Tumor Research Center The Hospital for Sick Children Toronto Ontario Canada Department of Anatomy and Cell Biology Kyoto University Kyoto Japan School of Computer Science McGill University Montreal Canada St. Judes Memphis USA Arnie Charbonneau Cancer Institute Cumming School of Medicine University of Calgary Calgary Canada Department of Pediatrics McGill University Montreal Canada Department of Pathology and Laboratory Medicine Mayo Clinic Rochester MN USA Duke University Medical Center DURHAM NC USA Department of Pediatrics Semmelweis University Budapest Hungary Department of Neurosurgery Division of Pediatric Neurosurgery Seoul National University Children’s Hospital Seoul Republic of Korea Department of Pathology The Children’s Memorial Health Institute University of Warsaw Warsaw Poland Department of Neurosurgery University of Pittsburgh Medical Center Pittsburgh USA Department of Pathology Centre Hospitalier Universitaire Sainte-Justine Université de Montréal Montreal Canada Department of Human Genetics McGill University Montreal USA Arnie Charbonneau Cancer Institute Cumming School of Medicine University of Calgary Calgary Alberta Canada Calgary Alberta Canada Princess Margaret Cancer Centre University Health Network Toronto Canada McGill University Montreal Canada The Research Institute of the McGill University Health Center Montréal Canada The Hospital for Sick Children Toronto Canada

Posterior Fossa Group A (PFA) ependymomas are pediatric brain tumors with extremely poor survival outcomes. As protein-coding mutations in PFA are exceedingly rare, the underlying etiology of these tumors remains elusive. Elevated CpG island methylation and depletion of H3K27me3 have been described in PFA, leading to the hypothesis that PFA may be driven by a dysregulated epigenetic state. In this study, we sought to determine how three-dimensional (3D) genome features (such as DNA loops, domains, and compartments) differ between pediatric brain tumors. We performed Hi-C sequencing on a collection of 64 patient specimens and patient-derived primary cultures that collectively span multiple subgroups of ependymoma, medulloblastoma, high-grade glioma, and non-neoplastic brain. For certain samples, we further performed RNA-seq, histone modification ChIP-seq, or whole-genome bisulfite sequencing to allow multiomic data integration. Overall, the 3D genome organization of PFA samples appeared distinct from other tumor types. We identified and defined TULIPs: a subset of type B compartments, separated by genomic distances greater than 10 Mbp, that exhibit a striking fivefold increase in reciprocal interaction strength. These TULIPs recurred at the same genomic positions across the vast majority of PFA samples with minimal representation among other tumor or non-tumor samples. TULIPs displayed enrichment for heterochromatic features such as H3K9me3 and late replication timing and were depleted of euchromatic features such as H3K27ac and protein-coding genes. By using immuno-fluorescence for H3K9me3 and oligo-FISH to label TULIP regions, we demonstrated that TULIP regions are more compact in PFA than other tumors. Finally, by applying inhibitors of H3K9 lysine methylation to PFA cultures we showed that TULIPs become more diffuse and cell viability is reduced. Altogether, this work defines TULIPs as highly recurrent epigenetic features of PFA tumors.

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A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology

arXiv

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arXiv 2018年

作者： Iglesias, Juan Eugenio Insausti, Ricardo Lerma-Usabiaga, Garikoitz Bocchetta, Martina van Leemput, Koen Greve, Douglas N. van der Kouwe, Andre Fischl, Bruce Caballero-Gaudes, César Paz-Alonso, Pedro M. Department of Medical Physics and Biomedical Engineering University College London United Kingdom BCBL. Basque Center on Cognition Brain and Language Spain Human Neuroanatomy Laboratory University of Castilla-La Mancha Spain Dementia Research Centre Department of Neurodegenerative Disease Institute of Neurology University College London United Kingdom Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School United States Department of Applied Mathematics and Computer Science Technical University of Denmark MIT Computer Science and Artificial Intelligence Laboratory United States

The human thalamus is a brain structure that comprises numerous, highly specific nuclei. Since these nuclei are known to have different functions and to be connected to different areas of the cerebral cortex, it is of great interest for the neuroimaging community to study their volume, shape and connectivity in vivo with MRI. In this study, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histological data, as well as the application of the atlas to in vivo MRI segmentation. The atlas was built using manual delineation of 26 thalamic nuclei on the serial histology of 12 whole thalami from six autopsy samples, combined with manual segmentations of the whole thalamus and surrounding structures (caudate, putamen, hippocampus, etc.) made on in vivo brain MR data from 39 subjects. The 3D structure of the histological data and corresponding manual segmentations was recovered using the ex vivo MRI as reference frame, and stacks of blockface photographs acquired during the sectioning as intermediate target. The atlas, which was encoded as an adaptive tetrahedral mesh, shows a good agreement with with previous histological studies of the thalamus in terms of volumes of representative nuclei. When applied to segmentation of in vivo scans using Bayesian inference, the atlas shows excellent test-retest reliability, robustness to changes in input MRI contrast, and ability to detect differential thalamic effects in subjects with Alzheimer’s disease. The probabilistic atlas and companion segmentation tool are publicly available as part of the neuroimaging package FreeSurfer. Copyright © 2018, The Authors. All rights reserved.

关键词： Brain

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Publisher Correction: A vaccine targeting the RBD of the S protein of SARS-CoV-2 induces protective immunity

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Nature 2021年第7844期590卷 E23页

作者： Jingyun Yang Wei Wang Zimin Chen Shuaiyao Lu Fanli Yang Zhenfei Bi Linlin Bao Fei Mo Xue Li Yong Huang Weiqi Hong Yun Yang Yuan Zhao Fei Ye Sheng Lin Wei Deng Hua Chen Hong Lei Ziqi Zhang Min Luo Hong Gao Yue Zheng Yanqiu Gong Xiaohua Jiang Yanfeng Xu Qi Lv Dan Li Manni Wang Fengdi Li Shunyi Wang Guanpeng Wang Pin Yu Yajin Qu Li Yang Hongxin Deng Aiping Tong Jiong Li Zhenling Wang Jinliang Yang Guobo Shen Zhiwei Zhao Yuhua Li Jingwen Luo Hongqi Liu Wenhai Yu Mengli Yang Jingwen Xu Junbin Wang Haiyan Li Haixuan Wang Dexuan Kuang Panpan Lin Zhengtao Hu Wei Guo Wei Cheng Yanlin He Xiangrong Song Chong Chen Zhihong Xue Shaohua Yao Lu Chen Xuelei Ma Siyuan Chen Maling Gou Weijin Huang Youchun Wang Changfa Fan Zhixin Tian Ming Shi Fu-Sheng Wang Lunzhi Dai Min Wu Gen Li Guangyu Wang Yong Peng Zhiyong Qian Canhua Huang Johnson Yiu-Nam Lau Zhenglin Yang Yuquan Wei Xiaobo Cen Xiaozhong Peng Chuan Qin Kang Zhang Guangwen Lu Xiawei Wei Laboratory of Aging Research and Cancer Drug Target State Key Laboratory of Biotherapy and Cancer Center National Clinical Research Center for Geriatrics West China Hospital Sichuan University Chengdu China. National Kunming High-level Biosafety Primate Research Center Institute of Medical Biology Chinese Academy of Medical Sciences and Peking Union Medical College Yunnan China. Key Laboratory of Human Disease Comparative Medicine Chinese Ministry of Health Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases Institute of Laboratory Animal Science Chinese Academy of Medical Sciences and Comparative Medicine Center Peking Union Medical College Beijing China. National Institutes for Food and Drug Control (NIFDC) Beijing China. National Chengdu Center for Safety Evaluation of Drugs State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University Collaborative Innovation Center for Biotherapy Chengdu China. Shanghai Key Laboratory of Chemical Assessment and Sustainability School of Chemical Science & Engineering Tongji University Shanghai China. Treatment and Research Center for Infectious Diseases The Fifth Medical Center of PLA General Hospital National Clinical Research Center for Infectious Diseases Beijing China. Center for Biomedicine and Innovations Faculty of Medicine Macau University of Science and Technology Macau China. Department of Computer Science and Technology Tsinghua University Beijing China. Department of Applied Biology and Chemical Technology Hong Kong Polytechnic University Hong Kong China. Sichuan Provincial Key Laboratory for Human Disease Gene Study and Institute of Laboratory Medicine Sichuan Provincial People's Hospital University of Electronic Science and Technology of China Chengdu China. State Key Laboratory of Medical Molecular Biology Chinese Academy of Medical Sciences School of Basic Medicine Peking Union Medical College Beijing China. Center for Biomedicine and Innovation

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Precise object detection using local feature for robot manipulator

Precise object detection using local feature for robot manip...

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International Conference on Ubiquitous Robots and Ambient Intelligence (URAI)

作者： Jae Min Cho KyeKyung Kim Department of Computer Software Korea University of Science and Technology Daejeon Korea ETRI Human Machine Interaction Research Group Daejeon Korea

It is difficult to apply object recognition technology to manufacturing industry because the intrinsic characteristics of an object is easily influenced by the surrounding environment such as lighting condition, background complexity and object shape. This paper proposes a precise object detection method for assembling components by more stable feature extraction. To accomplish it, two images are captured by fine-tuning exposure time for the purpose of complementation of features. Adaptive binarization and differential of Gaussian methods are applied to extracting edge information from each image. In the next step, primary features such as contour lines are extracted from the object using the Fast Hough Transform and candidate lines are selected to become geometric conditions of the object. The precise object region is detected by shape analysis using the four vertices computed by the candidate lines. In addition, the internal features of the object are employed to increase the precision of object detection. As a result, the proposed method improved the accuracy of object detection so that it can be useful in the visual servoing using the robot manipulator.

关键词： Feature extraction Object detection Shape Image edge detection Manipulators Lighting

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Megacity: A collaborative virtual reality environment for emergency response, training, and decision making

Megacity: A collaborative virtual reality environment for em...

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Visualization and Data Analysis 2017, VDA 2017

作者： Sharma, Sharad Devreaux, Phillip Scribner, David Grynovicki, Jock Grazaitis, Peter Department of Computer Science Bowie State University BowieMD20715 United States Army Research Laboratory Human Research and Engineering Direct. Aberdeen Proving GroundMD21005 United States

The simulation of human behavior with avatars and agents in virtual reality (VR) has led to an explosion of training and educational research. The use of avatars (user-controlled characters) or agents (computer-controlled characters) may influence the engagements of the user experience for emergency response, and training in emergency scenarios. Our proposed collaborative VR megacity environment offers flexibility to run multiple scenarios and evacuation drills for disaster preparedness and response. Modeling such an environment is very important because in the real-time emergencies we experience in day-to-day life, there is a need for preparation to extreme events. These emergencies could be the result of fire, smoke, gunman threat, or a bomb blast in a city block. The collaborative virtual environment (CVE) can act as a platform for training and decision making for SWAT teams, fire responders, and traffic clearance personnel. The novelty of our work lies in modeling behaviors (hostile, non-hostile, selfish, leader-following) for computer-controlled agents so that they can interact with user-controlled agents in a CVE. We have used game creation as a metaphor for creating an experimental setup to study human behavior in a megacity for emergency response, decision-making strategies, and what-if scenarios. Our proposed collaborative VR environment includes both immersive and non-immersive environments. The participant can enter the CVE setup on the cloud and participate in the emergency evacuation drill, which leads to considerable cost advantages over large-scale, real-life exercises. We present two ways for controlling crowd behavior. The first defines rules for agents, and the second provides controls to the users as avatars to navigate in the VR environment as autonomous agents. Our contribution lies in our approach to combine these two approaches of behavior to perform virtual drills for emergency response and decision making. © 2017, Society for Imaging science

关键词： Decision making

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How to be Helpful? Supportive Behaviors and Personalization for human-Robot Collaboration

arXiv

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arXiv 2017年

作者： Mangin, Olivier Roncone, Alessandro Scassellati, Brian Social Robotics Lab Computer Science Department Yale University New HavenCT United States Human Interaction and Robotics Group Computer Science Department University of Colorado Boulder BoulderCO United States

The field of human-Robot Collaboration (HRC) has seen a considerable amount of progress in recent years. Thanks in part to advances in control and perception algorithms, robots have started to work in increasingly unstructured environments, where they operate side by side with humans to achieve shared tasks. However, little progress has been made toward the development of systems that are truly effective in supporting the human, proactive in their collaboration, and that can autonomously take care of part of the task. In this work, we present a collaborative system capable of assisting a human worker despite limited manipulation capabilities, incomplete model of the task, and partial observability of the environment. Our framework leverages information from a high-level, hierarchical model that is shared between the human and robot and that enables transparent synchronization between the peers and mutual understanding of each other’s plan. More precisely, we firstly derive a partially observable Markov model from the high-level task representation;we then use an online Monte-Carlo solver to compute a short-horizon robot-executable plan. The resulting policy is capable of interactive replanning on-the-fly, dynamic error recovery, and identification of hidden user preferences. We demonstrate that the system is capable of robustly providing support to the human in a realistic furniture construction task. Copyright © 2017, The Authors. All rights reserved.

关键词： Markov processes

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The most efficient sequence of study depends on the type of test 39

The most efficient sequence of study depends on the type of ...

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39th Annual Meeting of the Cognitive science Society: Computational Foundations of Cognition, CogSci 2017

作者： Carvalho, Paulo F. Goldstone, Robert L. Human-Computer Interaction Institute Carnegie Mellon University 5000 Forbes Ave PittsburghPA15213 United States Department of Psychological and Brain Sciences Cognitive Science Program Indiana University 1100 E. 10th St. BloomingtonIN47405 United States

ISBN: (纸本)9780991196760

Previous research has shown that the sequence in which concepts are studied changes how well they are learned. In a series of experiments featuring naturalistic concepts (psychology concepts) and naïve learners, we extend previous research by showing that the sequence of study changes the representation the learner creates of the study materials. Interleaved study leads to the creation of relatively interrelated concepts that are represented by contrast to each other and based on discriminating properties. Blocked study, instead, leads to the creation of relatively isolated concepts that are represented in terms of their central and characteristic properties. The relative benefits of these representations depend on whether the test of conceptual knowledge requires contrastive or characteristic information. These results argue for the integrated investigation of the benefits of different sequences of study as depending on the characteristics of the study and testing situation as a whole. © CogSci 2017.

关键词： interleaving interrelated concepts study sequence

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Soft printing with fabric

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XRDS: Crossroads 2016年第3期22卷 50-53页

作者： Peng, Huaishu Hudson, Scott Mankoff, Jennifer McCann, James Information Science Department Cornell University United States Human-Computer Interaction Institute United States The School of Computer Science Carnegie Mellon University United States Human Computer Interaction Institute Carnegie Mellon University United States Carnegie Mellon University United States

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Mapping geographical inequalities in childhood diarrhoeal morbidity and mortality in low-income and middle-income countries, 2000-17: analysis for the Global Burden of Disease Study 2017 (vol 395, pg 1779, 2020)

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LANCET 2020年第10239期395卷 1762-1762页

作者： Reiner, R. C., Jr. Hay, S., I Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Global Health School of Medicine University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States College of Health and Medical Sciences Haramaya University Harar Ethiopia Department of Epidemiology and Biostatistics Haramaya University Harar Ethiopia Department of Medical Laboratory Sciences Haramaya University Harar Ethiopia School of Nursing and Midwifery Haramaya University Harar Ethiopia School of Pharmacy Haramaya University Harar Ethiopia School of Public Health Haramaya University Harar Ethiopia Haramaya University Harar Ethiopia Advanced Diagnostic and Interventional Radiology Research Center Tehran University of Medical Sciences Tehran Iran Cancer Biology Research Center Tehran University of Medical Sciences Tehran Iran Cancer Research Institute Tehran University of Medical Sciences Tehran Iran Department of Economics and Management Sciences for Health Tehran University of Medical Sciences Tehran Iran Department of Environmental Health Engineering Tehran University of Medical Sciences Tehran Iran Department of Epidemiology and Biostatistics Tehran University of Medical Sciences Tehran Iran Department of Health Management and Economics Tehran University of Medical Sciences Tehran Iran Department of Microbiology Tehran University of Medical Sciences Tehran Iran Department of Pharmacology Tehran University of Medical Sciences Tehran Iran Digestive Diseases Research Institute Tehran University of Medical Sciences Tehran Iran Endocrinology and Metabolism Research Center Tehran University of Medical Sciences Tehran Iran Hematology-Oncology and Stem Cell Transplantation Research Center Tehran University of Medical Sciences Tehran Iran Iran National Institute of Health Research Tehran University of Medical Sciences Tehran Iran Metabolomics and

Summary Background Across low-income and middle-income countries (LMICs), one in ten deaths in children younger than 5 years is attributable to diarrhoea. The substantial between-country variation in both diarrhoea incidence and mortality is attributable to interventions that protect children, prevent infection, and treat disease. Identifying subnational regions with the highest burden and mapping associated risk factors can aid in reducing preventable childhood *** We used Bayesian model-based geostatistics and a geolocated dataset comprising 15 072 746 children younger than 5 years from 466 surveys in 94 LMICs, in combination with findings of the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017, to estimate posterior distributions of diarrhoea prevalence, incidence, and mortality from 2000 to 2017. From these data, we estimated the burden of diarrhoea at varying subnational levels (termed units) by spatially aggregating draws, and we investigated the drivers of subnational patterns by creating aggregated risk factor *** The greatest declines in diarrhoeal mortality were seen in south and southeast Asia and South America, where 54·0% (95% uncertainty interval [UI] 38·1-65·8), 17·4% (7·7-28·4), and 59·5% (34·2-86·9) of units, respectively, recorded decreases in deaths from diarrhoea greater than 10%. Although children in much of Africa remain at high risk of death due to diarrhoea, regions with the most deaths were outside Africa, with the highest mortality units located in Pakistan. Indonesia showed the greatest within-country geographical inequality; some regions had mortality rates nearly four times the average country rate. Reductions in mortality were correlated to improvements in water, sanitation, and hygiene (WASH) or reductions in child growth failure (CGF). Similarly, most high-risk areas had poor WASH, high CGF, or low oral rehydration therapy *** By co-analysing geospatial trends in d

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Control strategy for stabilization of the biped trunk-SLIP walking model

Control strategy for stabilization of the biped trunk-SLIP w...

引用

International Conference on Ubiquitous Robots and Ambient Intelligence (URAI)

作者： Minh Nhat Vu Jongwoo Lee Yonghwan Oh Department of Human-Computer Interaction and Robotics University of Science and Technology (UST) Korea Center for Robotics Research Korea Institute of Science and Technology (KIST) Seoul Korea

In this paper, we present a new control strategy for the Bipedal Trunk Spring Loaded Inverted Pendulum (BTSLIP) model, consisting of springy legs and rigid trunk. Our walking controller is inspired from the Virtual Pendulum (VP) concept. In this concept, by intersecting the ground reaction forces (GRF) to a virtual pivot point (VPP), the trunk is provided the restoring moment to keep its balance and to behave like a virtual hanging pendulum. The simple hip torque control was presented with the name the VPP method. However, this approach is not reliable in terms of rejecting disturbances. Thus, we propose a new control strategy to achieve the robustness and stabilize the walking gait. Herein, the control is introduced with the combination of two strategies, 1) updating the position of the VPP by using Discrete Linear Quadratic Regulator controller and 2) controlling the stiffness of springy legs by feedback linearization controller to track both reference vertical position and velocity of the Center of Mass (CoM). We present the dynamic simulation of the BTSLIP model under the presence of external disturbances. The performance of the proposed control strategy shows stable, robust walking which is compared with the VPP method.

关键词： Legged locomotion Hip Force Trajectory Springs Torso Load modeling

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