1
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Kim SY, Zhang H, Rubio-Magnieto J. Operating Mechanism Principles and Advancements for Halide Perovskite-Based Memristors and Neuromorphic Devices. J Phys Chem Lett 2024; 15:10087-10103. [PMID: 39331473 PMCID: PMC11472375 DOI: 10.1021/acs.jpclett.4c02170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 09/22/2024] [Accepted: 09/24/2024] [Indexed: 09/29/2024]
Abstract
With the advent of the generation of artificial intelligence (AI) based on big data-processing technologies, next-generation memristor and memristive neuromorphic devices have been actively studied with great interest to overcome the von Neumann bottleneck limits. Among various candidates, halide perovskites (HPs) have been in the spotlight as potential candidates for these devices due to their unique switching characteristics with low energy consumption and flexible integration compatibility across various sources for scalability. We outline the characteristics and operating principles of HP-based memristors and their neuromorphic devices. We explain filamentary- and interface-type switching according to the type of conducting pathway occurring inside the active HP layer and the operating mechanisms depending on the species that make up this conducting pathway. We summarize the types and mechanisms of current changes beneficial for neuromorphic device applications and finally organize various suggested analysis tools and physical models to enable experimental determination of switching mechanisms from various perspectives.
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Affiliation(s)
- So-Yeon Kim
- Instituto
de Tecnología Química (ITQ), Universitat Politècnica de València-
Consejo Superior de Investigaciones Científicas (UPV-CSIC), 46022 València, Spain
| | - Heyi Zhang
- Instituto
de Tecnología Química (ITQ), Universitat Politècnica de València-
Consejo Superior de Investigaciones Científicas (UPV-CSIC), 46022 València, Spain
- Institute
of Advanced Materials (INAM), Universitat
Jaume I, 12006 Castelló, Spain
| | - Jenifer Rubio-Magnieto
- Instituto
de Tecnología Química (ITQ), Universitat Politècnica de València-
Consejo Superior de Investigaciones Científicas (UPV-CSIC), 46022 València, Spain
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2
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Susan S. Neuroscientific insights about computer vision models: a concise review. BIOLOGICAL CYBERNETICS 2024:10.1007/s00422-024-00998-9. [PMID: 39382577 DOI: 10.1007/s00422-024-00998-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 09/12/2024] [Indexed: 10/10/2024]
Abstract
The development of biologically-inspired computational models has been the focus of study ever since the artificial neuron was introduced by McCulloch and Pitts in 1943. However, a scrutiny of literature reveals that most attempts to replicate the highly efficient and complex biological visual system have been futile or have met with limited success. The recent state-of the-art computer vision models, such as pre-trained deep neural networks and vision transformers, may not be biologically inspired per se. Nevertheless, certain aspects of biological vision are still found embedded, knowingly or unknowingly, in the architecture and functioning of these models. This paper explores several principles related to visual neuroscience and the biological visual pathway that resonate, in some manner, in the architectural design and functioning of contemporary computer vision models. The findings of this survey can provide useful insights for building futuristic bio-inspired computer vision models. The survey is conducted from a historical perspective, tracing the biological connections of computer vision models starting with the basic artificial neuron to modern technologies such as deep convolutional neural network (CNN) and spiking neural networks (SNN). One spotlight of the survey is a discussion on biologically plausible neural networks and bio-inspired unsupervised learning mechanisms adapted for computer vision tasks in recent times.
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Affiliation(s)
- Seba Susan
- Department of Information Technology, Delhi Technological University, Delhi, India.
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3
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Nelson APK, Mole J, Pombo G, Gray RJ, Ruffle JK, Chan E, Rees GE, Cipolotti L, Nachev P. The minimal computational substrate of fluid intelligence. Cortex 2024; 179:62-76. [PMID: 39141936 DOI: 10.1016/j.cortex.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/08/2024] [Accepted: 07/01/2024] [Indexed: 08/16/2024]
Abstract
The quantification of cognitive powers rests on identifying a behavioural task that depends on them. Such dependence cannot be assured, for the powers a task invokes cannot be experimentally controlled or constrained a priori, resulting in unknown vulnerability to failure of specificity and generalisability. Evaluating a compact version of Raven's Advanced Progressive Matrices (RAPM), a widely used clinical test of fluid intelligence, we show that LaMa, a self-supervised artificial neural network trained solely on the completion of partially masked images of natural environmental scenes, achieves representative human-level test scores a prima vista, without any task-specific inductive bias or training. Compared with cohorts of healthy and focally lesioned participants, LaMa exhibits human-like variation with item difficulty, and produces errors characteristic of right frontal lobe damage under degradation of its ability to integrate global spatial patterns. LaMa's narrow training and limited capacity suggest matrix-style tests may be open to computationally simple solutions that need not necessarily invoke the substrates of reasoning.
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Affiliation(s)
- Amy P K Nelson
- High Dimensional Neurology Group, UCL Queen Square Institute of Neurology, University College London, Russell Square House, Bloomsbury, London, UK.
| | - Joe Mole
- Department of Neuropsychology, National Hospital for Neurology and Neurosurgery, London, UK; UCL Queen Square Institute of Neurology, London, UK
| | - Guilherme Pombo
- High Dimensional Neurology Group, UCL Queen Square Institute of Neurology, University College London, Russell Square House, Bloomsbury, London, UK
| | - Robert J Gray
- High Dimensional Neurology Group, UCL Queen Square Institute of Neurology, University College London, Russell Square House, Bloomsbury, London, UK
| | - James K Ruffle
- High Dimensional Neurology Group, UCL Queen Square Institute of Neurology, University College London, Russell Square House, Bloomsbury, London, UK
| | - Edgar Chan
- Department of Neuropsychology, National Hospital for Neurology and Neurosurgery, London, UK; UCL Queen Square Institute of Neurology, London, UK
| | - Geraint E Rees
- UCL Queen Square Institute of Neurology, London, UK; University College London, Gower Street, London, UK
| | - Lisa Cipolotti
- Department of Neuropsychology, National Hospital for Neurology and Neurosurgery, London, UK; UCL Queen Square Institute of Neurology, London, UK
| | - Parashkev Nachev
- High Dimensional Neurology Group, UCL Queen Square Institute of Neurology, University College London, Russell Square House, Bloomsbury, London, UK.
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4
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Shamul JG, Wang Z, Gong H, Ou W, White AM, Moniz-Garcia DP, Gu S, Clyne AM, Quiñones-Hinojosa A, He X. Meta-analysis of the make-up and properties of in vitro models of the healthy and diseased blood-brain barrier. Nat Biomed Eng 2024:10.1038/s41551-024-01250-2. [PMID: 39304761 DOI: 10.1038/s41551-024-01250-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/08/2024] [Indexed: 09/22/2024]
Abstract
In vitro models of the human blood-brain barrier (BBB) are increasingly used to develop therapeutics that can cross the BBB for treating diseases of the central nervous system. Here we report a meta-analysis of the make-up and properties of transwell and microfluidic models of the healthy BBB and of BBBs in glioblastoma, Alzheimer's disease, Parkinson's disease and inflammatory diseases. We found that the type of model, the culture method (static or dynamic), the cell types and cell ratios, and the biomaterials employed as extracellular matrix are all crucial to recapitulate the low permeability and high expression of tight-junction proteins of the BBB, and to obtain high trans-endothelial electrical resistance. Specifically, for models of the healthy BBB, the inclusion of endothelial cells and pericytes as well as physiological shear stresses (~10-20 dyne cm-2) are necessary, and when astrocytes are added, astrocytes or pericytes should outnumber endothelial cells. We expect this meta-analysis to facilitate the design of increasingly physiological models of the BBB.
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Affiliation(s)
- James G Shamul
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Zhiyuan Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Hyeyeon Gong
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Wenquan Ou
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Alisa M White
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | | | - Shuo Gu
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Alisa Morss Clyne
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA
- Brain and Behavior Institute, University of Maryland, College Park, MD, USA
| | | | - Xiaoming He
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA.
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA.
- Brain and Behavior Institute, University of Maryland, College Park, MD, USA.
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA.
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5
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Monk T, Dennler N, Ralph N, Rastogi S, Afshar S, Urbizagastegui P, Jarvis R, van Schaik A, Adamatzky A. Electrical Signaling Beyond Neurons. Neural Comput 2024; 36:1939-2029. [PMID: 39141803 DOI: 10.1162/neco_a_01696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/21/2024] [Indexed: 08/16/2024]
Abstract
Neural action potentials (APs) are difficult to interpret as signal encoders and/or computational primitives. Their relationships with stimuli and behaviors are obscured by the staggering complexity of nervous systems themselves. We can reduce this complexity by observing that "simpler" neuron-less organisms also transduce stimuli into transient electrical pulses that affect their behaviors. Without a complicated nervous system, APs are often easier to understand as signal/response mechanisms. We review examples of nonneural stimulus transductions in domains of life largely neglected by theoretical neuroscience: bacteria, protozoans, plants, fungi, and neuron-less animals. We report properties of those electrical signals-for example, amplitudes, durations, ionic bases, refractory periods, and particularly their ecological purposes. We compare those properties with those of neurons to infer the tasks and selection pressures that neurons satisfy. Throughout the tree of life, nonneural stimulus transductions time behavioral responses to environmental changes. Nonneural organisms represent the presence or absence of a stimulus with the presence or absence of an electrical signal. Their transductions usually exhibit high sensitivity and specificity to a stimulus, but are often slow compared to neurons. Neurons appear to be sacrificing the specificity of their stimulus transductions for sensitivity and speed. We interpret cellular stimulus transductions as a cell's assertion that it detected something important at that moment in time. In particular, we consider neural APs as fast but noisy detection assertions. We infer that a principal goal of nervous systems is to detect extremely weak signals from noisy sensory spikes under enormous time pressure. We discuss neural computation proposals that address this goal by casting neurons as devices that implement online, analog, probabilistic computations with their membrane potentials. Those proposals imply a measurable relationship between afferent neural spiking statistics and efferent neural membrane electrophysiology.
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Affiliation(s)
- Travis Monk
- International Centre for Neuromorphic Systems, MARCS Institute, Western Sydney University, Sydney, NSW 2747, Australia
| | - Nik Dennler
- International Centre for Neuromorphic Systems, MARCS Institute, Western Sydney University, Sydney, NSW 2747, Australia
- Biocomputation Group, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB, U.K.
| | - Nicholas Ralph
- International Centre for Neuromorphic Systems, MARCS Institute, Western Sydney University, Sydney, NSW 2747, Australia
| | - Shavika Rastogi
- International Centre for Neuromorphic Systems, MARCS Institute, Western Sydney University, Sydney, NSW 2747, Australia
- Biocomputation Group, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB, U.K.
| | - Saeed Afshar
- International Centre for Neuromorphic Systems, MARCS Institute, Western Sydney University, Sydney, NSW 2747, Australia
| | - Pablo Urbizagastegui
- International Centre for Neuromorphic Systems, MARCS Institute, Western Sydney University, Sydney, NSW 2747, Australia
| | - Russell Jarvis
- International Centre for Neuromorphic Systems, MARCS Institute, Western Sydney University, Sydney, NSW 2747, Australia
| | - André van Schaik
- International Centre for Neuromorphic Systems, MARCS Institute, Western Sydney University, Sydney, NSW 2747, Australia
| | - Andrew Adamatzky
- Unconventional Computing Laboratory, University of the West of England, Bristol BS16 1QY, U.K.
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6
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Urbizagastegui P, van Schaik A, Wang R. Memory-efficient neurons and synapses for spike-timing-dependent-plasticity in large-scale spiking networks. Front Neurosci 2024; 18:1450640. [PMID: 39308944 PMCID: PMC11412959 DOI: 10.3389/fnins.2024.1450640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 08/12/2024] [Indexed: 09/25/2024] Open
Abstract
This paper addresses the challenges posed by frequent memory access during simulations of large-scale spiking neural networks involving synaptic plasticity. We focus on the memory accesses performed during a common synaptic plasticity rule since this can be a significant factor limiting the efficiency of the simulations. We propose neuron models that are represented by only three state variables, which are engineered to enforce the appropriate neuronal dynamics. Additionally, memory retrieval is executed solely by fetching postsynaptic variables, promoting a contiguous memory storage and leveraging the capabilities of burst mode operations to reduce the overhead associated with each access. Different plasticity rules could be implemented despite the adopted simplifications, each leading to a distinct synaptic weight distribution (i.e., unimodal and bimodal). Moreover, our method requires fewer average memory accesses compared to a naive approach. We argue that the strategy described can speed up memory transactions and reduce latencies while maintaining a small memory footprint.
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Affiliation(s)
- Pablo Urbizagastegui
- International Centre for Neuromorphic Systems, The MARCS Institute for Brain, Behavior, and Development, Western Sydney University, Kingswood, NSW, Australia
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7
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Rabeling A, van der Hoven A, Andersen N, Goolam M. Neural Tube Organoids: A Novel System to Study Developmental Timing. Stem Cell Rev Rep 2024:10.1007/s12015-024-10785-5. [PMID: 39230820 DOI: 10.1007/s12015-024-10785-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2024] [Indexed: 09/05/2024]
Abstract
The neural tube (NT) is a transient structure formed during embryogenesis which develops into the brain and spinal cord. While mouse models have been commonly used in place of human embryos to study NT development, species-specific differences limit their applicability. One major difference is developmental timing, with NT formation from the neural plate in 16 days in humans compared to 4 days in mice, as well as differences in the time taken to form neuronal subtypes and complete neurogenesis. Neural tube organoids (NTOs) represent a new way to study NT development in vitro. While mouse and human NTOs have been shown to recapitulate the major developmental events of NT formation; it is unknown whether species-specific developmental timing, also termed allochrony, is also recapitulated. This review summarises current research using both mouse and human NTOs and compares developmental timing events in order to assess if allochrony is maintained in organoids.
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Affiliation(s)
- Alexa Rabeling
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
- UCT Neuroscience Institute, Cape Town, South Africa
| | - Amy van der Hoven
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
- UCT Neuroscience Institute, Cape Town, South Africa
| | - Nathalie Andersen
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
- UCT Neuroscience Institute, Cape Town, South Africa
| | - Mubeen Goolam
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.
- UCT Neuroscience Institute, Cape Town, South Africa.
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8
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Berry JA, Guhle DC, Davis RL. Active forgetting and neuropsychiatric diseases. Mol Psychiatry 2024; 29:2810-2820. [PMID: 38532011 PMCID: PMC11420092 DOI: 10.1038/s41380-024-02521-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024]
Abstract
Recent and pioneering animal research has revealed the brain utilizes a variety of molecular, cellular, and network-level mechanisms used to forget memories in a process referred to as "active forgetting". Active forgetting increases behavioral flexibility and removes irrelevant information. Individuals with impaired active forgetting mechanisms can experience intrusive memories, distressing thoughts, and unwanted impulses that occur in neuropsychiatric diseases. The current evidence indicates that active forgetting mechanisms degrade, or mask, molecular and cellular memory traces created in synaptic connections of "engram cells" that are specific for a given memory. Combined molecular genetic/behavioral studies using Drosophila have uncovered a complex system of cellular active-forgetting pathways within engram cells that is regulated by dopamine neurons and involves dopamine-nitric oxide co-transmission and reception, endoplasmic reticulum Ca2+ signaling, and cytoskeletal remodeling machinery regulated by small GTPases. Some of these molecular cellular mechanisms have already been found to be conserved in mammals. Interestingly, some pathways independently regulate forgetting of distinct memory types and temporal phases, suggesting a multi-layering organization of forgetting systems. In mammals, active forgetting also involves modulation of memory trace synaptic strength by altering AMPA receptor trafficking. Furthermore, active-forgetting employs network level mechanisms wherein non-engram neurons, newly born-engram neurons, and glial cells regulate engram synapses in a state and experience dependent manner. Remarkably, there is evidence for potential coordination between the network and cellular level forgetting mechanisms. Finally, subjects with several neuropsychiatric diseases have been tested and shown to be impaired in active forgetting. Insights obtained from research on active forgetting in animal models will continue to enrich our understanding of the brain dysfunctions that occur in neuropsychiatric diseases.
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Affiliation(s)
- Jacob A Berry
- Department of Biological Sciences, University of Alberta, Edmonton, AL, T6G 2E9, Canada.
| | - Dana C Guhle
- Department of Biological Sciences, University of Alberta, Edmonton, AL, T6G 2E9, Canada
| | - Ronald L Davis
- Department of Neuroscience, UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL, 33458, USA.
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9
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Molska M, Mruczyk K, Cisek-Woźniak A, Prokopowicz W, Szydełko P, Jakuszewska Z, Marzec K, Trocholepsza M. The Influence of Intestinal Microbiota on BDNF Levels. Nutrients 2024; 16:2891. [PMID: 39275207 PMCID: PMC11397622 DOI: 10.3390/nu16172891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/24/2024] [Accepted: 08/26/2024] [Indexed: 09/16/2024] Open
Abstract
The regulation of neurogenesis, the complex process of producing and differentiating new brain tissue cells, is influenced by a complex interaction of internal and external factors. Over the past decade, extensive research has been conducted on neurotrophins and their key role in adult neurogenesis, as well as their impact on diseases such as depression. Among neurotrophins, the brain-derived neurotrophic factor (BDNF) has been the subject of comprehensive studies on adult neurogenesis, and scientific evidence supports its necessity for neurogenesis in the subventricular zone of the hippocampus. A novel area of research is the emerging role of gut microbiota as a significant contributor to neurogenesis and neurotrophin production. Studies have shown that reduced BDNF levels can lead to mood disorders, which are observed in intestinal dysbiosis, characterized by an imbalance in the composition and quantity of the intestinal microbiota. There is evidence in the literature that there is a link between brain function and gut microbiota. Physical activity, and especially the regularity and intensity of exercise, is important in relation to the level of BDNF and the intestinal microbiota. Probiotics, prebiotics and physical activity may have a positive effect on the intestinal microbiota, and therefore also on the level of the brain-derived neurotrophic factor.
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Affiliation(s)
- Marta Molska
- Department of Dietetics, Faculty of Physical Culture in Gorzow Wlkp., Poznan University of Physical Education, Estkowskiego 13, 66-400 Gorzow Wielkopolski, Poland; (K.M.); (A.C.-W.); (P.S.); (Z.J.); (K.M.); (M.T.)
| | - Kinga Mruczyk
- Department of Dietetics, Faculty of Physical Culture in Gorzow Wlkp., Poznan University of Physical Education, Estkowskiego 13, 66-400 Gorzow Wielkopolski, Poland; (K.M.); (A.C.-W.); (P.S.); (Z.J.); (K.M.); (M.T.)
| | - Angelika Cisek-Woźniak
- Department of Dietetics, Faculty of Physical Culture in Gorzow Wlkp., Poznan University of Physical Education, Estkowskiego 13, 66-400 Gorzow Wielkopolski, Poland; (K.M.); (A.C.-W.); (P.S.); (Z.J.); (K.M.); (M.T.)
| | - Wojciech Prokopowicz
- GSP Clinic Limited Liability Company, Kostrzyńska Street 12, 66-400 Gorzow Wielkopolski, Poland;
| | - Patrycja Szydełko
- Department of Dietetics, Faculty of Physical Culture in Gorzow Wlkp., Poznan University of Physical Education, Estkowskiego 13, 66-400 Gorzow Wielkopolski, Poland; (K.M.); (A.C.-W.); (P.S.); (Z.J.); (K.M.); (M.T.)
| | - Zuzanna Jakuszewska
- Department of Dietetics, Faculty of Physical Culture in Gorzow Wlkp., Poznan University of Physical Education, Estkowskiego 13, 66-400 Gorzow Wielkopolski, Poland; (K.M.); (A.C.-W.); (P.S.); (Z.J.); (K.M.); (M.T.)
| | - Karolina Marzec
- Department of Dietetics, Faculty of Physical Culture in Gorzow Wlkp., Poznan University of Physical Education, Estkowskiego 13, 66-400 Gorzow Wielkopolski, Poland; (K.M.); (A.C.-W.); (P.S.); (Z.J.); (K.M.); (M.T.)
| | - Martyna Trocholepsza
- Department of Dietetics, Faculty of Physical Culture in Gorzow Wlkp., Poznan University of Physical Education, Estkowskiego 13, 66-400 Gorzow Wielkopolski, Poland; (K.M.); (A.C.-W.); (P.S.); (Z.J.); (K.M.); (M.T.)
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10
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Kang R, Park S, Shin S, Bak G, Park JC. Electrophysiological insights with brain organoid models: a brief review. BMB Rep 2024; 57:311-317. [PMID: 38919012 PMCID: PMC11289503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/19/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024] Open
Abstract
Brain organoid is a three-dimensional (3D) tissue derived from stem cells such as induced pluripotent stem cells (iPSCs) embryonic stem cells (ESCs) that reflect real human brain structure. It replicates the complexity and development of the human brain, enabling studies of the human brain in vitro. With emerging technologies, its application is various, including disease modeling and drug screening. A variety of experimental methods have been used to study structural and molecular characteristics of brain organoids. However, electrophysiological analysis is necessary to understand their functional characteristics and complexity. Although electrophysiological approaches have rapidly advanced for monolayered cells, there are some limitations in studying electrophysiological and neural network characteristics due to the lack of 3D characteristics. Herein, electrophysiological measurement and analytical methods related to neural complexity and 3D characteristics of brain organoids are reviewed. Overall, electrophysiological understanding of brain organoids allows us to overcome limitations of monolayer in vitro cell culture models, providing deep insights into the neural network complex of the real human brain and new ways of disease modeling. [BMB Reports 2024; 57(7): 311-317].
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Affiliation(s)
- Rian Kang
- Institute of Quantum Biophysics, Sungkyunkwan University, Suwon 16419, Korea
- Department of Metabiohealth, Sungkyunkwan University, Suwon 16419, Korea
| | - Soomin Park
- Institute of Quantum Biophysics, Sungkyunkwan University, Suwon 16419, Korea
- Department of Biophysics, Sungkyunkwan University, Suwon 16419, Korea
| | - Saewoon Shin
- Institute of Quantum Biophysics, Sungkyunkwan University, Suwon 16419, Korea
| | - Gyusoo Bak
- Institute of Quantum Biophysics, Sungkyunkwan University, Suwon 16419, Korea
- Department of Metabiohealth, Sungkyunkwan University, Suwon 16419, Korea
| | - Jong-Chan Park
- Institute of Quantum Biophysics, Sungkyunkwan University, Suwon 16419, Korea
- Department of Metabiohealth, Sungkyunkwan University, Suwon 16419, Korea
- Department of Biophysics, Sungkyunkwan University, Suwon 16419, Korea
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11
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Gkotsoulias DG, Jäger C, Müller R, Gräßle T, Olofsson KM, Møller T, Unwin S, Crockford C, Wittig RM, Bilgic B, Möller HE. Chaos and COSMOS-Considerations on QSM methods with multiple and single orientations and effects from local anisotropy. Magn Reson Imaging 2024; 110:104-111. [PMID: 38631534 DOI: 10.1016/j.mri.2024.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/07/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
PURPOSE Field-to-susceptibility inversion in quantitative susceptibility mapping (QSM) is ill-posed and needs numerical stabilization through either regularization or oversampling by acquiring data at three or more object orientations. Calculation Of Susceptibility through Multiple Orientations Sampling (COSMOS) is an established oversampling approach and regarded as QSM gold standard. It achieves a well-conditioned inverse problem, requiring rotations by 0°, 60° and 120° in the yz-plane. However, this is impractical in vivo, where head rotations are typically restricted to a range of ±25°. Non-ideal sampling degrades the conditioning with residual streaking artifacts whose mitigation needs further regularization. Moreover, susceptibility anisotropy in white matter is not considered in the COSMOS model, which may introduce additional bias. The current work presents a thorough investigation of these effects in primate brain. METHODS Gradient-recalled echo (GRE) data of an entire fixed chimpanzee brain were acquired at 7 T (350 μm resolution, 10 orientations) including ideal COSMOS sampling and realistic rotations in vivo. Comparisons of the results included ideal COSMOS, in-vivo feasible acquisitions with 3-8 orientations and single-orientation iLSQR QSM. RESULTS In-vivo feasible and optimal COSMOS yielded high-quality susceptibility maps with increased SNR resulting from averaging multiple acquisitions. COSMOS reconstructions from non-ideal rotations about a single axis required additional L2-regularization to mitigate residual streaking artifacts. CONCLUSION In view of unconsidered anisotropy effects, added complexity of the reconstruction, and the general challenge of multi-orientation acquisitions, advantages of sub-optimal COSMOS schemes over regularized single-orientation QSM appear limited in in-vivo settings.
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Affiliation(s)
- Dimitrios G Gkotsoulias
- Nuclear Magnetic Resonance Methods & Development Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
| | - Carsten Jäger
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Roland Müller
- Nuclear Magnetic Resonance Methods & Development Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Tobias Gräßle
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany
| | | | | | - Steve Unwin
- Wildlife Health Australia, Canberra, Australia
| | - Catherine Crockford
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; The Ape Social Mind Lab, Institut des Sciences Cognitives Marc Jeannerod, Bron, France; Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Roman M Wittig
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; The Ape Social Mind Lab, Institut des Sciences Cognitives Marc Jeannerod, Bron, France; Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Berkin Bilgic
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Harvard/MIT Health Sciences and Technology, Cambridge, MA, United States
| | - Harald E Möller
- Nuclear Magnetic Resonance Methods & Development Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
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12
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Nehme R, Pietiläinen O, Barrett LE. Genomic, molecular, and cellular divergence of the human brain. Trends Neurosci 2024; 47:491-505. [PMID: 38897852 DOI: 10.1016/j.tins.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/29/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
While many core biological processes are conserved across species, the human brain has evolved with unique capacities. Current understanding of the neurobiological mechanisms that endow human traits as well as associated vulnerabilities remains limited. However, emerging data have illuminated species divergence in DNA elements and genome organization, in molecular, morphological, and functional features of conserved neural cell types, as well as temporal differences in brain development. Here, we summarize recent data on unique features of the human brain and their complex implications for the study and treatment of brain diseases. We also consider key outstanding questions in the field and discuss the technologies and foundational knowledge that will be required to accelerate understanding of human neurobiology.
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Affiliation(s)
- Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Olli Pietiläinen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Lindy E Barrett
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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13
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Wang Y, Cheng L, Li D, Lu Y, Wang C, Wang Y, Gao C, Wang H, Vanduffel W, Hopkins WD, Sherwood CC, Jiang T, Chu C, Fan L. Comparative Analysis of Human-Chimpanzee Divergence in Brain Connectivity and its Genetic Correlates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597252. [PMID: 38895242 PMCID: PMC11185649 DOI: 10.1101/2024.06.03.597252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Chimpanzees (Pan troglodytes) are humans' closest living relatives, making them the most directly relevant comparison point for understanding human brain evolution. Zeroing in on the differences in brain connectivity between humans and chimpanzees can provide key insights into the specific evolutionary changes that might have occured along the human lineage. However, conducting comparisons of brain connectivity between humans and chimpanzees remains challenging, as cross-species brain atlases established within the same framework are currently lacking. Without the availability of cross-species brain atlases, the region-wise connectivity patterns between humans and chimpanzees cannot be directly compared. To address this gap, we built the first Chimpanzee Brainnetome Atlas (ChimpBNA) by following a well-established connectivity-based parcellation framework. Leveraging this new resource, we found substantial divergence in connectivity patterns across most association cortices, notably in the lateral temporal and dorsolateral prefrontal cortex between the two species. Intriguingly, these patterns significantly deviate from the patterns of cortical expansion observed in humans compared to chimpanzees. Additionally, we identified regions displaying connectional asymmetries that differed between species, likely resulting from evolutionary divergence. Genes associated with these divergent connectivities were found to be enriched in cell types crucial for cortical projection circuits and synapse formation. These genes exhibited more pronounced differences in expression patterns in regions with higher connectivity divergence, suggesting a potential foundation for brain connectivity evolution. Therefore, our study not only provides a fine-scale brain atlas of chimpanzees but also highlights the connectivity divergence between humans and chimpanzees in a more rigorous and comparative manner and suggests potential genetic correlates for the observed divergence in brain connectivity patterns between the two species. This can help us better understand the origins and development of uniquely human cognitive capabilities.
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Affiliation(s)
- Yufan Wang
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Luqi Cheng
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin 541004, China
- Research Center for Augmented Intelligence, Zhejiang Lab, Hangzhou 311100, China
| | - Deying Li
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yuheng Lu
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Changshuo Wang
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yaping Wang
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Chaohong Gao
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Haiyan Wang
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- Department of Neurosciences, Laboratory of Neuro- and Psychophysiology, KU Leuven Medical School, 3000 Leuven, Belgium
| | - Wim Vanduffel
- Department of Neurosciences, Laboratory of Neuro- and Psychophysiology, KU Leuven Medical School, 3000 Leuven, Belgium
- Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Radiology, Harvard Medical School, Boston, MA 02144, USA
| | - William D. Hopkins
- Department of Comparative Medicine, University of Texas MD Anderson Cancer Center, Bastrop, TX 78602, USA
| | - Chet C. Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Tianzi Jiang
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100190, China
- Research Center for Augmented Intelligence, Zhejiang Lab, Hangzhou 311100, China
| | - Congying Chu
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Lingzhong Fan
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100190, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100190, China
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao 266000, China
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14
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Yan Y, Cho AN. Human Brain In Vitro Model for Pathogen Infection-Related Neurodegeneration Study. Int J Mol Sci 2024; 25:6522. [PMID: 38928228 PMCID: PMC11204318 DOI: 10.3390/ijms25126522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/21/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Recent advancements in stem cell biology and tissue engineering have revolutionized the field of neurodegeneration research by enabling the development of sophisticated in vitro human brain models. These models, including 2D monolayer cultures, 3D organoids, organ-on-chips, and bioengineered 3D tissue models, aim to recapitulate the cellular diversity, structural organization, and functional properties of the native human brain. This review highlights how these in vitro brain models have been used to investigate the effects of various pathogens, including viruses, bacteria, fungi, and parasites infection, particularly in the human brain cand their subsequent impacts on neurodegenerative diseases. Traditional studies have demonstrated the susceptibility of different 2D brain cell types to infection, elucidated the mechanisms underlying pathogen-induced neuroinflammation, and identified potential therapeutic targets. Therefore, current methodological improvement brought the technology of 3D models to overcome the challenges of 2D cells, such as the limited cellular diversity, incomplete microenvironment, and lack of morphological structures by highlighting the need for further technological advancements. This review underscored the significance of in vitro human brain cell from 2D monolayer to bioengineered 3D tissue model for elucidating the intricate dynamics for pathogen infection modeling. These in vitro human brain cell enabled researchers to unravel human specific mechanisms underlying various pathogen infections such as SARS-CoV-2 to alter blood-brain-barrier function and Toxoplasma gondii impacting neural cell morphology and its function. Ultimately, these in vitro human brain models hold promise as personalized platforms for development of drug compound, gene therapy, and vaccine. Overall, we discussed the recent progress in in vitro human brain models, their applications in studying pathogen infection-related neurodegeneration, and future directions.
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Affiliation(s)
- Yuwei Yan
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Darlington, NSW 2008, Australia;
- The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, Camperdown, NSW 2050, Australia
| | - Ann-Na Cho
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Darlington, NSW 2008, Australia;
- The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, Camperdown, NSW 2050, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW 2006, Australia
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15
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Xiong GJ, Sheng ZH. Presynaptic perspective: Axonal transport defects in neurodevelopmental disorders. J Cell Biol 2024; 223:e202401145. [PMID: 38568173 PMCID: PMC10988239 DOI: 10.1083/jcb.202401145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
Disruption of synapse assembly and maturation leads to a broad spectrum of neurodevelopmental disorders. Presynaptic proteins are largely synthesized in the soma, where they are packaged into precursor vesicles and transported into distal axons to ensure precise assembly and maintenance of presynapses. Due to their morphological features, neurons face challenges in the delivery of presynaptic cargos to nascent boutons. Thus, targeted axonal transport is vital to build functional synapses. A growing number of mutations in genes encoding the transport machinery have been linked to neurodevelopmental disorders. Emerging lines of evidence have started to uncover presynaptic mechanisms underlying axonal transport defects, thus broadening the view of neurodevelopmental disorders beyond postsynaptic mechanisms. In this review, we discuss presynaptic perspectives of neurodevelopmental disorders by focusing on impaired axonal transport and disturbed assembly and maintenance of presynapses. We also discuss potential strategies for restoring axonal transport as an early therapeutic intervention.
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Affiliation(s)
- Gui-Jing Xiong
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Zu-Hang Sheng
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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16
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Fedorenko E, Piantadosi ST, Gibson EAF. Language is primarily a tool for communication rather than thought. Nature 2024; 630:575-586. [PMID: 38898296 DOI: 10.1038/s41586-024-07522-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/03/2024] [Indexed: 06/21/2024]
Abstract
Language is a defining characteristic of our species, but the function, or functions, that it serves has been debated for centuries. Here we bring recent evidence from neuroscience and allied disciplines to argue that in modern humans, language is a tool for communication, contrary to a prominent view that we use language for thinking. We begin by introducing the brain network that supports linguistic ability in humans. We then review evidence for a double dissociation between language and thought, and discuss several properties of language that suggest that it is optimized for communication. We conclude that although the emergence of language has unquestionably transformed human culture, language does not appear to be a prerequisite for complex thought, including symbolic thought. Instead, language is a powerful tool for the transmission of cultural knowledge; it plausibly co-evolved with our thinking and reasoning capacities, and only reflects, rather than gives rise to, the signature sophistication of human cognition.
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Affiliation(s)
- Evelina Fedorenko
- Massachusetts Institute of Technology, Cambridge, MA, USA.
- Speech and Hearing in Bioscience and Technology Program at Harvard University, Boston, MA, USA.
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17
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Hodgdon EA, Anderson R, Azzawi HA, Wilson TW, Calhoun VD, Wang YP, Solis I, Greve DN, Stephen JM, Ciesielski KTR. MRI morphometry of the anterior and posterior cerebellar vermis and its relationship to sensorimotor and cognitive functions in children. Dev Cogn Neurosci 2024; 67:101385. [PMID: 38713999 PMCID: PMC11096723 DOI: 10.1016/j.dcn.2024.101385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 05/09/2024] Open
Abstract
INTRODUCTION The human cerebellum emerges as a posterior brain structure integrating neural networks for sensorimotor, cognitive, and emotional processing across the lifespan. Developmental studies of the cerebellar anatomy and function are scant. We examine age-dependent MRI morphometry of the anterior cerebellar vermis, lobules I-V and posterior neocortical lobules VI-VII and their relationship to sensorimotor and cognitive functions. METHODS Typically developing children (TDC; n=38; age 9-15) and healthy adults (HAC; n=31; 18-40) participated in high-resolution MRI. Rigorous anatomically informed morphometry of the vermis lobules I-V and VI-VII and total brain volume (TBV) employed manual segmentation computer-assisted FreeSurfer Image Analysis Program [http://surfer.nmr.mgh.harvard.edu]. The neuropsychological scores (WASI-II) were normalized and related to volumes of anterior, posterior vermis, and TBV. RESULTS TBVs were age independent. Volumes of I-V and VI-VII were significantly reduced in TDC. The ratio of VI-VII to I-V (∼60%) was stable across age-groups; I-V correlated with visual-spatial-motor skills; VI-VII with verbal, visual-abstract and FSIQ. CONCLUSIONS In TDC neither anterior I-V nor posterior VI-VII vermis attained adult volumes. The "inverted U" developmental trajectory of gray matter peaking in adolescence does not explain this finding. The hypothesis of protracted development of oligodendrocyte/myelination is suggested as a contributor to TDC's lower cerebellar vermis volumes.
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Affiliation(s)
- Elizabeth A Hodgdon
- Pediatric Neuroscience Laboratory, Psychology Clinical Neuroscience Center, Department of Psychology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Ryan Anderson
- Pediatric Neuroscience Laboratory, Psychology Clinical Neuroscience Center, Department of Psychology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Hussein Al Azzawi
- Pediatric Neuroscience Laboratory, Psychology Clinical Neuroscience Center, Department of Psychology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Tony W Wilson
- Institute of Human Neuroscience, Boys Town National Research Hospital, 14090 Mother Teresa Lane, Boys Town, NE 68010, USA
| | - Vince D Calhoun
- Mind Research Network and Lovelace Biomedical and Environmental Research Institute, 1101 Yale Blvd N.E., Albuquerque, NM 87106, USA; Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia Tech, Emory, Atlanta, GA, USA
| | - Yu-Ping Wang
- Department of Biomedical Engineering, Tulane University, 6823 St. Charles Ave, New Orleans, LA 70118, USA
| | - Isabel Solis
- Pediatric Neuroscience Laboratory, Psychology Clinical Neuroscience Center, Department of Psychology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Douglas N Greve
- MGH/MIT Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Julia M Stephen
- Mind Research Network and Lovelace Biomedical and Environmental Research Institute, 1101 Yale Blvd N.E., Albuquerque, NM 87106, USA
| | - Kristina T R Ciesielski
- Pediatric Neuroscience Laboratory, Psychology Clinical Neuroscience Center, Department of Psychology, University of New Mexico, Albuquerque, NM 87131, USA; MGH/MIT Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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18
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Pratt HE, Andrews G, Shedd N, Phalke N, Li T, Pampari A, Jensen M, Wen C, Consortium P, Gandal MJ, Geschwind DH, Gerstein M, Moore J, Kundaje A, Colubri A, Weng Z. Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. SCIENCE ADVANCES 2024; 10:eadj4452. [PMID: 38781344 PMCID: PMC11114231 DOI: 10.1126/sciadv.adj4452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Most genetic variants associated with psychiatric disorders are located in noncoding regions of the genome. To investigate their functional implications, we integrate epigenetic data from the PsychENCODE Consortium and other published sources to construct a comprehensive atlas of candidate brain cis-regulatory elements. Using deep learning, we model these elements' sequence syntax and predict how binding sites for lineage-specific transcription factors contribute to cell type-specific gene regulation in various types of glia and neurons. The elements' evolutionary history suggests that new regulatory information in the brain emerges primarily via smaller sequence mutations within conserved mammalian elements rather than entirely new human- or primate-specific sequences. However, primate-specific candidate elements, particularly those active during fetal brain development and in excitatory neurons and astrocytes, are implicated in the heritability of brain-related human traits. Additionally, we introduce PsychSCREEN, a web-based platform offering interactive visualization of PsychENCODE-generated genetic and epigenetic data from diverse brain cell types in individuals with psychiatric disorders and healthy controls.
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Affiliation(s)
- Henry E. Pratt
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gregory Andrews
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicole Shedd
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nishigandha Phalke
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tongxin Li
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Khoury College of Computer Science, Northeastern University, Boston, MA 02115, USA
| | - Anusri Pampari
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Jensen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Cindy Wen
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Michael J. Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Daniel H. Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Jill Moore
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Andrés Colubri
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Zhiping Weng
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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19
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Cheng S, Chang S, Li Y, Novoseltseva A, Lin S, Wu Y, Zhu J, McKee AC, Rosene DL, Wang H, Bigio IJ, Boas DA, Tian L. Enhanced Multiscale Human Brain Imaging by Semi-supervised Digital Staining and Serial Sectioning Optical Coherence Tomography. RESEARCH SQUARE 2024:rs.3.rs-4014687. [PMID: 38562721 PMCID: PMC10984089 DOI: 10.21203/rs.3.rs-4014687/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
A major challenge in neuroscience is to visualize the structure of the human brain at different scales. Traditional histology reveals micro- and meso-scale brain features, but suffers from staining variability, tissue damage and distortion that impedes accurate 3D reconstructions. Here, we present a new 3D imaging framework that combines serial sectioning optical coherence tomography (S-OCT) with a deep-learning digital staining (DS) model. We develop a novel semi-supervised learning technique to facilitate DS model training on weakly paired images. The DS model performs translation from S-OCT to Gallyas silver staining. We demonstrate DS on various human cerebral cortex samples with consistent staining quality. Additionally, we show that DS enhances contrast across cortical layer boundaries. Furthermore, we showcase geometry-preserving 3D DS on cubic-centimeter tissue blocks and visualization of meso-scale vessel networks in the white matter. We believe that our technique offers the potential for high-throughput, multiscale imaging of brain tissues and may facilitate studies of brain structures.
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Affiliation(s)
- Shiyi Cheng
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
| | - Shuaibin Chang
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
| | - Yunzhe Li
- Department of Electrical Engineering and Computer Sciences, University of California, Cory Hall, Berkeley, California, 94720, USA
| | - Anna Novoseltseva
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA, 02215, USA
| | - Sunni Lin
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA, 02215, USA
| | - Yicun Wu
- Department of Computer Science, Boston University, 665 Commonwealth Ave, Boston, MA, 02215, USA
| | - Jiahui Zhu
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
| | - Ann C. McKee
- Boston University Alzheimer’s Disease Research Center and CTE Center, Boston University, Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
- Department of Neurology, Boston University, Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
- VA Boston Healthcare System, U.S. Department of Veteran Affairs, Jamaica Plain, MA, 02130, USA
- Department of Psychiatry and Ophthalmology, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Douglas L. Rosene
- Department of Anatomy & Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Hui Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA, 02129, USA
| | - Irving J. Bigio
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA, 02215, USA
- Neurophotonics Center, Boston University, Boston, MA, 02215, USA
| | - David A. Boas
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA, 02215, USA
- Neurophotonics Center, Boston University, Boston, MA, 02215, USA
| | - Lei Tian
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA, 02215, USA
- Neurophotonics Center, Boston University, Boston, MA, 02215, USA
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20
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Cook PF, Reichmuth C. An Ecological and Neural Argument for Developing Pursuit-Based Cognitive Enrichment for Sea Lions in Human Care. Animals (Basel) 2024; 14:797. [PMID: 38473182 DOI: 10.3390/ani14050797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
While general enrichment strategies for captive animals attempt to elicit variable and species-typical behaviors, approaches to cognitive enrichment have been disappointingly one-size-fits-all. In this commentary, we address the potential benefit of tailoring cognitive enrichment to the "cognitive niche" of the species, with a particular focus on a reasonably well-studied marine carnivore, the sea lion. Sea lions likely share some cognitive evolutionary pressures with primates, including complex social behavior. Their foraging ecology, however, like that of many terrestrial carnivores, is based on the rapid and behaviorally flexible pursuit of avoidant prey. Unlike terrestrial carnivores, sea lions carry out this pursuit in a truly fluid three-dimensional field, computing and executing sensorimotor transformations from any solid angle to any other. The cognitive demands of flexible prey pursuit are unlikely to be fully elicited by typical stationary puzzle box style foraging enrichment devices or screen-based interactive games. With this species, we recommend exploring more water-based movement activities generally, and complex pursuit challenges specifically.
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Affiliation(s)
- Peter F Cook
- Social Sciences Division, New College of Florida, Sarasota, FL 34243, USA
| | - Colleen Reichmuth
- Long Marine Laboratory, Institute for Marine Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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21
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Kong X, Yu F, Yao W, Cai S, Zhang J, Lin H. Memristor-induced hyperchaos, multiscroll and extreme multistability in fractional-order HNN: Image encryption and FPGA implementation. Neural Netw 2024; 171:85-103. [PMID: 38091767 DOI: 10.1016/j.neunet.2023.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 11/06/2023] [Accepted: 12/04/2023] [Indexed: 01/29/2024]
Abstract
Fractional-order differentiation (FOD) can record information from the past, present, and future. Compared with integer-order systems, FOD systems have higher complexity and more accurate ability to describe the real world. In this paper, two types of fractional-order memristors are proposed and one type is proved to have extreme multistability, local activity, and non-volatility. By using memristors to simulate the autapse of a neuron and to describe the phenomenon of electromagnetic induction caused by electromagnetic radiation, we establish a new 5D FOD memristive HNN (FOMHNN). Through dynamic simulation, rich dynamic behaviors are found, such as hyperchaos, multiscroll, extreme multistability, and "overclocking" behavior caused by order reduction. To the best of our knowledge, this is the first time that such rich dynamic behaviors are found in FOMHNN simultaneously. Based on this FOMHNN, a very efficient and secure image encryption scheme is designed. Security analysis shows that the encrypted Lena image has extremely low adjacent pixel correlation and high randomness, with information entropy of 7.9995. Despite discarding diffusion and scrambling, it has excellent plaintext sensitivity, with NCPR = 99.6095% and UACI = 33.4671%. Finally, this paper implements the proposed FOMHNN and image encryption on field programmable gate array (FPGA). To our knowledge, the related work of fully hardware implementation of fractional-order neural networks and image encryption schemes based on this is rare.
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Affiliation(s)
- Xinxin Kong
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, 410114, Hunan, China.
| | - Fei Yu
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, 410114, Hunan, China.
| | - Wei Yao
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, 410114, Hunan, China.
| | - Shuo Cai
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, 410114, Hunan, China.
| | - Jin Zhang
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, 410114, Hunan, China.
| | - Hairong Lin
- School of Computer and Communication Engineering, Hunan University, Changsha, 410082, Hunan, China.
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22
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Sunny MM, Thamankar R. Spike rate dependent synaptic characteristics in lamellar, multilayered alpha-MoO 3 based two-terminal devices - efficient way to control the synaptic amplification. RSC Adv 2024; 14:2518-2528. [PMID: 38226148 PMCID: PMC10788777 DOI: 10.1039/d3ra07757h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024] Open
Abstract
Brain-inspired computing systems require a rich variety of neuromorphic devices using multi-functional materials operating at room temperature. Artificial synapses which can be operated using optical and electrical stimuli are in high demand. In this regard, layered materials have attracted a lot of attention due to their tunable energy gap and exotic properties. In the current study, we report the growth of layered MoO3 using the chemical vapor deposition (CVD) technique. MoO3 has an energy gap of 3.22 eV and grows with a large aspect ratio, as seen through optical and scanning electron microscopy. We used transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy for complete characterisation. The two-terminal devices using platinum (Pt/MoO3/Pt) exhibit superior memory with the high-resistance state (HRS) and low-resistance state (LRS) differing by a large resistance (∼MΩ). The devices also show excellent synaptic characteristics. Both optical and electrical pulses can be utilised to stimulate the synapse. Consistent learning (potentiation) and forgetting (depression) curves are measured. Transition from long term depression to long term potentiation can be achieved using the spike frequency dependent pulsing scheme. We have found that the amplification of postsynaptic current can be tuned using such frequency dependent spikes. This will help us to design neuromorphic devices with the required synaptic amplification.
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Affiliation(s)
- Meenu Maria Sunny
- Department of Physics, Vellore Institute of Technology Vellore TN India
- Centre for Functional Materials, Vellore Institute of Technology Vellore TN India
| | - R Thamankar
- Centre for Functional Materials, Vellore Institute of Technology Vellore TN India
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23
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Usui N. Possible roles of deep cortical neurons and oligodendrocytes in the neural basis of human sociality. Anat Sci Int 2024; 99:34-47. [PMID: 38010534 PMCID: PMC10771383 DOI: 10.1007/s12565-023-00747-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/17/2023] [Indexed: 11/29/2023]
Abstract
Sociality is an instinctive property of organisms that live in relation to others and is a complex characteristic of higher order brain functions. However, the evolution of the human brain to acquire higher order brain functions, such as sociality, and the neural basis for executing these functions and their control mechanisms are largely unknown. Several studies have attempted to evaluate how human sociality was acquired during the course of evolution and the mechanisms controlling sociality from a neurodevelopment viewpoint. This review discusses these findings in the context of human brain evolution and the pathophysiology of autism spectrum disorder (ASD). Comparative genomic studies of postmortem primate brains have demonstrated human-specific regulatory mechanisms underlying higher order brain functions, providing evidence for the contribution of oligodendrocytes to human brain function. Functional analyses of the causative genes of ASD in animal models have demonstrated that the neural basis of social behavior is associated with layer 6 (L6) of the neocortex and oligodendrocytes. These findings demonstrate that both neurons and oligodendrocytes contribute to the neural basis and molecular mechanisms underlying human brain evolution and social functioning. This review provides novel insights into sociability and the corresponding neural bases of brain disorders and evolution.
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Affiliation(s)
- Noriyoshi Usui
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, 565-0871, Japan.
- Omics Center, Center of Medical Innovation and Translational Research, Graduate School of Medicine, Osaka University, Suita, 565-0871, Japan.
- United Graduate School of Child Development, Osaka University, Suita, 565-0871, Japan.
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, 565-0871, Japan.
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka, 541-8567, Japan.
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24
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Nolan M, Scott C, Hof PR, Ansorge O. Betz cells of the primary motor cortex. J Comp Neurol 2024; 532:e25567. [PMID: 38289193 PMCID: PMC10952528 DOI: 10.1002/cne.25567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/11/2023] [Accepted: 11/17/2023] [Indexed: 02/01/2024]
Abstract
Betz cells, named in honor of Volodymyr Betz (1834-1894), who described them as "giant pyramids" in the primary motor cortex of primates and other mammalian species, are layer V extratelencephalic projection (ETP) neurons that directly innervate α-motoneurons of the brainstem and spinal cord. Despite their large volume and circumferential dendritic architecture, to date, no single molecular criterion has been established that unequivocally distinguishes adult Betz cells from other layer V ETP neurons. In primates, transcriptional signatures suggest the presence of at least two ETP neuron clusters that contain mature Betz cells; these are characterized by an abundance of axon guidance and oxidative phosphorylation transcripts. How neurodevelopmental programs drive the distinct positional and morphological features of Betz cells in humans remains unknown. Betz cells display a distinct biphasic firing pattern involving early cessation of firing followed by delayed sustained acceleration in spike frequency and magnitude. Few cell type-specific transcripts and electrophysiological characteristics are conserved between rodent layer V ETP neurons of the motor cortex and primate Betz cells. This has implications for the modeling of disorders that affect the motor cortex in humans, such as amyotrophic lateral sclerosis (ALS). Perhaps vulnerability to ALS is linked to the evolution of neural networks for fine motor control reflected in the distinct morphomolecular architecture of the human motor cortex, including Betz cells. Here, we discuss histological, molecular, and functional data concerning the position of Betz cells in the emerging taxonomy of neurons across diverse species and their role in neurological disorders.
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Affiliation(s)
- Matthew Nolan
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Department of NeurologyMassachusetts General HospitalBostonMassachusettsUSA
| | - Connor Scott
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
| | - Patrick. R. Hof
- Nash Family Department of Neuroscience and Friedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Olaf Ansorge
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
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25
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Bi Z. Cognition of Time and Thinking Beyond. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1455:171-195. [PMID: 38918352 DOI: 10.1007/978-3-031-60183-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
A common research protocol in cognitive neuroscience is to train subjects to perform deliberately designed experiments while recording brain activity, with the aim of understanding the brain mechanisms underlying cognition. However, how the results of this protocol of research can be applied in technology is seldom discussed. Here, I review the studies on time processing of the brain as examples of this research protocol, as well as two main application areas of neuroscience (neuroengineering and brain-inspired artificial intelligence). Time processing is a fundamental dimension of cognition, and time is also an indispensable dimension of any real-world signal to be processed in technology. Therefore, one may expect that the studies of time processing in cognition profoundly influence brain-related technology. Surprisingly, I found that the results from cognitive studies on timing processing are hardly helpful in solving practical problems. This awkward situation may be due to the lack of generalizability of the results of cognitive studies, which are under well-controlled laboratory conditions, to real-life situations. This lack of generalizability may be rooted in the fundamental unknowability of the world (including cognition). Overall, this paper questions and criticizes the usefulness and prospect of the abovementioned research protocol of cognitive neuroscience. I then give three suggestions for future research. First, to improve the generalizability of research, it is better to study brain activity under real-life conditions instead of in well-controlled laboratory experiments. Second, to overcome the unknowability of the world, we can engineer an easily accessible surrogate of the object under investigation, so that we can predict the behavior of the object under investigation by experimenting on the surrogate. Third, the paper calls for technology-oriented research, with the aim of technology creation instead of knowledge discovery.
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Affiliation(s)
- Zedong Bi
- Lingang Laboratory, Shanghai, China.
- Institute for Future, Qingdao University, Qingdao, China.
- School of Automation, Shandong Key Laboratory of Industrial Control Technology, Qingdao University, Qingdao, China.
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26
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Castrillon G, Epp S, Bose A, Fraticelli L, Hechler A, Belenya R, Ranft A, Yakushev I, Utz L, Sundar L, Rauschecker JP, Preibisch C, Kurcyus K, Riedl V. An energy costly architecture of neuromodulators for human brain evolution and cognition. SCIENCE ADVANCES 2023; 9:eadi7632. [PMID: 38091393 PMCID: PMC10848727 DOI: 10.1126/sciadv.adi7632] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
In comparison to other species, the human brain exhibits one of the highest energy demands relative to body metabolism. It remains unclear whether this heightened energy demand uniformly supports an enlarged brain or if specific signaling mechanisms necessitate greater energy. We hypothesized that the regional distribution of energy demands will reveal signaling strategies that have contributed to human cognitive development. We measured the energy distribution within the brain functional connectome using multimodal brain imaging and found that signaling pathways in evolutionarily expanded regions have up to 67% higher energetic costs than those in sensory-motor regions. Additionally, histology, transcriptomic data, and molecular imaging independently reveal an up-regulation of signaling at G-protein-coupled receptors in energy-demanding regions. Our findings indicate that neuromodulator activity is predominantly involved in cognitive functions, such as reading or memory processing. This study suggests that an up-regulation of neuromodulator activity, alongside increased brain size, is a crucial aspect of human brain evolution.
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Affiliation(s)
- Gabriel Castrillon
- Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Research Group in Medical Imaging, SURA Ayudas Diagnósticas, Medellin, Colombia
- Department of Neuroradiology at Uniklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Samira Epp
- Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Antonia Bose
- Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Laura Fraticelli
- Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - André Hechler
- Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roman Belenya
- Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andreas Ranft
- Department of Anesthesiology and Intensive Care Medicine at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Igor Yakushev
- Department of Nuclear Medicine at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Lukas Utz
- Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Lalith Sundar
- Quantitative Imaging and Medical Physics Team, Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Josef P Rauschecker
- Center for Neuroengineering, Georgetown University, Washington, DC, USA
- Institute for Advanced Study, Technical University of Munich, Munich, Germany
| | - Christine Preibisch
- Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Department of Neurology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Katarzyna Kurcyus
- Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Valentin Riedl
- Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Department of Neuroradiology at Uniklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
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27
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Magielse N, Heuer K, Toro R, Schutter DJLG, Valk SL. A Comparative Perspective on the Cerebello-Cerebral System and Its Link to Cognition. CEREBELLUM (LONDON, ENGLAND) 2023; 22:1293-1307. [PMID: 36417091 PMCID: PMC10657313 DOI: 10.1007/s12311-022-01495-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 11/24/2022]
Abstract
The longstanding idea that the cerebral cortex is the main neural correlate of human cognition can be elaborated by comparative analyses along the vertebrate phylogenetic tree that support the view that the cerebello-cerebral system is suited to support non-motor functions more generally. In humans, diverse accounts have illustrated cerebellar involvement in cognitive functions. Although the neocortex, and its transmodal association cortices such as the prefrontal cortex, have become disproportionately large over primate evolution specifically, human neocortical volume does not appear to be exceptional relative to the variability within primates. Rather, several lines of evidence indicate that the exceptional volumetric increase of the lateral cerebellum in conjunction with its connectivity with the cerebral cortical system may be linked to non-motor functions and mental operation in primates. This idea is supported by diverging cerebello-cerebral adaptations that potentially coevolve with cognitive abilities across other vertebrates such as dolphins, parrots, and elephants. Modular adaptations upon the vertebrate cerebello-cerebral system may thus help better understand the neuroevolutionary trajectory of the primate brain and its relation to cognition in humans. Lateral cerebellar lobules crura I-II and their reciprocal connections to the cerebral cortical association areas appear to have substantially expanded in great apes, and humans. This, along with the notable increase in the ventral portions of the dentate nucleus and a shift to increased relative prefrontal-cerebellar connectivity, suggests that modular cerebellar adaptations support cognitive functions in humans. In sum, we show how comparative neuroscience provides new avenues to broaden our understanding of cerebellar and cerebello-cerebral functions in the context of cognition.
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Affiliation(s)
- Neville Magielse
- Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour), Research Center Jülich, Jülich, Germany
- Otto Hahn Cognitive Neurogenetics Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Institute of Systems Neuroscience, Heinrich Heine University, Düsseldorf, Germany
| | - Katja Heuer
- Institute Pasteur, Unité de Neuroanatomie Appliquée et Théorique, Université Paris Cité, Paris, France
- Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Roberto Toro
- Institute Pasteur, Unité de Neuroanatomie Appliquée et Théorique, Université Paris Cité, Paris, France
| | - Dennis J L G Schutter
- Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, The Netherlands
| | - Sofie L Valk
- Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour), Research Center Jülich, Jülich, Germany.
- Otto Hahn Cognitive Neurogenetics Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
- Institute of Systems Neuroscience, Heinrich Heine University, Düsseldorf, Germany.
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28
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Hale WD, Romero AM, Gonzalez CU, Jayaraman V, Lau AY, Huganir RL, Twomey EC. Allosteric Competition and Inhibition in AMPA Receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569057. [PMID: 38076818 PMCID: PMC10705377 DOI: 10.1101/2023.11.28.569057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Excitatory neurotransmission is principally mediated by AMPA-subtype ionotropic glutamate receptors (AMPARs). Dysregulation of AMPARs is the cause of many neurological disorders and how therapeutic candidates such as negative allosteric modulators inhibit AMPARs is unclear. Here, we show that non-competitive inhibition desensitizes AMPARs to activation and prevents positive allosteric modulation. We dissected the noncompetitive inhibition mechanism of action by capturing AMPARs bound to glutamate and the prototypical negative allosteric modulator, GYKI-52466, with cryo-electron microscopy. Noncompetitive inhibition by GYKI-52466, which binds in the transmembrane collar region surrounding the ion channel, negatively modulates AMPARs by decoupling glutamate binding in the ligand binding domain from the ion channel. Furthermore, during allosteric competition between negative and positive modulators, negative allosteric modulation by GKYI-52466 outcompetes positive allosteric modulators to control AMPAR function. Our data provide a new framework for understanding allostery of AMPARs and foundations for rational design of therapeutics targeting AMPARs in neurological diseases.
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Affiliation(s)
- W. Dylan Hale
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Alejandra Montaño Romero
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Cuauhtemoc U. Gonzalez
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, TX, USA
| | - Albert Y. Lau
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Richard L. Huganir
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Edward C. Twomey
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA
- The Beckman Center for Cryo-EM at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA USA
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29
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Magielse N, Toro R, Steigauf V, Abbaspour M, Eickhoff SB, Heuer K, Valk SL. Phylogenetic comparative analysis of the cerebello-cerebral system in 34 species highlights primate-general expansion of cerebellar crura I-II. Commun Biol 2023; 6:1188. [PMID: 37993596 PMCID: PMC10665558 DOI: 10.1038/s42003-023-05553-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023] Open
Abstract
The reciprocal connections between the cerebellum and the cerebrum have been suggested to simultaneously play a role in brain size increase and to support a broad array of brain functions in primates. The cerebello-cerebral system has undergone marked functionally relevant reorganization. In particular, the lateral cerebellar lobules crura I-II (the ansiform) have been suggested to be expanded in hominoids. Here, we manually segmented 63 cerebella (34 primate species; 9 infraorders) and 30 ansiforms (13 species; 8 infraorders) to understand how their volumes have evolved over the primate lineage. Together, our analyses support proportional cerebellar-cerebral scaling, whereas ansiforms have expanded faster than the cerebellum and cerebrum. We did not find different scaling between strepsirrhines and haplorhines, nor between apes and non-apes. In sum, our study shows primate-general structural reorganization of the ansiform, relative to the cerebello-cerebral system, which is relevant for specialized brain functions in an evolutionary context.
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Grants
- RT and KH are supported by the French Agence Nationale de la Recherche, projects NeuroWebLab (ANR-19-DATA-0025) and DMOBE (ANR-21-CE45-0016). KH received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No101033485 (Individual Fellowship). Last, this work was funded in part by Helmholtz Association’s Initiative and Networking Fund under the Helmholtz International Lab grant agreement InterLabs-0015, and the Canada First Research Excellence Fund (CFREF Competition 2, 2015–2016), awarded to the Healthy Brains, Healthy Lives initiative at McGill University, through the Helmholtz International BigBrain Analytics and Learning Laboratory (HIBALL), including NM, SBE, and SLV.
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Affiliation(s)
- Neville Magielse
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center Jülich, Wilhelm-Johnen-Straße, 52428, Jülich, Germany.
- Otto Hahn Cognitive Neurogenetics Group, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstraße 1A, 04103, Leipzig, Germany.
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstraße 5, 40225, Düsseldorf, Germany.
| | - Roberto Toro
- Institut Pasteur, Unité de Neuroanatomie Appliquée et Théorique, Université Paris Cité, 25 rue du Dr. Roux, 75724, Paris, France
| | - Vanessa Steigauf
- Department of Biology, Northern Michigan University, 1401 Presque Isle Ave, MI, 49855, Marquette, USA
| | - Mahta Abbaspour
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Luisenstraße 56, Haus 1, 10117, Berlin, Germany
- Department of Neurology, Charité - Universitätsmedizin Berlin, Bonhoefferweg 3, 10117, Berlin, Germany
| | - Simon B Eickhoff
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center Jülich, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Katja Heuer
- Institut Pasteur, Unité de Neuroanatomie Appliquée et Théorique, Université Paris Cité, 25 rue du Dr. Roux, 75724, Paris, France
- Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstraße 1A, 04103, Leipzig, Germany
| | - Sofie L Valk
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center Jülich, Wilhelm-Johnen-Straße, 52428, Jülich, Germany.
- Otto Hahn Cognitive Neurogenetics Group, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstraße 1A, 04103, Leipzig, Germany.
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstraße 5, 40225, Düsseldorf, Germany.
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30
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Zhang R, Quan H, Wang Y, Luo F. Neurogenesis in primates versus rodents and the value of non-human primate models. Natl Sci Rev 2023; 10:nwad248. [PMID: 38025664 PMCID: PMC10659238 DOI: 10.1093/nsr/nwad248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/21/2023] [Accepted: 09/10/2023] [Indexed: 12/01/2023] Open
Abstract
Neurogenesis, the process of generating neurons from neural stem cells, occurs during both embryonic and adult stages, with each stage possessing distinct characteristics. Dysfunction in either stage can disrupt normal neural development, impair cognitive functions, and lead to various neurological disorders. Recent technological advancements in single-cell multiomics and gene-editing have facilitated investigations into primate neurogenesis. Here, we provide a comprehensive overview of neurogenesis across rodents, non-human primates, and humans, covering embryonic development to adulthood and focusing on the conservation and diversity among species. While non-human primates, especially monkeys, serve as valuable models with closer neural resemblance to humans, we highlight the potential impacts and limitations of non-human primate models on both physiological and pathological neurogenesis research.
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Affiliation(s)
- Runrui Zhang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Hongxin Quan
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Yinfeng Wang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Fucheng Luo
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
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31
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Li Y, Zhang B, Liu Z, Wang R. Neural energy computations based on Hodgkin-Huxley models bridge abnormal neuronal activities and energy consumption patterns of major depressive disorder. Comput Biol Med 2023; 166:107500. [PMID: 37797488 DOI: 10.1016/j.compbiomed.2023.107500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/07/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023]
Abstract
Limited by the current experimental techniques and neurodynamical models, the dysregulation mechanisms of decision-making related neural circuits in major depressive disorder (MDD) are still not clear. In this paper, we proposed a neural coding methodology using energy to further investigate it, which has been proven to strongly complement the neurodynamical methodology. We augmented the previous neural energy calculation method, and applied it to our VTA-NAc-mPFC neurodynamical H-H models. We particularly focused on the peak power and energy consumption of abnormal ion channel (ionic) currents under different concentrations of dopamine input, and investigated the abnormal energy consumption patterns for the MDD group. The results revealed that the energy consumption of medium spiny neurons (MSNs) in the NAc region were lower in the MDD group than that of the normal control group despite having the same firing frequencies, peak action potentials, and average membrane potentials in both groups. Dopamine concentration was also positively correlated with the energy consumption of the pyramidal neurons, but the patterns of different interneuron types were distinct. Additionally, the ratio of mPFC's energy consumption to total energy consumption of the whole network in MDD group was lower than that in normal control group, revealing that the mPFC region in MDD group encoded less neural information, which matched the energy consumption patterns of BOLD-fMRI results. It was also in line with the behavioral characteristics that MDD patients demonstrated in the form of reward insensitivity during decision-making tasks. In conclusion, the model in this paper was the first neural network energy computational model for MDD, which showed success in explaining its dynamical mechanisms with an energy consumption perspective. To build on this, we demonstrated that energy consumption levels can be used as a potential indicator for MDD, which also showed a promising pipeline to use an energy methodology for studying other neuropsychiatric disorders.
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Affiliation(s)
- Yuanxi Li
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, Shanghai, China; Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA.
| | - Bing Zhang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Zhiqiang Liu
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China; Anesthesia and Brain Function Research Institute, Tongji University School of Medicine, Shanghai, China.
| | - Rubin Wang
- Institute for Cognitive Neurodynamics, School of Mathematics, East China University of Science and Technology, Shanghai, China.
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Kagan BJ, Gyngell C, Lysaght T, Cole VM, Sawai T, Savulescu J. The technology, opportunities, and challenges of Synthetic Biological Intelligence. Biotechnol Adv 2023; 68:108233. [PMID: 37558186 PMCID: PMC7615149 DOI: 10.1016/j.biotechadv.2023.108233] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/15/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
Integrating neural cultures developed through synthetic biology methods with digital computing has enabled the early development of Synthetic Biological Intelligence (SBI). Recently, key studies have emphasized the advantages of biological neural systems in some information processing tasks. However, neither the technology behind this early development, nor the potential ethical opportunities or challenges, have been explored in detail yet. Here, we review the key aspects that facilitate the development of SBI and explore potential applications. Considering these foreseeable use cases, various ethical implications are proposed. Ultimately, this work aims to provide a robust framework to structure ethical considerations to ensure that SBI technology can be both researched and applied responsibly.
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Affiliation(s)
| | - Christopher Gyngell
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Tamra Lysaght
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Victor M Cole
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tsutomu Sawai
- Graduate School of Humanities and Social Sciences, Hiroshima University, Hiroshima, Japan; Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
| | - Julian Savulescu
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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33
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Maugoust J, Orliac MJ. Anatomical correlates and nomenclature of the chiropteran endocranial cast. Anat Rec (Hoboken) 2023; 306:2791-2829. [PMID: 37018745 DOI: 10.1002/ar.25206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 04/07/2023]
Abstract
Bats form a diverse group of mammals that are highly specialized in active flight and ultrasound echolocation. These specializations rely on adaptations that reflect on their morphoanatomy and have been tentatively linked to brain morphology and volumetry. Despite their small size and fragility, bat crania and natural braincase casts ("endocasts") have been preserved in the fossil record, which allows for investigating brain evolution and inferring paleobiology. Advances in imaging techniques have allowed virtual extraction of internal structures, assuming that the shape of the endocast reflects soft organ morphology. However, there is no direct correspondence between the endocast and internal structures because meninges and vascular tissues mark the inner braincase together with the brain they surround, resulting in a mosaic morphology of the endocast. The hypothesis suggesting that the endocast reflects the brain in terms of both external shape and volume has drastic implications when addressing brain evolution, but it has been rarely discussed. To date, only a single study addressed the correspondence between the brain and braincase in bats. Taking advantage of the advent of imaging techniques, we reviewed the anatomical, neuroanatomical, and angiological literature and compare this knowledge available on bat's braincase anatomy with anatomical observations using a sample of endocranial casts representing most modern bat families. Such comparison allows to propose a Chiroptera-scale nomenclature for future descriptions and comparisons among bat endocasts. Describing the imprints of the tissues surrounding the brain also allows to address to what extent brain features can be blurred or hidden (e.g., hypophysis, epiphysis, colliculi, flocculus). Furthermore, this approach encourages further study to formally test the proposed hypotheses.
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Affiliation(s)
- Jacob Maugoust
- Institut des Sciences de l'Evolution de Montpellier, département CHANGE, équipe Paléontologie, UMR 5554 Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, Montpellier Cedex 5, 34095, France
| | - Maeva Judith Orliac
- Institut des Sciences de l'Evolution de Montpellier, département CHANGE, équipe Paléontologie, UMR 5554 Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, Montpellier Cedex 5, 34095, France
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Zaongo SD, Harypursat V, Rashid F, Dahourou DL, Ouedraogo AS, Chen Y. Influence of HIV infection on cognition and overall intelligence in HIV-infected individuals: advances and perspectives. Front Behav Neurosci 2023; 17:1261784. [PMID: 37953826 PMCID: PMC10637382 DOI: 10.3389/fnbeh.2023.1261784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023] Open
Abstract
It is now well understood that HIV-positive individuals, even those under effective ART, tend to develop a spectrum of cognitive, motor, and/or mood conditions which are contemporarily referred to as HIV-associated neurocognitive disorder (HAND), and which is directly related to HIV-1 infection and HIV-1 replication in the central nervous system (CNS). As HAND is known to induce difficulties associated with attention, concentration, and memory, it is thus legitimate and pertinent to speculate upon the possibility that HIV infection may well influence human cognition and intelligence. We therefore propose herein to review the concept of intelligence, the concept of cells of intelligence, the influence of HIV on these particular cells, and the evidence pointing to differences in observed intelligence quotient (IQ) scores between HIV-positive and HIV-negative individuals. Additionally, cumulative research evidence continues to draw attention to the influence of the gut on human intelligence. Up to now, although it is known that HIV infection profoundly alters both the composition and diversity of the gut microbiota and the structural integrity of the gut, the influence of the gut on intelligence in the context of HIV infection remains poorly described. As such, we also provide herein a review of the different ways in which HIV may influence human intelligence via the gut-brain axis. Finally, we provide a discourse on perspectives related to HIV and human intelligence which may assist in generating more robust evidence with respect to this issue in future studies. Our aim is to provide insightful knowledge for the identification of novel areas of investigation, in order to reveal and explain some of the enigmas related to HIV infection.
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Affiliation(s)
- Silvere D. Zaongo
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Vijay Harypursat
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Farooq Rashid
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Désiré Lucien Dahourou
- Département Biomédical/Santé Publique, Institut de Recherche en Sciences de la Santé/CNRST, Ouagadougou, Burkina Faso
| | - Abdoul-Salam Ouedraogo
- Centre Muraz, Bobo-Dioulasso, Burkina Faso
- Department of Bacteriology and Virology, Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | - Yaokai Chen
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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Gentile F. The effective enhancement of information in 3D small-world networks of biological neuronal cells. Biomed Phys Eng Express 2023; 9:065019. [PMID: 37802049 DOI: 10.1088/2057-1976/ad00c0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/06/2023] [Indexed: 10/08/2023]
Abstract
The cardiovascular system, the kidney, or the brain, are examples of complex systems - where the properties of the systems arise because of the layout of cells in those systems. One way to characterize systems is using networks, where elements and interactions of the systems are represented as nodes and links of a graph. Network's topology can be, in turn, measured by the small-world coefficient. Small world networks feature increased clustering and shorter paths compared to random or periodic networks of the same size. This suggests that systems with small world attributes can also efficiently transport signals, nutrients, or information within their body. While several reports in literature have illustrated that real biological systems are small-world, yet little is known about how information varies as a function of the small-world-ness (sw) of three dimensional graphs. Here, we used a model of the brain to estimate quantitatively the information processed in 3D networks. In the model, nodes of the graph are neuronal units capable to receive, integrate and transmit signals to other neurons of the system in parallel. The information encoded in the signals was then extracted using the techniques of information theory. In simulations where the topology of networks of400nodes was varied over large intervals, we found that in the0-9swrange information scales linearly with the small world coefficient, with a five-fold increase. Results of the paper and review of the existing literature on model organisms suggest that a small-world architecture may offer an evolutionary advantage to biological systems.
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Affiliation(s)
- F Gentile
- Nanotechnology Research Center, Department of Experimental and Clinical Medicine, University of Magna Graecia, 88100 Catanzaro, Italy
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Gentili PL, Stano P. Tracing a new path in the field of AI and robotics: mimicking human intelligence through chemistry. Part II: systems chemistry. Front Robot AI 2023; 10:1266011. [PMID: 37915426 PMCID: PMC10616823 DOI: 10.3389/frobt.2023.1266011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023] Open
Abstract
Inspired by some traits of human intelligence, it is proposed that wetware approaches based on molecular, supramolecular, and systems chemistry can provide valuable models and tools for novel forms of robotics and AI, being constituted by soft matter and fluid states as the human nervous system and, more generally, life, is. Bottom-up mimicries of intelligence range from the molecular world to the multicellular level, i.e., from the Ångström (10 - 10 meters) to the micrometer scales (10 - 6 meters), and allows the development of unconventional chemical robotics. Whereas conventional robotics lets humans explore and colonise otherwise inaccessible environments, such as the deep oceanic abysses and other solar system planets, chemical robots will permit us to inspect and control the microscopic molecular and cellular worlds. This article suggests that systems made of properly chosen molecular compounds can implement all those modules that are the fundamental ingredients of every living being: sensory, processing, actuating, and metabolic networks. Autonomous chemical robotics will be within reach when such modules are compartmentalised and assembled. The design of a strongly intertwined web of chemical robots, with or without the involvement of living matter, will give rise to collective forms of intelligence that will probably reproduce, on a minimal scale, some sophisticated performances of the human intellect and will implement forms of "general AI." These remarkable achievements will require a productive interdisciplinary collaboration among chemists, biotechnologists, computer scientists, engineers, physicists, neuroscientists, cognitive scientists, and philosophers to be achieved. The principal purpose of this paper is to spark this revolutionary collaborative scientific endeavour.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, Università degli Studi di Perugia, Perugia, Italy
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DISTeBA), University of Salento, Lecce, Italy
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37
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Bao B, Sun Y, Lin J, Gao T, Shen J, Hu W, Zhu H, Zhu T, Li J, Wang Z, Wei H, Zheng X. Altered cortical thickness and structural covariance networks in upper limb amputees: A graph theoretical analysis. CNS Neurosci Ther 2023; 29:2901-2911. [PMID: 37122148 PMCID: PMC10493660 DOI: 10.1111/cns.14226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 04/03/2023] [Accepted: 04/09/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND The extensive functional and structural remodeling that occurs in the brain after amputation often results in phantom limb pain (PLP). These closely related phenomena are still not fully understood. METHODS Using magnetic resonance imaging (MRI) and graph theoretical analysis (GTA), we explored how alterations in brain cortical thickness (CTh) and structural covariance networks (SCNs) in upper limb amputees (ULAs) relate to PLP. In all, 45 ULAs and 45 healthy controls (HCs) underwent structural MRI. Regional network properties, including nodal degree, betweenness centrality (BC), and node efficiency, were analyzed with GTA. Similarly, global network properties, including global efficiency (Eglob), local efficiency (Eloc), clustering coefficient (Cp), characteristic path length (Lp), and the small-worldness index, were evaluated. RESULTS Compared with HCs, ULAs had reduced CThs in the postcentral and precentral gyri contralateral to the amputated limb; this decrease in CTh was negatively correlated with PLP intensity in ULAs. ULAs showed varying degrees of change in node efficiency in regional network properties compared to HCs (p < 0.005). There were no group differences in Eglob, Eloc, Cp, and Lp properties (all p > 0.05). The real-worldness SCN of ULAs showed a small-world topology ranging from 2% to 34%, and the area under the curve of the small-worldness index in ULAs was significantly different compared to HCs (p < 0.001). CONCLUSION These results suggest that the topological organization of human CNS functional networks is altered after amputation of the upper limb, providing further support for the cortical remapping theory of PLP.
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Affiliation(s)
- Bingbo Bao
- Department of Orthopedic SurgeryShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Yi Sun
- Department of Orthopedic SurgeryShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Junqing Lin
- Department of Orthopedic SurgeryShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Tao Gao
- Department of Orthopedic SurgeryShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Junjie Shen
- Department of Orthopedic SurgeryShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Wencheng Hu
- Department of Orthopedic SurgeryShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Hongyi Zhu
- Department of Orthopedic SurgeryShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Tianhao Zhu
- Department of Orthopedic SurgeryShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Jing Li
- Institute of Diagnostic and Interventional RadiologyShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Zhibin Wang
- Institute of Diagnostic and Interventional RadiologyShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Haifeng Wei
- Department of Orthopedic SurgeryShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Xianyou Zheng
- Department of Orthopedic SurgeryShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
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Kim E, Carreira Figueiredo I, Simmons C, Randall K, Rojo Gonzalez L, Wood T, Ranieri B, Sureda-Gibert P, Howes O, Pariante C, Nima Consortium, Pasternak O, Dell'Acqua F, Turkheimer F, Cash D. Mapping acute neuroinflammation in vivo with diffusion-MRI in rats given a systemic lipopolysaccharide challenge. Brain Behav Immun 2023; 113:289-301. [PMID: 37482203 DOI: 10.1016/j.bbi.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/19/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023] Open
Abstract
It is becoming increasingly apparent that neuroinflammation plays a critical role in an array of neurological and psychiatric disorders. Recent studies have demonstrated the potential of diffusion MRI (dMRI) to characterize changes in microglial density and morphology associated with neuroinflammation, but these were conducted mostly ex vivo and/or in extreme, non-physiological animal models. Here, we build upon these studies by investigating the utility of well-established dMRI methods to detect neuroinflammation in vivo in a more clinically relevant animal model of sickness behavior. We show that diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI) indicate widespread increases in diffusivity in the brains of rats given a systemic lipopolysaccharide challenge (n = 20) vs. vehicle-treated controls (n = 12). These diffusivity changes correlated with histologically measured changes in microglial morphology, confirming the sensitivity of dMRI to neuroinflammatory processes. This study marks a further step towards establishing a noninvasive indicator of neuroinflammation, which would greatly facilitate early diagnosis and treatment monitoring in various neurological and psychiatric diseases.
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Affiliation(s)
- Eugene Kim
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom.
| | - Ines Carreira Figueiredo
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom.
| | - Camilla Simmons
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Karen Randall
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Loreto Rojo Gonzalez
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Tobias Wood
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom.
| | - Brigida Ranieri
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Paula Sureda-Gibert
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom.
| | - Oliver Howes
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Carmine Pariante
- Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom.
| | - Nima Consortium
- The Wellcome Trust Consortium for the Neuroimmunology of Mood Disorders and Alzheimer's Disease (NIMA), United Kingdom
| | - Ofer Pasternak
- Departments of Psychiatry and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Flavio Dell'Acqua
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom.
| | - Federico Turkheimer
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom.
| | - Diana Cash
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom.
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Geerts H, Bergeler S, Walker M, van der Graaf PH, Courade JP. Analysis of clinical failure of anti-tau and anti-synuclein antibodies in neurodegeneration using a quantitative systems pharmacology model. Sci Rep 2023; 13:14342. [PMID: 37658103 PMCID: PMC10474108 DOI: 10.1038/s41598-023-41382-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/25/2023] [Indexed: 09/03/2023] Open
Abstract
Misfolded proteins in Alzheimer's disease and Parkinson's disease follow a well-defined connectomics-based spatial progression. Several anti-tau and anti-alpha synuclein (aSyn) antibodies have failed to provide clinical benefit in clinical trials despite substantial target engagement in the experimentally accessible cerebrospinal fluid (CSF). The proposed mechanism of action is reducing neuronal uptake of oligomeric protein from the synaptic cleft. We built a quantitative systems pharmacology (QSP) model to quantitatively simulate intrasynaptic secretion, diffusion and antibody capture in the synaptic cleft, postsynaptic membrane binding and internalization of monomeric and oligomeric tau and aSyn proteins. Integration with a physiologically based pharmacokinetic (PBPK) model allowed us to simulate clinical trials of anti-tau antibodies gosuranemab, tilavonemab, semorinemab, and anti-aSyn antibodies cinpanemab and prasineuzumab. Maximal target engagement for monomeric tau was simulated as 45% (semorinemab) to 99% (gosuranemab) in CSF, 30% to 99% in ISF but only 1% to 3% in the synaptic cleft, leading to a reduction of less than 1% in uptake of oligomeric tau. Simulations for prasineuzumab and cinpanemab suggest target engagement of free monomeric aSyn of only 6-8% in CSF, 4-6% and 1-2% in the ISF and synaptic cleft, while maximal target engagement of aggregated aSyn was predicted to reach 99% and 80% in the synaptic cleft with similar effects on neuronal uptake. The study generates optimal values of selectivity, sensitivity and PK profiles for antibodies. The study identifies a gradient of decreasing target engagement from CSF to the synaptic cleft as a key driver of efficacy, quantitatively identifies various improvements for drug design and emphasizes the need for QSP modelling to support the development of tau and aSyn antibodies.
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Affiliation(s)
- Hugo Geerts
- Certara US, 100 Overlook Centre, Suite 101, Princeton, NJ, 08540, USA.
| | - Silke Bergeler
- Certara US, 100 Overlook Centre, Suite 101, Princeton, NJ, 08540, USA
- Bristol-Meyers-Squibb, Lawrenceville, NJ, 08648, USA
| | - Mike Walker
- Certara UK, Canterbury Innovation Centre, University Road, Canterbury, CT2 7FG, Kent, UK
| | - Piet H van der Graaf
- Certara UK, Canterbury Innovation Centre, University Road, Canterbury, CT2 7FG, Kent, UK
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40
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Li Z, Zhou J, Wani KA, Yu T, Ronan EA, Piggott BJ, Liu J, Xu XS. A C. elegans neuron both promotes and suppresses motor behavior to fine tune motor output. Front Mol Neurosci 2023; 16:1228980. [PMID: 37680582 PMCID: PMC10482346 DOI: 10.3389/fnmol.2023.1228980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/31/2023] [Indexed: 09/09/2023] Open
Abstract
How neural circuits drive behavior is a central question in neuroscience. Proper execution of motor behavior requires precise coordination of many neurons. Within a motor circuit, individual neurons tend to play discrete roles by promoting or suppressing motor output. How exactly neurons function in specific roles to fine tune motor output is not well understood. In C. elegans, the interneuron RIM plays important yet complex roles in locomotion behavior. Here, we show that RIM both promotes and suppresses distinct features of locomotion behavior to fine tune motor output. This dual function is achieved via the excitation and inhibition of the same motor circuit by electrical and chemical neurotransmission, respectively. Additionally, this bi-directional regulation contributes to motor adaptation in animals placed in novel environments. Our findings reveal that individual neurons within a neural circuit may act in opposing ways to regulate circuit dynamics to fine tune behavioral output.
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Affiliation(s)
- Zhaoyu Li
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Jiejun Zhou
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
- College of Life Science and Technology, Key laboratory of Molecular Biophysics of MOE, International Research Center for Sensory Biology and Technology of MOST, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Khursheed A. Wani
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
| | - Teng Yu
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
- College of Life Science and Technology, Key laboratory of Molecular Biophysics of MOE, International Research Center for Sensory Biology and Technology of MOST, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Elizabeth A. Ronan
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Beverly J. Piggott
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Jianfeng Liu
- College of Life Science and Technology, Key laboratory of Molecular Biophysics of MOE, International Research Center for Sensory Biology and Technology of MOST, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - X.Z. Shawn Xu
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
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41
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Wu X, Li Z, Wang ZQ, Xu X. The neurological and non-neurological roles of the primary microcephaly-associated protein ASPM. Front Neurosci 2023; 17:1242448. [PMID: 37599996 PMCID: PMC10436222 DOI: 10.3389/fnins.2023.1242448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
Primary microcephaly (MCPH), is a neurological disorder characterized by small brain size that results in numerous developmental problems, including intellectual disability, motor and speech delays, and seizures. Hitherto, over 30 MCPH causing genes (MCPHs) have been identified. Among these MCPHs, MCPH5, which encodes abnormal spindle-like microcephaly-associated protein (ASPM), is the most frequently mutated gene. ASPM regulates mitotic events, cell proliferation, replication stress response, DNA repair, and tumorigenesis. Moreover, using a data mining approach, we have confirmed that high levels of expression of ASPM correlate with poor prognosis in several types of tumors. Here, we summarize the neurological and non-neurological functions of ASPM and provide insight into its implications for the diagnosis and treatment of MCPH and cancer.
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Affiliation(s)
- Xingxuan Wu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Zheng Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Zhao-Qi Wang
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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Gkotsoulias DG, Müller R, Jäger C, Schlumm T, Mildner T, Eichner C, Pampel A, Jaffe J, Gräßle T, Alsleben N, Chen J, Crockford C, Wittig R, Liu C, Möller HE. High angular resolution susceptibility imaging and estimation of fiber orientation distribution functions in primate brain. Neuroimage 2023; 276:120202. [PMID: 37247762 DOI: 10.1016/j.neuroimage.2023.120202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/21/2023] [Accepted: 05/27/2023] [Indexed: 05/31/2023] Open
Abstract
Uncovering brain-tissue microstructure including axonal characteristics is a major neuroimaging research focus. Within this scope, anisotropic properties of magnetic susceptibility in white matter have been successfully employed to estimate primary axonal trajectories using mono-tensorial models. However, anisotropic susceptibility has not yet been considered for modeling more complex fiber structures within a voxel, such as intersecting bundles, or an estimation of orientation distribution functions (ODFs). This information is routinely obtained by high angular resolution diffusion imaging (HARDI) techniques. In applications to fixed tissue, however, diffusion-weighted imaging suffers from an inherently low signal-to-noise ratio and limited spatial resolution, leading to high demands on the performance of the gradient system in order to mitigate these limitations. In the current work, high angular resolution susceptibility imaging (HARSI) is proposed as a novel, phase-based methodology to estimate ODFs. A multiple gradient-echo dataset was acquired in an entire fixed chimpanzee brain at 61 orientations by reorienting the specimen in the magnetic field. The constant solid angle method was adapted for estimating phase-based ODFs. HARDI data were also acquired for comparison. HARSI yielded information on whole-brain fiber architecture, including identification of peaks of multiple bundles that resembled features of the HARDI results. Distinct differences between both methods suggest that susceptibility properties may offer complementary microstructural information. These proof-of-concept results indicate a potential to study the axonal organization in post-mortem primate and human brain at high resolution.
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Affiliation(s)
- Dimitrios G Gkotsoulias
- Nuclear Magnetic Resonance Methods & Development Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
| | - Roland Müller
- Nuclear Magnetic Resonance Methods & Development Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Carsten Jäger
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Torsten Schlumm
- Nuclear Magnetic Resonance Methods & Development Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Toralf Mildner
- Nuclear Magnetic Resonance Methods & Development Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Cornelius Eichner
- Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - André Pampel
- Nuclear Magnetic Resonance Methods & Development Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Jennifer Jaffe
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Côte d'Ivoire
| | - Tobias Gräßle
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Côte d'Ivoire; Helmholtz Institute for One Health, Greifswald, Germany; Robert Koch Institute, Epidemiology of Highly Pathogenic Microorganisms, Berlin, Germany
| | - Niklas Alsleben
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Jingjia Chen
- Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Catherine Crockford
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Côte d'Ivoire; Institute of Cognitive Sciences, CNRS UMR5229 University of Lyon, Bron, France
| | - Roman Wittig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Côte d'Ivoire; Institute of Cognitive Sciences, CNRS UMR5229 University of Lyon, Bron, France
| | - Chunlei Liu
- Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
| | - Harald E Möller
- Nuclear Magnetic Resonance Methods & Development Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
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43
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Wahlster W. Understanding computational dialogue understanding. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2023; 381:20220049. [PMID: 37271176 DOI: 10.1098/rsta.2022.0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/20/2023] [Indexed: 06/06/2023]
Abstract
In this paper, we first explain why human-like dialogue understanding is so difficult for artificial intelligence (AI). We discuss various methods for testing the understanding capabilities of dialogue systems. Our review of the development of dialogue systems over five decades focuses on the transition from closed-domain to open-domain systems and their extension to multi-modal, multi-party and multi-lingual dialogues. From being somewhat of a niche topic of AI research for the first 40 years, it has made newspaper headlines in recent years and is now being discussed by political leaders at events such as the World Economic Forum in Davos. We ask whether large language models are super-parrots or a milestone towards human-like dialogue understanding and how they relate to what we know about language processing in the human brain. Using ChatGPT as an example, we present some limitations of this approach to dialogue systems. Finally, we present some lessons learned from our 40 years of research in this field about system architecture principles: symmetric multi-modality, no presentation without representation and anticipation feedback loops. We conclude with a discussion of grand challenges such as satisfying conversational maxims and the European Language Equality Act through massive digital multi-linguality-perhaps enabled by interactive machine learning with human trainers. This article is part of a discussion meeting issue 'Cognitive artificial intelligence'.
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Affiliation(s)
- Wolfgang Wahlster
- German Research Center for Artificial Intelligence (DFKI), Alt-Moabit 91c, D-10559 Berlin, Germany
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44
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Barron AB, Mourmourakis F. The Relationship between Cognition and Brain Size or Neuron Number. BRAIN, BEHAVIOR AND EVOLUTION 2023; 99:109-122. [PMID: 37487478 DOI: 10.1159/000532013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]
Abstract
The comparative approach is a powerful way to explore the relationship between brain structure and cognitive function. Thus far, the field has been dominated by the assumption that a bigger brain somehow means better cognition. Correlations between differences in brain size or neuron number between species and differences in specific cognitive abilities exist, but these correlations are very noisy. Extreme differences exist between clades in the relationship between either brain size or neuron number and specific cognitive abilities. This means that correlations become weaker, not stronger, as the taxonomic diversity of sampled groups increases. Cognition is the outcome of neural networks. Here we propose that considering plausible neural network models will advance our understanding of the complex relationships between neuron number and different aspects of cognition. Computational modelling of networks suggests that adding pathways, or layers, or changing patterns of connectivity in a network can all have different specific consequences for cognition. Consequently, models of computational architecture can help us hypothesise how and why differences in neuron number might be related to differences in cognition. As methods in connectomics continue to improve and more structural information on animal brains becomes available, we are learning more about natural network structures in brains, and we can develop more biologically plausible models of cognitive architecture. Natural animal diversity then becomes a powerful resource to both test the assumptions of these models and explore hypotheses for how neural network structure and network size might delimit cognitive function.
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Affiliation(s)
- Andrew B Barron
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Faelan Mourmourakis
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
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45
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Driessens SLW, Galakhova AA, Heyer DB, Pieterse IJ, Wilbers R, Mertens EJ, Waleboer F, Heistek TS, Coenen L, Meijer JR, Idema S, de Witt Hamer PC, Noske DP, de Kock CPJ, Lee BR, Smith K, Ting JT, Lein ES, Mansvelder HD, Goriounova NA. Genes associated with cognitive ability and HAR show overlapping expression patterns in human cortical neuron types. Nat Commun 2023; 14:4188. [PMID: 37443107 PMCID: PMC10345092 DOI: 10.1038/s41467-023-39946-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
GWAS have identified numerous genes associated with human cognition but their cell type expression profiles in the human brain are unknown. These genes overlap with human accelerated regions (HARs) implicated in human brain evolution and might act on the same biological processes. Here, we investigated whether these gene sets are expressed in adult human cortical neurons, and how their expression relates to neuronal function and structure. We find that these gene sets are preferentially expressed in L3 pyramidal neurons in middle temporal gyrus (MTG). Furthermore, neurons with higher expression had larger total dendritic length (TDL) and faster action potential (AP) kinetics, properties previously linked to intelligence. We identify a subset of genes associated with TDL or AP kinetics with predominantly synaptic functions and high abundance of HARs.
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Affiliation(s)
- Stan L W Driessens
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Djai B Heyer
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Isabel J Pieterse
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - René Wilbers
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Eline J Mertens
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Femke Waleboer
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Tim S Heistek
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Loet Coenen
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Julia R Meijer
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Sander Idema
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081HV, Amsterdam, the Netherlands
| | - Philip C de Witt Hamer
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081HV, Amsterdam, the Netherlands
| | - David P Noske
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081HV, Amsterdam, the Netherlands
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Brian R Lee
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Kimberly Smith
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Ed S Lein
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA, 98109, USA
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands.
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46
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Shabani K, Pigeon J, Benaissa Touil Zariouh M, Liu T, Saffarian A, Komatsu J, Liu E, Danda N, Becmeur-Lefebvre M, Limame R, Bohl D, Parras C, Hassan BA. The temporal balance between self-renewal and differentiation of human neural stem cells requires the amyloid precursor protein. SCIENCE ADVANCES 2023; 9:eadd5002. [PMID: 37327344 PMCID: PMC10275593 DOI: 10.1126/sciadv.add5002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/11/2023] [Indexed: 06/18/2023]
Abstract
Neurogenesis in the developing human cerebral cortex occurs at a particularly slow rate owing in part to cortical neural progenitors preserving their progenitor state for a relatively long time, while generating neurons. How this balance between the progenitor and neurogenic state is regulated, and whether it contributes to species-specific brain temporal patterning, is poorly understood. Here, we show that the characteristic potential of human neural progenitor cells (NPCs) to remain in a progenitor state as they generate neurons for a prolonged amount of time requires the amyloid precursor protein (APP). In contrast, APP is dispensable in mouse NPCs, which undergo neurogenesis at a much faster rate. Mechanistically, APP cell-autonomously contributes to protracted neurogenesis through suppression of the proneurogenic activator protein-1 transcription factor and facilitation of canonical WNT signaling. We propose that the fine balance between self-renewal and differentiation is homeostatically regulated by APP, which may contribute to human-specific temporal patterns of neurogenesis.
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Affiliation(s)
- Khadijeh Shabani
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Julien Pigeon
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Marwan Benaissa Touil Zariouh
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Tengyuan Liu
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Azadeh Saffarian
- Scipio bioscience, iPEPS-ICM, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jun Komatsu
- Scipio bioscience, iPEPS-ICM, Hôpital Pitié-Salpêtrière, Paris, France
| | - Elise Liu
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Natasha Danda
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Mathilde Becmeur-Lefebvre
- Genetics and Foetopathology, Centre Hospitalier Regional d’Orleans–Hôpital de la Source, Orleans, France
| | - Ridha Limame
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Delphine Bohl
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Carlos Parras
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Bassem A. Hassan
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
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47
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Zeng B, Liu Z, Lu Y, Zhong S, Qin S, Huang L, Zeng Y, Li Z, Dong H, Shi Y, Yang J, Dai Y, Ma Q, Sun L, Bian L, Han D, Chen Y, Qiu X, Wang W, Marín O, Wu Q, Wang Y, Wang X. The single-cell and spatial transcriptional landscape of human gastrulation and early brain development. Cell Stem Cell 2023; 30:851-866.e7. [PMID: 37192616 PMCID: PMC10241223 DOI: 10.1016/j.stem.2023.04.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 05/18/2023]
Abstract
The emergence of the three germ layers and the lineage-specific precursor cells orchestrating organogenesis represent fundamental milestones during early embryonic development. We analyzed the transcriptional profiles of over 400,000 cells from 14 human samples collected from post-conceptional weeks (PCW) 3 to 12 to delineate the dynamic molecular and cellular landscape of early gastrulation and nervous system development. We described the diversification of cell types, the spatial patterning of neural tube cells, and the signaling pathways likely involved in transforming epiblast cells into neuroepithelial cells and then into radial glia. We resolved 24 clusters of radial glial cells along the neural tube and outlined differentiation trajectories for the main classes of neurons. Lastly, we identified conserved and distinctive features across species by comparing early embryonic single-cell transcriptomic profiles between humans and mice. This comprehensive atlas sheds light on the molecular mechanisms underlying gastrulation and early human brain development.
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Affiliation(s)
- Bo Zeng
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China; Changping Laboratory, Beijing 102206, China
| | - Zeyuan Liu
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China; Changping Laboratory, Beijing 102206, China
| | - Yufeng Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Suijuan Zhong
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China; Changping Laboratory, Beijing 102206, China
| | - Shenyue Qin
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Luwei Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Zeng
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Zixiao Li
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China; Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing 100069, China
| | - Hao Dong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingchao Shi
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Guangdong Institute of Intelligence Science and Technology, Guangdong 519031, China
| | - Jialei Yang
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China; Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Yalun Dai
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China; Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Qiang Ma
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Le Sun
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing 100069, China
| | - Lihong Bian
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Dan Han
- Department of Obstetrics & Gynecology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Youqiao Chen
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
| | - Xin Qiu
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China; Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Wei Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK.
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China; Changping Laboratory, Beijing 102206, China.
| | - Yongjun Wang
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China; Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing 100069, China.
| | - Xiaoqun Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China; State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute of Brain Disorders, Capital Medical University, Beijing 100069, China; Guangdong Institute of Intelligence Science and Technology, Guangdong 519031, China; Changping Laboratory, Beijing 102206, China; New Cornerstone Science Laboratory, Beijing Normal University, Beijing 100875, China.
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48
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Maksimovic K, Youssef M, You J, Sung HK, Park J. Evidence of Metabolic Dysfunction in Amyotrophic Lateral Sclerosis (ALS) Patients and Animal Models. Biomolecules 2023; 13:biom13050863. [PMID: 37238732 DOI: 10.3390/biom13050863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that affects motor neurons, leading to muscle weakness, paralysis, and eventual death. Research from the past few decades has appreciated that ALS is not only a disease of the motor neurons but also a disease that involves systemic metabolic dysfunction. This review will examine the foundational research of understanding metabolic dysfunction in ALS and provide an overview of past and current studies in ALS patients and animal models, spanning from full systems to various metabolic organs. While ALS-affected muscle tissue exhibits elevated energy demand and a fuel preference switch from glycolysis to fatty acid oxidation, adipose tissue in ALS undergoes increased lipolysis. Dysfunctions in the liver and pancreas contribute to impaired glucose homeostasis and insulin secretion. The central nervous system (CNS) displays abnormal glucose regulation, mitochondrial dysfunction, and increased oxidative stress. Importantly, the hypothalamus, a brain region that controls whole-body metabolism, undergoes atrophy associated with pathological aggregates of TDP-43. This review will also cover past and present treatment options that target metabolic dysfunction in ALS and provide insights into the future of metabolism research in ALS.
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Affiliation(s)
- Katarina Maksimovic
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mohieldin Youssef
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Justin You
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Hoon-Ki Sung
- Translational Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeehye Park
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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49
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Hadiyal K, Ganesan R, Rastogi A, Thamankar R. Bio-inspired artificial synapse for neuromorphic computing based on NiO nanoparticle thin film. Sci Rep 2023; 13:7481. [PMID: 37160948 PMCID: PMC10169867 DOI: 10.1038/s41598-023-33752-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023] Open
Abstract
The unprecedented need for data processing in the modern technological era has created opportunities in neuromorphic devices and computation. This is primarily due to the extensive parallel processing done in our human brain. Data processing and logical decision-making at the same physical location are an exciting aspect of neuromorphic computation. For this, establishing reliable resistive switching devices working at room temperature with ease of fabrication is important. Here, a reliable analog resistive switching device based on Au/NiO nanoparticles/Au is discussed. The application of positive and negative voltage pulses of constant amplitude results in enhancement and reduction of synaptic current, which is consistent with potentiation and depression, respectively. The change in the conductance resulting in such a process can be fitted well with double exponential growth and decay, respectively. Consistent potentiation and depression characteristics reveal that non-ideal voltage pulses can result in a linear dependence of potentiation and depression. Long-term potentiation (LTP) and Long-term depression (LTD) characteristics have been established, which are essential for mimicking the biological synaptic applications. The NiO nanoparticle-based devices can also be used for controlled synaptic enhancement by optimizing the electric pulses, displaying typical learning-forgetting-relearning characteristics.
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Affiliation(s)
- Keval Hadiyal
- Centre for Functional Materials, Vellore Institute of Technology, Vellore, TN, 632014, India
- Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Ramakrishnan Ganesan
- Department of Chemistry, Birla Institute of Technology and Science (BITS), Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India
| | - A Rastogi
- Centre for Functional Materials, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - R Thamankar
- Centre for Functional Materials, Vellore Institute of Technology, Vellore, TN, 632014, India.
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50
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Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 PMCID: PMC10322212 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/23/2023] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
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Affiliation(s)
- Irene M. Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J. Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E. Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H. Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E. Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N. Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R. Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P. Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Elinor K. Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K. Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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