Cortical model with reinforcement learning drives realistic virtual arm (Dura-Bernal et al 2015)

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Accession:183014
We developed a 3-layer sensorimotor cortical network of consisting of 704 spiking model-neurons, including excitatory, fast-spiking and low-threshold spiking interneurons. Neurons were interconnected with AMPA/NMDA, and GABAA synapses. We trained our model using spike-timing-dependent reinforcement learning to control a virtual musculoskeletal human arm, with realistic anatomical and biomechanical properties, to reach a target. Virtual arm position was used to simultaneously control a robot arm via a network interface.
References:
1 . Dura-Bernal S, Zhou X, Neymotin SA, Przekwas A, Francis JT, Lytton WW (2015) Cortical Spiking Network Interfaced with Virtual Musculoskeletal Arm and Robotic Arm. Front Neurorobot 9:13 [PubMed]
2 . Dura-Bernal S, Li K, Neymotin SA, Francis JT, Principe JC, Lytton WW (2016) Restoring Behavior via Inverse Neurocontroller in a Lesioned Cortical Spiking Model Driving a Virtual Arm. Front Neurosci 10:28 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Neocortex M1 L5B pyramidal pyramidal tract GLU cell; Neocortex M1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex M1 interneuron basket PV GABA cell; Neocortex fast spiking (FS) interneuron; Neostriatum fast spiking interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON; Python (web link to model);
Model Concept(s): Synaptic Plasticity; Learning; Reinforcement Learning; STDP; Reward-modulated STDP; Sensory processing; Motor control; Touch;
Implementer(s): Neymotin, Sam [Samuel.Neymotin at nki.rfmh.org]; Dura, Salvador [ salvadordura at gmail.com];
Search NeuronDB for information about:  Neocortex M1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex M1 L5B pyramidal pyramidal tract GLU cell; Neocortex M1 interneuron basket PV GABA cell; GabaA; AMPA; NMDA; Gaba; Glutamate;
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									<body>humerus</body>
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									<coordinate>arm_flex</coordinate>
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								<ConditionalPathPoint name="default">
									<location> -0.0126011 0.00810135 -0.0322038</location>
									<body>humerus</body>
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								<ConditionalPathPoint name="default">
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									<body>humerus</body>
									<range> 2.61799 3.2</range>
									<coordinate>arm_flex</coordinate>
								</ConditionalPathPoint>
								<PathPoint name="LAT1-P2">
									<location> -0.08854 -0.06153 0.14488</location>
									<body>thorax</body>
								</PathPoint>
								<PathPoint name="LAT1-P3">
									<location> -0.11939 -0.07953 0.11232</location>
									<body>thorax</body>
								</PathPoint>
								<PathPoint name="LAT1-P4">
									<location> -0.11828 -0.10118 0.03316</location>
									<body>thorax</body>
								</PathPoint>
								<PathPoint name="LAT1-P5">
									<location> -0.09578 -0.11724 0.00882</location>
									<body>thorax</body>
								</PathPoint>
							</objects>
					</PathPointSet>
					</GeometryPath>
					
							<max_isometric_force>2334.6</max_isometric_force>
					
							<optimal_fiber_length>       0.25400000 </optimal_fiber_length>
					
							<tendon_slack_length>       0.12000000 </tendon_slack_length>
					
							<pennation_angle>       0.43633231 </pennation_angle>
				</Schutte1993Muscle>
				<Schutte1993Muscle name="Latissimus_dorsi_2">
					<GeometryPath name="">
					<PathPointSet name="">
							<objects>
								<PathPoint name="LAT2-P1">
									<location> 0.00968 -0.04071 -0.00611</location>
									<body>humerus</body>
								</PathPoint>
								<PathPoint name="Latissimus_dorsi_2-P2">
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									<body>humerus</body>
								</PathPoint>
								<ConditionalPathPoint name="default">
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								<ConditionalPathPoint name="default">
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									<body>humerus</body>
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								<ConditionalPathPoint name="default">
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									<body>humerus</body>
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								<PathPoint name="LAT2-P2">
									<location> -0.0805 -0.06686 0.16486</location>
									<body>thorax</body>
								</PathPoint>
								<PathPoint name="LAT2-P3">
									<location> -0.10517 -0.1267 0.1194</location>
									<body>thorax</body>
								</PathPoint>
								<PathPoint name="LAT2-P4">
									<location> -0.10992 -0.16908 0.02878</location>
									<body>thorax</body>
								</PathPoint>
								<PathPoint name="LAT2-P5">
									<location> -0.07186 -0.18818 0.00815</location>
									<body>thorax</body>
								</PathPoint>
							</objects>
					</PathPointSet>
					</GeometryPath>
					
							<max_isometric_force>2334.6</max_isometric_force>
					
							<optimal_fiber_length>       0.23240000 </optimal_fiber_length>
					
							<tendon_slack_length>       0.17650000 </tendon_slack_length>
					
							<pennation_angle>       0.33161256 </pennation_angle>
				</Schutte1993Muscle>
				<Schutte1993Muscle name="Latissimus_dorsi_3">
					<GeometryPath name="">
					<PathPointSet name="">
							<objects>
								<PathPoint name="LAT3-P1">
									<location> 0.01208 -0.03922 -0.00416</location>
									<body>humerus</body>
								</PathPoint>
								<PathPoint name="Latissimus_dorsi_3-P2">
									<location> 0.00439304 -0.0372487 -0.0152687</location>
									<body>humerus</body>
								</PathPoint>
								<ConditionalPathPoint name="default">
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									<body>humerus</body>
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									<coordinate>arm_flex</coordinate>
								</ConditionalPathPoint>
								<ConditionalPathPoint name="default">
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									<body>humerus</body>
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									<coordinate>arm_flex</coordinate>
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								<ConditionalPathPoint name="default">
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									<body>humerus</body>
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									<coordinate>arm_flex</coordinate>
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								<PathPoint name="LAT3-P2">
									<location> -0.06702 -0.09303 0.1686</location>
									<body>thorax</body>
								</PathPoint>
								<PathPoint name="LAT3-P3">
									<location> -0.08567 -0.14961 0.12246</location>
									<body>thorax</body>
								</PathPoint>
								<PathPoint name="LAT3-P4">
									<location> -0.11157 -0.19387 0.05532</location>
									<body>thorax</body>
								</PathPoint>
								<PathPoint name="LAT3-P5">
									<location> -0.07117 -0.24858 0.00907</location>
									<body>thorax</body>
								</PathPoint>
							</objects>
					</PathPointSet>
					</GeometryPath>
					
							<max_isometric_force>844.98</max_isometric_force>
					
							<optimal_fiber_length>       0.27890000 </optimal_fiber_length>
					
							<tendon_slack_length>       0.14030000 </tendon_slack_length>
					
							<pennation_angle>       0.36651914 </pennation_angle>
				</Schutte1993Muscle>
				<Schutte1993Muscle name="Coracobrachialis">
					<GeometryPath name="">
					<PathPointSet name="">
					<objects>
						<PathPoint name="CORB-P1">
							<location>       0.01250000      -0.04127000      -0.02652000 </location>
							<body> scapula </body>
						</PathPoint>
						<PathPoint name="CORB-P2">
							<location>       0.00483000      -0.06958000      -0.01563000 </location>
							<body> scapula </body>
						</PathPoint>
						<PathPoint name="CORB-P3">
							<location>       0.00743000      -0.15048000      -0.00782000 </location>
							<body> humerus </body>
						</PathPoint>
					</objects>
					</PathPointSet>
					</GeometryPath>
					
							<max_isometric_force>727.38</max_isometric_force>
					
							<optimal_fiber_length>       0.09320000 </optimal_fiber_length>
					
							<tendon_slack_length>       0.09700000 </tendon_slack_length>
					
							<pennation_angle>       0.00000000 </pennation_angle>
				</Schutte1993Muscle>

				<Schutte1993Muscle name="Teres_minor">
					<GeometryPath name="">
					<PathPointSet name="">
							<objects>
								<PathPoint name="TMIN-P1">
									<location> -0.0011 -0.01264 0.02156</location>
									<body>humerus</body>
								</PathPoint>
								<ConditionalPathPoint name="default">
									<location> -0.0150882 -0.00443819 0.0117292</location>
									<body>humerus</body>
									<range> -0.174533 3.2</range>
									<coordinate>arm_flex</coordinate>
								</ConditionalPathPoint>
								<ConditionalPathPoint name="default">
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									<body>humerus</body>
									<range> 0.698132 3.2</range>
									<coordinate>arm_flex</coordinate>
								</ConditionalPathPoint>
								<ConditionalPathPoint name="default">
									<location> -0.00737528 0.0182568 -0.00476424</location>
									<body>humerus</body>
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									<coordinate>arm_flex</coordinate>
								</ConditionalPathPoint>
								<ConditionalPathPoint name="default">
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									<body>humerus</body>
									<range> 2.61799 3.2</range>
									<coordinate>arm_flex</coordinate>
								</ConditionalPathPoint>
								<PathPoint name="TMIN-P2">
									<location> -0.09473 -0.07991 -0.04737</location>
									<body>scapula</body>
								</PathPoint>
								<PathPoint name="TMIN-P3">
									<location> -0.09643 -0.08121 -0.05298</location>
									<body>scapula</body>
								</PathPoint>
							</objects>
					</PathPointSet>
					</GeometryPath>
					
							<max_isometric_force>2125.5</max_isometric_force>
					
							<optimal_fiber_length>       0.07410000 </optimal_fiber_length>
					
							<tendon_slack_length>       0.07130000 </tendon_slack_length>
					
							<pennation_angle>       0.41887902 </pennation_angle>
				</Schutte1993Muscle>

				<Schutte1993Muscle name="PronatorTeres">
					<GeometryPath name="">
					<PathPointSet name="">
					<objects>
						<PathPoint name="PT-P1">
							<location>       0.00360000      -0.27590000      -0.03650000 </location>
							<body> humerus </body>
						</PathPoint>
						<PathPoint name="PT-P2">
							<location>       0.00846000      -0.03373000      -0.01432000 </location>
							<body> ulna </body>
						</PathPoint>
						<PathPoint name="PT-P3">
							<location>       0.01382      -0.06411      -0.00042 </location>
							<body> ulna </body>
						</PathPoint>
						<PathPoint name="PT-P4">
							<location>       0.02360000      -0.09340000       0.00940000 </location>
							<body> radius </body>
						</PathPoint>
						<PathPoint name="PT-P5">
							<location>       0.02540000      -0.10880000       0.01980000 </location>
							<body> radius </body>
						</PathPoint>
					</objects>
					</PathPointSet>
					</GeometryPath>
					
							<max_isometric_force>     566.22000000 </max_isometric_force>
					
							<optimal_fiber_length>       0.04920000 </optimal_fiber_length>
					
							<tendon_slack_length>       0.09800000 </tendon_slack_length>
					
							<pennation_angle>       0.17453293 </pennation_angle>
				</Schutte1993Muscle>
				
				<Schutte1993Muscle name="ECRL">
					<GeometryPath name="">
					<PathPointSet name="">
					<objects>
						<PathPoint name="ECRL-P1">
							<location>      -0.00730000      -0.26090000       0.00910000 </location>
							<body> humerus </body>
						</PathPoint>
						<ConditionalPathPoint name="ECRL-P1.5">
							<location>       0.01450     -0.00346       0.00680 </location>
							<body> radius </body>
							<coordinate> elbow_flex </coordinate>
							<range>     -1.0       0.6981317 </range>
						</ConditionalPathPoint>
						<PathPoint name="ECRL-P2">
							<location>       0.03195000      -0.13463000       0.02779000 </location>
							<body> radius </body>
						</PathPoint>
						<PathPoint name="ECRL-P3">
							<location>       0.04243000      -0.23684000       0.03620000 </location>
							<body> radius </body>
						</PathPoint>
						<PathPoint name="ECRL-P4">
							<location>       -0.00816      -0.03627      0.02117 </location>
							<body> hand </body>
						</PathPoint>
					</objects>
					</PathPointSet>
					</GeometryPath>
					
							<max_isometric_force>     304.89000000 </max_isometric_force>
					
							<optimal_fiber_length>       0.08100000 </optimal_fiber_length>
					
							<tendon_slack_length>       0.22400000 </tendon_slack_length>
					
							<pennation_angle>       0.00000000 </pennation_angle>
				</Schutte1993Muscle>
				<Schutte1993Muscle name="ANC">
					<GeometryPath name="">
					<PathPointSet name="">
					<objects>
						<PathPoint name="ANC-P1">
							<location>      -0.00744000      -0.28359000       0.00979000 </location>
							<body> humerus </body>
						</PathPoint>
						<ConditionalPathPoint name="ANC-P1.5">
							<location>       -0.013185    0.007605    0.01356 </location>
							<body> ulna </body>
							<coordinate> elbow_flex </coordinate>
							<range>     1.0472       3.2 </range>
						</ConditionalPathPoint>
						<PathPoint name="ANC-P2">
							<location>      -0.02532000      -0.00124000       0.00600000 </location>
							<body> ulna </body>
						</PathPoint>
					</objects>
					</PathPointSet>
					</GeometryPath>
					
							<max_isometric_force>     350.00000000 </max_isometric_force>
					
							<optimal_fiber_length>       0.02700000 </optimal_fiber_length>
					
							<tendon_slack_length>       0.01800000 </tendon_slack_length>
					
							<pennation_angle>       0.00000000 </pennation_angle>
				</Schutte1993Muscle>
				<Schutte1993Muscle name="BRD">
					<GeometryPath name="">
					<PathPointSet name="">
					<objects>
						<PathPoint name="BRD-P1">
							<location>      -0.00980000      -0.19963000       0.00223000 </location>
							<body> humerus </body>
						</PathPoint>
						<ConditionalPathPoint name="BRD-P1.5">
							<location>       0.0197017    0.0041987    0.0061355 </location>
							<body> radius </body>
							<coordinate> elbow_flex </coordinate>
							<range>     -1.0       0.2617994   </range>
						</ConditionalPathPoint>
						<PathPoint name="BRD-P2">
							<location>       0.03577000      -0.12742000       0.02315000 </location>
							<body> radius </body>
						</PathPoint>
						<PathPoint name="BRD-P3">
							<location>       0.04190000      -0.22100000       0.02240000 </location>
							<body> radius </body>
						</PathPoint>
					</objects>
					</PathPointSet>
					</GeometryPath>
					
							<max_isometric_force>2421.68</max_isometric_force>
					
							<optimal_fiber_length>       0.17260000 </optimal_fiber_length>
					
							<tendon_slack_length>       0.13300000 </tendon_slack_length>
					
							<pennation_angle>       0.00000000 </pennation_angle>
				</Schutte1993Muscle>

		</objects>
			<groups>
				<ObjectGroup name="shoulder">
					<members> DELT1 DELT2 DELT3 PECM1 PECM2 PECM3 Infraspinatus Latissimus_dorsi_1 Latissimus_dorsi_2 Latissimus_dorsi_3 Teres_minor Coracobrachialis </members>
				</ObjectGroup>
				<ObjectGroup name="elbow">
					<members> BIClong BICshort TRIlat TRIlong TRImed BRA ANC BRD ECRL PronatorTeres</members>
				</ObjectGroup>
			</groups>
			<datafile>  </datafile>
		</ForceSet>
		<length_units> meters </length_units>
		<force_units> N </force_units>
		
		
		<gravity>     0.00000000    0.000000     0.00000000 </gravity>
		
		<BodySet name="">
			<objects>
				<Body name="ground">
					<mass>       0.00000000 </mass>
					<mass_center>       0.00000000       0.00000000       0.00000000 </mass_center>
					<inertia_xx>       0.00000000 </inertia_xx>
					<inertia_yy>       0.00000000 </inertia_yy>
					<inertia_zz>       0.00000000 </inertia_zz>
					<inertia_xy>       0.00000000 </inertia_xy>
					<inertia_xz>       0.00000000 </inertia_xz>
					<inertia_yz>       0.00000000 </inertia_yz>
					
					<Joint />
					<VisibleObject name="">
						
						<GeometrySet name="">
							<objects>
								<DisplayGeometry name="">
									
									<geometry_file> sphere2.vtp </geometry_file>
									
									<color>       1.00000000       0.00000000       0.00000000 </color>
									
									<texture_file>  </texture_file>
									
									<transform>0 0 0 -0.308836 -0.05 -0.290886</transform>
									
									<scale_factors>       1.00000000       1.00000000       1.00000000 </scale_factors>
									
									<display_preference> 4 </display_preference>
									
									<opacity>       1.00000000 </opacity>
								</DisplayGeometry>
							</objects>
							<groups />
						</GeometrySet>
						
						<scale_factors>       1.00000000       1.00000000       1.00000000 </scale_factors>
						
						<transform>      -0.00000000       0.00000000      -0.00000000       0.00000000       0.00000000       0.00000000 </transform>
						
						<show_axes> false </show_axes>
						
						<display_preference> 0 </display_preference>
					</VisibleObject>
					<WrapObjectSet name="">
						<objects />
						<groups />
					</WrapObjectSet>
				</Body>
				<Body name="thorax">
					<mass>       0.00000000 </mass>
					<mass_center>       0.00000000       0.00000000       0.00000000 </mass_center>
					<inertia_xx>       0.00000000 </inertia_xx>
					<inertia_yy>       0.00000000 </inertia_yy>
					<inertia_zz>       0.00000000 </inertia_zz>
					<inertia_xy>       0.00000000 </inertia_xy>
					<inertia_xz>       0.00000000 </inertia_xz>
					<inertia_yz>       0.00000000 </inertia_yz>
					
					<Joint>
						<WeldJoint name="ground_thorax">
							<parent_body> ground </parent_body>
							<location_in_parent>       0.00000000       0.00000000       0.00000000 </location_in_parent>
							<orientation_in_parent>       0.00000000       0.00000000       0.00000000 </orientation_in_parent>
							<location>       0.00000000       0.00000000       0.00000000 </location>
							<orientation>       0.00000000       0.00000000       0.00000000 </orientation>
							
							<CoordinateSet name="">
								<objects />
								<groups />
							</CoordinateSet>
							<reverse> false </reverse>
						</WeldJoint>
					</Joint>
					<VisibleObject name="">
						
						<GeometrySet name="">
							<objects>
								<DisplayGeometry name="">
									
									
									
									<color>       1.00000000       1.00000000       1.00000000 </color>
									
									<texture_file>  </texture_file>
									
									<transform>      -0.00000000       0.00000000      -0.00000000       0.00000000       0.00000000       0.00000000 </transform>
									
									<scale_factors>       1.00000000       1.00000000       1.00000000 </scale_factors>
									
									<display_preference> 4 </display_preference>
									
									<opacity>       1.00000000 </opacity>
								</DisplayGeometry>
							</objects>
							<groups />
						</GeometrySet>
						
						<scale_factors>       1.00000000       1.00000000       1.00000000 </scale_factors>
						
						<transform>      -0.00000000       0.00000000      -0.00000000       0.00000000       0.00000000       0.00000000 </transform>
						
						<show_axes> false </show_axes>
						
						<display_preference> 4 </display_preference>
					</VisibleObject>
				</Body>
				<Body name="clavicle">
					<mass>       0.00000000 </mass>
					<mass_center>       0.00000000       0.00000000       0.00000000 </mass_center>
					<inertia_xx>       0.00000000 </inertia_xx>
					<inertia_yy>       0.00000000 </inertia_yy>
					<inertia_zz>       0.00000000 </inertia_zz>
					<inertia_xy>       0.00000000 </inertia_xy>
					<inertia_xz>       0.00000000 </inertia_xz>
					<inertia_yz>       0.00000000 </inertia_yz>
					
					<Joint>
						<WeldJoint name="sternoclavicular">
							<parent_body> thorax </parent_body>
							<location_in_parent>       0.00632500       0.00693000       0.02546500 </location_in_parent>
							<orientation_in_parent>       0.00000000       0.00000000       0.00000000 </orientation_in_parent>
							<location>       0.00000000       0.00000000       0.00000000 </location>
							<orientation>       0.00000000       0.00000000       0.00000000 </orientation>
							
							<CoordinateSet name="">
								<objects />
								<groups />
							</CoordinateSet>
							<reverse> false </reverse>
						</WeldJoint>
					</Joint>
					<VisibleObject name="">
						
						<GeometrySet name="">
							<objects>
								<DisplayGeometry name="">
									
									<geometry_file> clavicle.vtp </geometry_file>
									
									<color>       1.00000000       1.00000000       1.00000000 </color>
									
									<texture_file>  </texture_file>
									
									<transform>      -0.00000000       0.00000000      -0.00000000       0.00000000       0.00000000       0.00000000 </transform>
									
									<scale_factors>       1.00000000       1.00000000       1.00000000 </scale_factors>
									
									<display_preference> 4 </display_preference>
									
									<opacity>       1.00000000 </opacity>
								</DisplayGeometry>
							</objects>
							<groups />
						</GeometrySet>
						
						<scale_factors>       1.00000000       1.00000000       1.00000000 </scale_factors>
						
						<transform>      -0.00000000       0.00000000      -0.00000000       0.00000000       0.00000000       0.00000000 </transform>
						
						<show_axes> false </show_axes>
						
						<display_preference> 4 </display_preference>
					</VisibleObject>
					<WrapObjectSet name="">
						<objects />
						<groups />
					</WrapObjectSet>
				</Body>
				<Body name="scapula">
					<mass>       0.00000000 </mass>
					<mass_center>       0.00000000       0.00000000       0.00000000 </mass_center>
					<inertia_xx>       0.00000000 </inertia_xx>
					<inertia_yy>       0.00000000 </inertia_yy>
					<inertia_zz>       0.00000000 </inertia_zz>
					<inertia_xy>       0.00000000 </inertia_xy>
					<inertia_xz>       0.00000000 </inertia_xz>
					<inertia_yz>       0.00000000 </inertia_yz>
					
					<Joint>
						<WeldJoint name="acromioclavicular">
							<parent_body> thorax </parent_body>
							<location_in_parent>      -0.01000000       0.03000000       0.16100000 </location_in_parent>
							<orientation_in_parent>       0.00000000      -0.00000000      -0.00000000 </orientation_in_parent>
							<location>       0.00000000       0.00000000       0.00000000 </location>
							<orientation>       0.00000000       0.00000000       0.00000000 </orientation>
							
							<CoordinateSet name="">
								<objects />
								<groups />
							</CoordinateSet>
							<reverse> false </reverse>
						</WeldJoint>
					</Joint>
					<VisibleObject name="">
						
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