Young Researchers Event 2019

Jan Bjaalie, M.D., Ph.D., is professor at the Institute of Basic Medical Sciences, University of Oslo, and Infrastructure Operations Director and leader of the Neuroinformatics Platform of the EU Human Brain Project. He was founding Executive Director of the International Neuroinformatics Coordinating Facility (INCF) and is currently head of the INCF Norwegian Node and member of the INCF Council for Training, Science, and Infrastructure. His research group has studied wiring patterns of the brain and developed data systems for organizing and managing heterogeneous neuroscience research data by use of a new generation of digital brain atlases. The group develops software and workflows for analysis of data integrated in the atlases. Jan Bjaalie is Chief editor of Frontiers in Neuroinformatics and Section editor of Brain Structure and Function.

Lecture title: EBRAINS - towards a European research infrastructure

No abstract provided.

Simisola Akintoye is the Interim Data Protection Officer for the European Union Future and Emerging Technologies Human Brain Project. She is an international privacy practitioner, data protection consultant and law lecturer at De Montfort University Institute of Evidence-based Law Reform where she is the convenor of Privacy, Ethics and Responsibility.

Her work involves continuous, up-to-date collaborative research in privacy and data protection. As a legal expert, she regularly sits on panels involved in critical dialogues on balancing the competing interests of privacy and innovation at national and international levels. She holds a Phd in Law – Corporate Governance and Regulation in Emerging Economies (Sheffield), LLM International Commercial Law (Dundee), LLM Business Law and Taxation (France), Certified Data Protection Practitioner (PC.dp) on European Union General Data protection Regulation (EU GDPR) from Privacy and Data Protection (PdP) London.

Lecture title: Ethics in neuroscience research

No abstract provided.

Katrin Amunts did a postdoctoral fellowship at the C. & O. Vogt Institute of Brain Research at Düsseldorf University, Germany. In 1999, she set up a new research unit for Brain Mapping at the Research Center Juelich, Germany. In 2004, she became professor for Structural-Functional Brain Mapping, and in 2008 a full professor at the Department of Psychiatry, Psychotherapy and Psychosomatics at the RWTH Aachen University as well as director of the Institute of Neuroscience and Medicine (INM-1) at Research Center Juelich. Since 2013, she is a full professor for Brain Research, director of the C. and O. Vogt Institute of Brain Research, Heinrich-Heine University Düsseldorf and director of the Institute of Neuroscience and Medicine (INM-1), Research Center Juelich.

Katrin Amunts is a member of the editorial board of Brain Structure and Function. She is a member of the German Ethics Council since 2012, and has been elected vice chair in 2016. Katrin Amunts is the programme speaker of the programme Decoding the Human Brain of the Helmholtz Association, Germany. She is leading Subproject 2 Human Brain Organisation of the European Flagship Project The Human Brain Project (HBP). In 2016, she has been elected Scientific Research Director and Chair of the Science and Infrastructure Board (SIB) of the HBP. Since 2017 Katrin Amunts is co-speaker of the graduate school Max-Planck School of Cognition and since 2018 she is a member of the International Advisory Council Healthy Brains for Healthy Lives, Canada.

In order to better understand the organisational principles of the human brain, she and her team aim to develop a multi-level and multi-scale brain atlas, and use methods of high-performance computing to generate ultra-high resolution human brain models.

Lecture title: Welcome and introduction to the European Human Brain Project

The human brain has a multi-level organisation and high complexity. New approaches are necessary to decode the brain with its 86 billion nerve cells, which form complex networks. Ultra-high resolution models and simulation pose massive challenges in terms of data processing, visualisation and analysis. For example, high-resolution data obtained in post-mortem brains supplement information about structural and functional connectivity as obtained by Magnetic Resonance Imaging, which can be acquired from the living human brain, with a spatial resolution in the millimetre range. 3D Polarized Light Imaging elucidates the connectional architecture of the brain at the level of axons at the micrometre range, while keeping the topography of the whole organ; it results in data sets of several petabytes per brain, which should be actively accessible while minimizing their transport. By bringing together different aspects of connectivity in one and the same atlas, it is feasible to combine the advantages of the different approaches, and to address the different spatial (and temporal) scales.

The Human Brain Project is developing a multimodal human brain atlas, which integrates the information of brain organisation from multiple levels including cellular architecture, connectivity, molecular and genetic maps, and results from neuroimaging studies of the brain from healthy subjects and patients. Empirical research is supplemented by modelling and simulation, resulting in new data that is stimulating new experiments.

The Human Brain Project [1, 2] creates a cutting-edge European infrastructure to enable cloud-based collaboration among researchers coming from different disciplines around the world, to create development platforms with databases, workflow systems, petabyte storage, and supercomputers opening new perspective to decode the human brain.

References

[1] K. Amunts, A. Knoll, T. Lippert, C.M. Pennartz, P. Ryvlin, A. Destexhe, V.K. Jirsa, E. D’Angelo, J.G. Bjaalie, The Human Brain Project – synergy between neuroscience, computing, informatics and brain inspired technologies, PLoS Biol, in press (2019).

[2] A. Salles, J.G. Bjaalie, K. Evers, M. Farisco, B.T. Fothergill, M. Guerrero, H. Maslen, J. Muller, T. Prescott, B.C. Stahl, H. Walter, K. Zilles, K. Amunts, The Human Brain Project: Responsible brain research for the benefit of society, Neuron, 101 (2019) 380-384.

Karin Grasenick graduated in Computer Science and Biomedical Engineering. Her thesis on innovative non-invasive techniques to measure stroke volume led to a growing interest in inter- and transdisciplinary research, diversity in research content and equal opportunities in science. She lectures, coaches and supports teams, universities and international projects in diversity and change management. In HBP, she actively supports the recognition of diversity as a success factor for research and innovation. Together with her team she provides tools and techniques for researchers accordingly. 

Lecture title: Hands-on career development: Insights into supportive measures of the HBP

Keynote Speakers will give insights on  success factors and challenges for scientific careers and answer questions of participants. General rules and differences will be explored in the context of equal opportunities in the global scientific community. Specific focus will be set on HBP best practices and measures to support career development regardless of gender and further diversity traits.

Aleksandar Maliković

is a Full Professor of Anatomy at the Faculty of Medicine at the University of Belgrade and his research focus is on the brain mapping and the architectonics of human visual cortex. He is a doctor of medicine (M.D.), Master of Medical Science (M.Sc.) and Doctor of Science (D.Sc. or Ph.D.). Aleksandar was awarded fellowship of the European Federation for Experimental Morphology (1996) and Heinrich Heine University (1997), C. and O. Vogt Institute of Brain Research, Dϋsseldorf, Germany. He spent 2 years as Visiting Fellow at C. and O. Vogt Institute of Brain Research, Heinrich Heine University, Dϋsseldorf, Germany under the supervision of Prof. Karl Zilles who had a strong influence on him and who created many opportunities for him. Also, he spent 2 years working as Visiting Scientist at the Research Centre Jϋlich, Institute of Neuroscience and Medicine (INM-1) - Structural and Functional Organization of the Brain where he collaborated with Prof. Katrin Amunts. Aleksandar is leading a project Structure and function of the Visual System (Ministry of Education, Science and Technological Development, Serbia) and he was a collaborator in the following projects: Human Brain Model (Helmholtz Gemeinschaft, Germany), Grant 01GO0204 (Brain Imaging Center West, Bundesministerium für Bildung und Forschung, Germany), Human Brain Project/Neuroinformatics (National Institute of Biomedical Imaging and Bioengineering, National Institute of Neurological Disorders and Stroke and National Institute of Mental Health, USA) and Morphological Investigations of the Brain (Ministry of Education, Science and Technological Development, Serbia). He is a member of Serbian Anatomical Society, Serbian Neuroscience Society, Federation of European Neuroscience Societies, European Federation for Experimental Morphology (board member) and Anatomische Gesellschaft. Aleksandar is the author or co-author of approximately 50 peer-reviewed articles, 3 monographs, 9 textbooks and 11 anatomical atlases.

Lecture title: The visual cortex: When structure meets function

Considerable technological progress in noninvasive functional investigations of the human visual cortex enabled the discovery of new visual areas and their further precise functional mapping. Since the beginning of the 1990s, the use of functional magnetic resonance imaging (fMRI) and positron emission tomography (PET) enabled the functional mapping of 13 occipital visual areas: V1, V2, V3 (V3d/V3v), V3A, V4, VО1, V5, hMST, V6, V7, LO1, LO2. This significant scientific progress in the functional mapping of the human visual cortex was not followed by the corresponding architectonic investigations so it was not possible to establish anatomical correlates of these new functionally defined visual areas. During the past two decades, our enthusiastic and dedicated group performed cytoarchitectonic mapping of 11 occipital areas (hOc1, hOc2, hOc3v, hOc4v, hOc3d, hOc4d, hOc4la, hOc4lp, hOc5, FG1 and FG2) which are visual in their function. Continuous probabilistic maps of these cytoarchitectonic areas have been generated to characterise their location, extent, size and variability. These maps are easily available to the whole scientific community (JuBrain, Human Brain Project) and their verification is ongoing. Convergent evidence from a standpoint of location, topography, size, functional properties and connectivity suggests that these cytoarchitectonic areas are the anatomical correlates of the functionally defined visual areas.

No bio and pic provided. 

Lecture title: Hands-on session II: Simulation in neuroscience

No abstract provided. 

Vladimir S. Kostić, Professor of Neurology at the Medical School of Belgrade, has focused his scientific interest in degenerative disorders of the central nervous system, mainly etiopathogenesis and treatment. In the course of his training and subsequent academic carrier he worked apprx. 3 years in the Neurological Institute of the Columbia Univesity (New York; USA). He is the author of 7 textbooks and editor of 12 monographs. He is also the author or co-author of >300 peer-reviewed papers. He is heading several scientific projects mainly devoted to the genetic background of neurodegenerative disorders. He is the member of the Serbian Academy of Science and Arts and Honorary President of the Serbian Neurological Society.

Lecture title: Cognition and motion: Space to be fulfilled

In several studies, including one recruiting 28,808 community-dwelling adults, it has been shown an association between poor cognitive function and reduced mobility (gait, balance and chair stands). Such interdependence between mobility and cognition has been suggested to reflect age-dependent changes in shared neural mechanisms and an increased demand for cognitive monitoring in motor control with age. Indeed,  safe and independent negotiation of complex environments requires integration of external sensory information with neural networks involving cortical, subcortical, brainstem, and spinal cord structures (some of these share common substrates with cognition). A substantial corpus of evidence suggests that the cognitive involvement in postural control and gait increases with aging. A large portion of such studies were based on dual-task experimental designs, which typically use the simultaneous performance of a motor task (e.g., static or dynamic balancing, walking) and a continuous cognitive task (e.g., mental arithmetic, tone detection). Resolution of similar interferences requires executive functions, which schedule processing order of the tasks, interrupt or reinstale task processing, and switch between the processing streams of the tasks. Even in cognitively normal, older adults, there is a robust association of gait speed and gait variability with executive function, attention, and (to a lesser extent) memory and visuospatial function. These associations are more emphatic under dual-task conditions. Moreover, gait impairment precedes and predicts cognitive decline and may be a more sensitive marker of cognitive decline than cognitive tests.

We have examined this association in patients with Parkinsonʼs disease (PD) using gait and freezing of gait (FoG) as models. In PD patients during the mental dual-task we observed furher deterioration in gait parameters which reflect gait automaticity (eg. an increase in stride variability and gait asymmetry, in parallel with decrease in gait rhythmicity). In PD patients with FoG we conducted multimodal MRI investigations and found (a) functional decoupling between coordinated motor and cognitive neural networks (“interference model” of FoG) and (b) altered functional connectivity not only in the locomotor but also in “cognitive” circuits such as the attention-related frontoparietal and visual occipito-temporal networks („network-wide dysfunction“).

Camilla Hagen Blixhavn is a researcher at the University of Oslo and team coordinator for atlas integration of rodent brain research data in the Human Brain Project. She couples her experience from organisational and creative leadership positions together with her studies in psychology, biology, didactics and neuroscience, and continues to strategise towards the needs of researchers in science and health. Camilla is MSc in neuroscience and is preparing for an interdisciplinary PhD in neuroscience data management.

Lecture title: Hands-on session I: Open Science: How to

Open Science is a continuation of practices which began centuries ago with the advent of academic journal publications. The most recent developments in Open Science is Open Data, recently made possible by new technological capabilities to store large amounts of data, and to access and work on the data online. Leading journals are already now requiring posting of research data in public repositories, to complement the traditional journal article containing the interpretations of the data. Several general data repositories for sharing of research data are available – however, many lack the necessary stewardship and standards for making the research data easy to Find, Access, Interpret, and Re-use, in accordance with the FAIR principles (Wilkinson et al., Scientific Data 3:160018, 2016). To address these challenges, the Human Brain Project is developing a new research infrastructure, the EBRAINS FAIR data service, providing tools, workflows and data curation services tailored for integration and sharing of heterogeneous, multimodal neuroscience data and computational models. Three-dimensional open-access brain reference atlases provide the anatomical context for all data shared via the EBRAINS infrastructure, easing comparison and interpretation of findings.

Formerly involved in the music industry, David Kunzmann decided to change paths in 2013 and study Computer Science. After gaining experience in diverse startups, he joined the HBP Knowledge Graph team at the end of 2017 as a full stack developer.

Lecture title: Introduction to the HBP Knowledge Graph

Open science is all about making the scientific data that is produced findable, accessible, interoperable and re-usable by others. Discover how the Human Brain Project annotates its heterogeneous research data with metadata in the HBP Knowledge Graph and how this allows you to find and re-use existing high-quality research data and/or share your own.

Jonathan Villemaire-Krajden is a developer who has been with the Human Brain Project since 2018. He works on the Collaboratory tools and infrastructure with a few colleagues in Geneva, Switzerland. He grew up and studied in Canada as a computer scientist and physicist and worked as a developer and devops engineer since 2010. He is interested in science, the outdoors and software design.

Lecture title: Introduction to the HBP Collaboratory 

The Human Brain Project (HBP) Collaboratory is a central directory for tools developed by the HBP Platforms. At the core of the Collaboratory are Collabs. These are spaces designed for collaborative work where users can contribute content, integrate applications and run Jupyter notebooks. Collabs have at least a team, a landing page, and a navigation menu. As a user, you can organise content, which can be text or documents, manage the team members you want to work with and add interactive tools. The Collaboratory is a tool to help with the dissemination of science, collaboration, and project management. In this presentation, I will introduce the project and the vision behind it, show you where to find information,  give a demo of the HBP Collaboratory's features and present how to build a shared workspace for a simple project.

Lyuba Zehl studied Biology (BSc) and Neuroscience (MSc) at the University of Cologne under the supervision of Prof. Ansgar Büschges and Prof. Wolfgang Walkowiak, respectively. During this time of study, she worked on kinematic of insect legs during locomotion (BSc thesis), optimisation of peripheral nerve implantation of multi-electrode arrays in small mammals (internship at Blackrock Microsystems and the Center of Neural Interfaces of the University of Utah, USA), and the anatomical cartography of auditory nuclei in the brain stem of toothed whales using cluster analysis (MSc thesis). For her doctoral studies, she switched to RWTH Aachen University and joint the Statistical Neuroscience Group of Prof. Sonja Grün at the Institute for Neuroscience and Medicine (INM-6) of the Jülich Research Centre. In her thesis, she worked on analysing multi-electrode array recordings of monkey motor cortex and, in particular, on data and metadata management of complex neuroscience experiments. After receiving her doctorate degree (Dr. rer. nat.) in 2017, she started working as a junior scientist half-time under Timo Dickscheid in the Big Data Analytics Group at the INM-1 of the Jülich Research Centre and Molecular and half-time under Prof. Björn Kampa in the Systemic Neurophysiology Group at the Institute of Biology II at RWTH Aachen University. Since May 2019, she has worked full time in the Big Data Analytics Group at the INM-1 for the curation team of the Neuroinformatics Platform of the Human Brain Project (HBP). Having a high interdisciplinary orientation towards computational neuroscience and software development for data and metadata management and a broad experience in various neuroscience laboratories, she now focuses on developing and implementing concepts, standards and tools for neuroscience data and metadata management. With her current work, she strongly supports the integration of heterogeneous neuroscience data into the unified data sharing platform and the interactive atlas viewers of the HBP.

Lecture title: Hands-on session III: The HBP Human Brain Atlas: Integration and visualisation of heterogeneous neuroscience data

As a part of the Neuroinformatics Platform, the Human Brain Project (HBP) is developing a comprehensive multi-level Human Brain Atlas. This novel atlas consists of web-based services that allow users to discover, explore and access a unique selection of anatomical reference spaces and high-quality structural parcellations, down to a microscopic resolution. A diverse range of well curated human brain data at different scales and modalities is linked to this atlas, and can be discovered and downloaded by browsing brain regions. For integrating new data to the atlas, the platform provides support and tools for metadata curation, and spatial anchoring of non-image, 2D and 3D image data to the reference atlases. A rich interactive viewer allows users to display common types of data in anatomical context together with the reference atlas delineations (e.g., JuBrain cytoarchitectonic atlas, BigBrain microscopic model). During the hands-on session, participants learn how the BigBrain reference model can be interactively explored in 3D using the interactive atlas viewer, and how non-image data can be semantically linked to the JuBrain reference atlas, using cortical receptor densities as an example. We will also demonstrate spatial anchoring of 2D and 3D image data to the HBP’s reference atlases.

Kai Kiwitz graduated in Psychology and Cognitive Neuroscience at the Universities of Düsseldorf and Bochum in 2016. Since then, he performs his PhD work at the Cécile and Oskar Vogt Institute of Brain Research at the University of Düsseldorf under the supervision of Prof. Katrin Amunts in close collaboration with the Big Data Analytics Group led by Dr. Timo Dickscheid at the INM-1 of the Jülich Research Centre. In his research, Kai evaluates the use of machine learning solutions aimed at aiding neuroscientists in high-resolution cytoarchitectonic mapping approaches in the BigBrain. He is especially interested in analysing representations of cytoarchitectonic features within Convolutional Neural Networks to validate their use in the generation of a high-resolution anatomical reference framework of the human visual system.  

Lecture title: Hands-on session III: The HBP Human Brain Atlas: Integration and visualisation of heterogeneous neuroscience data

As a part of the Neuroinformatics Platform, the Human Brain Project (HBP) is developing a comprehensive multi-level Human Brain Atlas. This novel atlas consists of web-based services that allow users to discover, explore and access a unique selection of anatomical reference spaces and high-quality structural parcellations, down to a microscopic resolution. A diverse range of well-curated human brain data at different scales and modalities is linked to this atlas, and can be discovered and downloaded by browsing brain regions. For integrating new data to the atlas, the platform provides support and tools for metadata curation, and spatial anchoring of non-image, 2D and 3D image data to the reference atlases. A rich interactive viewer allows users to display common types of data in anatomical context together with the reference atlas delineations (e.g., JuBrain cytoarchitectonic atlas, BigBrain microscopic model). During the hands-on session, participants learn how the BigBrain reference model can be interactively explored in 3D using the interactive atlas viewer, and how non-image data can be semantically linked to the JuBrain reference atlas, using cortical receptor densities as an example. We will also demonstrate spatial anchoring of 2D and 3D image data to the HBP’s reference atlases.