Families
families
Open source FPGA tools for building research devices
Edmund will present why to use FPGAs when building scientific instruments, when and why to use open source FPGA tools, the history of their development, their development status, currently supported FPGA families and functions, current developments in design languages and tools, the community, freely available design blocks, and possible future developments.
The multi-phase plasticity supporting winner effect
Aggression is an innate behavior across animal species. It is essential for competing for food, defending territory, securing mates, and protecting families and oneself. Since initiating an attack requires no explicit learning, the neural circuit underlying aggression is believed to be genetically and developmentally hardwired. Despite being innate, aggression is highly plastic. It is influenced by a wide variety of experiences, particularly winning and losing previous encounters. Numerous studies have shown that winning leads to an increased tendency to fight while losing leads to flight in future encounters. In the talk, I will present our recent findings regarding the neural mechanisms underlying the behavioral changes caused by winning.
Theories of consciousness: beyond the first/higher-order distinction
Theories of consciousness are commonly grouped into "first-order" and "higher-order" families. As conventional wisdom has it, many more animals are likely to be conscious if a first-order theory is correct. But two recent developments have put pressure on the first/higher-order distinction. One is the argument (from Shea and Frith) that an effective global workspace mechanism must involve a form of metacognition. The second is Lau's "perceptual reality monitoring" (PRM) theory, a member of the "higher-order" family in which conscious sensory content is not re-represented, only tagged with a temporal index and marked as reliable. I argue that the first/higher-order distinction has become so blurred that it is no longer particularly useful. Moreover, the conventional wisdom about animals should not be trusted. It could be, for example, that the distribution of PRM in the animal kingdom is wider than the distribution of global broadcasting.
Design principles of adaptable neural codes
Behavior relies on the ability of sensory systems to infer changing properties of the environment from incoming sensory stimuli. However, the demands that detecting and adjusting to changes in the environment place on a sensory system often differ from the demands associated with performing a specific behavioral task. This necessitates neural coding strategies that can dynamically balance these conflicting needs. I will discuss our ongoing theoretical work to understand how this balance can best be achieved. We connect ideas from efficient coding and Bayesian inference to ask how sensory systems should dynamically allocate limited resources when the goal is to optimally infer changing latent states of the environment, rather than reconstruct incoming stimuli. We use these ideas to explore dynamic tradeoffs between the efficiency and speed of sensory adaptation schemes, and the downstream computations that these schemes might support. Finally, we derive families of codes that balance these competing objectives, and we demonstrate their close match to experimentally-observed neural dynamics during sensory adaptation. These results provide a unifying perspective on adaptive neural dynamics across a range of sensory systems, environments, and sensory tasks.
Retroviruses and retrotransposons interacting with the 3D genome in mouse and human brain
Repeat-rich sequence blocks are considered major determinants for 3D folding and structural genome organization in the cell nucleus in all higher eukaryotes. Here, we discuss how megabase-scale chromatin domain and chromosomal compartment organization in adult mouse cerebral cortex is linked, in highly cell type-specific fashion, to multiple retrotransposon superfamilies which comprise the vast majority of mobile DNA elements in the murine genome. We show that neuronal megadomain architectures include an evolutionarily adaptive heterochromatic organization which, upon perturbation, unleashes proviruses from the Long Terminal Repeat (LTR) Endogenous Retrovirus family that exhibit strong tropism in mature neurons. Furthermore, we mapped, in the human brain, cell type-specific genomic integration patterns of the human pathogen and exogenous retrovirus, HIV, together with changes in genome organization and function of the HIV infected brain. Our work highlights the critical importance of chromosomal conformations and the ‘spatial genome’ for neuron- and glia-specific regulatory mechanisms and defenses aimed at exogenous and endogenous retrotransposons in the brain
Design principles of adaptable neural codes
Behavior relies on the ability of sensory systems to infer changing properties of the environment from incoming sensory stimuli. However, the demands that detecting and adjusting to changes in the environment place on a sensory system often differ from the demands associated with performing a specific behavioral task. This necessitates neural coding strategies that can dynamically balance these conflicting needs. I will discuss our ongoing theoretical work to understand how this balance can best be achieved. We connect ideas from efficient coding and Bayesian inference to ask how sensory systems should dynamically allocate limited resources when the goal is to optimally infer changing latent states of the environment, rather than reconstruct incoming stimuli. We use these ideas to explore dynamic tradeoffs between the efficiency and speed of sensory adaptation schemes, and the downstream computations that these schemes might support. Finally, we derive families of codes that balance these competing objectives, and we demonstrate their close match to experimentally-observed neural dynamics during sensory adaptation. These results provide a unifying perspective on adaptive neural dynamics across a range of sensory systems, environments, and sensory tasks.
Global AND Scale-Free? Spontaneous cortical dynamics between functional networks and cortico-hippocampal communication
Recent advancements in anatomical and functional imaging emphasize the presence of whole-brain networks organized according to functional and connectivity gradients, but how such structure shapes activity propagation and memory processes still lacks asatisfactory model. We analyse the fine-grained spatiotemporal dynamics of spontaneous activity in the entire dorsal cortex. through simultaneous recordings of wide-field voltage sensitive dye transients (VS), cortical ECoG, and hippocampal LFP in anesthetized mice. Both VS and ECoG show cortical avalanches. When measuring avalanches from the VS signal, we find a major deviation of the size scaling from the power-law distribution predicted by the criticality hypothesis and well approximated by the results from the ECoG. Breaking from scale-invariance, avalanches can thus be grouped in two regimes. Small avalanches consists of a limited number of co-activation modes involving a sub-set of cortical networks (related to the Default Mode Network), while larger avalanches involve a substantial portion of the cortical surface and can be clustered into two families: one immediately preceded by Retrosplenial Cortex activation and mostly involving medial-posterior networks, the other initiated by Somatosensory Cortex and extending preferentially along the lateral-anterior region. Rather than only differing in terms of size, these two set of events appear to be associated with markedly different brain-wide dynamical states: they are accompaniedby a shift in the hippocampal LFP, from the ripple band (smaller) to the gamma band (larger avalanches), and correspond to opposite directionality in the cortex-to-hippocampus causal relationship. These results provide a concrete description of global cortical dynamics, and shows how cortex in its entirety is involved in bi-directional communication in the hippocampus even in sleep-like states.
“LIM Domain Proteins in Cell Mechanotransduction”
My lab studies the design principles of cytoskeletal materials the drive cellular morphogenesis, with a focus on contractile machinery in adherent cells. In addition to force generation, a key feature of these materials are distributed force sensors which allow for rapid assembly, adaptation, repair and disintegration. Here I will discuss our recent identification of 18 proteins from the zyxin, paxillin, Tes and Enigma families with mechanosensitive LIM (Lin11, Isl- 1 & Mec-3) domains. We developed a screen to assess the force-dependent localization of LIM domain-containing region (LCR) from ~30 genes to the actin cytoskeleton and identified features common to their force-sensitive localization. Through in vitro reconstitution, we found that the LCR binds directly to mechanically stressed actin filaments. Moreover, the LCR from the fission yeast protein paxillin-like 1 is also mechanosensitive, suggesting force-sensitivity is highly conserved. We speculate that the evolutionary emergence of contractile F-actin machinery coincided with, or required, proteins that could report on the stresses present there to maintain homeostasis of actively stressed networks.
Mechanical Homeostasis of the Actin Cytoskeleton
My lab studies the design principles of cytoskeletal materials the drive cellular morphogenesis, with a focus on contractile machinery in adherent cells. In addition to force generation, a key feature of these materials are distributed force sensors which allow for rapid assembly, adaptation, repair and disintegration. Here I will describe how optogenetic control of RhoA GTPase is a powerful and versatile force spectroscopy approach of cytoskeletal assemblies and its recent use to probe repair response in actomyosin stress fibers. I will also describe our recent identification of 18 proteins from the zyxin, paxillin, Tes and Enigma families with mechanosensitive LIM (Lin11, Isl- 1 & Mec-3) domains that bind exclusively to mechanically stressed actin filaments. Our results suggest that the evolutionary emergence of contractile F-actin machinery coincided with, or required, proteins that could report on the stresses present there to maintain homeostasis of actively stressed networks.
E-prop: A biologically inspired paradigm for learning in recurrent networks of spiking neurons
Transformative advances in deep learning, such as deep reinforcement learning, usually rely on gradient-based learning methods such as backpropagation through time (BPTT) as a core learning algorithm. However, BPTT is not argued to be biologically plausible, since it requires to a propagate gradients backwards in time and across neurons. Here, we propose e-prop, a novel gradient-based learning method with local and online weight update rules for recurrent neural networks, and in particular recurrent spiking neural networks (RSNNs). As a result, e-prop has the potential to provide a substantial fraction of the power of deep learning to RSNNs. In this presentation, we will motivate e-prop from the perspective of recent insights in neuroscience and show how these have to be combined to form an algorithm for online gradient descent. The mathematical results will be supported by empirical evidence in supervised and reinforcement learning tasks. We will also discuss how limitations that are inherited from gradient-based learning methods, such as sample-efficiency, can be addressed by considering an evolution-like optimization that enhances learning on particular task families. The emerging learning architecture can be used to learn tasks by a single demonstration, hence enabling one-shot learning.
The Genetics of Parkinson's Disease: Understanding the Differences Between European and African Populations
In this talk, Professor Hardy will discuss the different causes and predispositions of PD that exist in Africa, and the differences to European populations. He will go on to discuss the importance of highlighting these differences and the impact of this vital research to people living with PD in Africa, as well as their families and caregivers.