List of Figures and Tables. Figure 1. Vicinity map of the restoration project site located north of Houma, Louisiana and adjacent to the BGCMA 2 Figure 2. Layout of of sampling plots and monitoring parcels along the restoration project site. 11 Table 1. Performance Criteria and Standards during Period of Performance Monitoring 5 Table 2. Performance Monitoring and Forest Management Activities. 9 Table 3. Sampling Plots in each Monitoring Parcel. 12
List of Figures and Tables. Figure 1: Active areas for a set of reference contrasts in six representative subjects. The two rows represent two different sets of functional contrasts 5 Figure 2: Summary of the main functional contrasts acquired in the group of subjects so far. 7 Figure 3: Analysis of axon radius and diameter in the human corpus callosum (data averaged over ten subjects). 11
List of Figures and Tables. Figure 1: Flow chart of the public dissemination procedure 5 Figure 2: Screenshot of the SUNFLOWER webpage with public section consisting of various informative subfolders and the secured project intranet section 7 Figure 3: Konarka OPV demonstrator operates an LED in indoor conditions 9 Table 1: Matrix of SUNFLOWER communication and dissemination channels 12 Table 2: Timeline for Deliverables and Milestones 12 1 Introduction
List of Figures and Tables. Figure 1: Architectural diagram of the Brain Simulation Platform 9 Table 1: Collaboratory Integration/Portals 10 Table 3: Foundation Software 19 Table 4: Platform Use Case Status Summary 25 Table 5: Collaboratory Integration 44 Table 6: Services 46 Table 7: Foundation Software 52 Table 8: Technology Readiness Levels 58 Table 9: Remaining Bugs in the Single Cell Builder 60 Table 10: Remaining Bugs in the Microcircuit Builder 60 Table 11: Features to be added to the Microcircuit Builder 60 Table 12: Features to be added to the Subcellular Builder 61 Table 13: Features to be added to the Mesocircuit and Macrocircuit Builder 61 Table 14: Features to be added to CoreNeuron, Neurodamus, and ReportingLib 61 Table 15: Features to be added to STEPS & Parallel STEPS 62 Figure 2: The Technology Adoption Curve [1]. 64 Table 16: IPR Status, Ownership and Innovation Potential 71
List of Figures and Tables. Fig. 1: Differential interference contrast image of Chlamydomonas reinhardtii. Fig. 2: Model for I1 dynein regulation Fig. 3: Cross section of the ciliary/flagellar axoneme Fig. 4: Model for I1 dynein Fig. 5: The axonemal “96nm repeat” Fig. 6: Model of the PP2A heterotrimer
List of Figures and Tables. Figure 1: HPC Platform Architectural Diagram 11 Table 1: HPC Platform Architecture: Core Platform Services 12 Table 2: New software features added after M18 release 18 Table 3: Export from Collaboratory Software Catalog: Cube 25 Table 4: Export from Collaboratory Software Catalog: Deflect Client Library 27 Table 5: Export from Collaboratory Software Catalog: DisplayCluster 29 Table 6: Export from Collaboratory Software Catalog: DLB 31 Table 7: Export from Collaboratory Software Catalog: Equalizer 33 Table 8: Export from Collaboratory Software Catalog: Extrae 35 Table 9: Export from Collaboratory Software Catalog: FLAT 37 Table 10: Export from Collaboratory Software Catalog: HCFFT 39 Table 11: Export from Collaboratory Software Catalog: InDiProv 40 Table 12: Export from Collaboratory Software Catalog: Livre 42 Table 13: Export from Collaboratory Software Catalog: MonetDB 44 Table 14: Export from Collaboratory Software Catalog: Monsteer 46 Table 15: Export from Collaboratory Software Catalog: MSPViz 48 Table 16: Export from Collaboratory Software Catalog: NeuroLOTs 50 Table 17: Export from Collaboratory Software Catalog: NeuroScheme 51 Table 18: Export from Collaboratory Software Catalog: OmpSs 52 Table 19: Export from Collaboratory Software Catalog: Paraver 54 Table 20: Export from Collaboratory Software Catalog: PyCOMPSs 56 Table 21: Export from Collaboratory Software Catalog: NeuroFiReS 58 Table 22: Export from Collaboratory Software Catalog: Remote Connection Manager (RCM) ....................................................................................................... 59 Table 23: Export from Collaboratory Software Catalog: RTNeuron 61 Table 24: Export from Collaboratory Software Catalog: RUBIK 62 Table 25: Export from Collaboratory Software Catalog: Scalasca 65 Table 26: Export from Collaboratory Software Catalog: Score-P 67 Table 27: Export from Collaboratory Software Catalog: SCOUT 69 Table 28: Export from Collaboratory Software Catalog: TOUCH 71 Table 29: Export from Collaboratory Software Catalog: TRANSFORMERS 74 Table 30: Export from Collaboratory Software Catalog: T-Storm 76 Table 31: Export from Collaboratory Software Catalog: UG4 78 Table 32: Export from Collaboratory Software Catalog: VisNEST 80 Table 33: Export from Collaboratory Software Catalog: ViSTA 81 Table 34: Export from Collaboratory Software Catalog: XXXXX 83 Table 35: Export from Collaboratory Software Catalog: ZeroBuf 85 Table 36: Export from Collaboratory Software Catalog: Z...
List of Figures and Tables. Table 1: SP1 tools and methodologies 6 Figure 1: Heat map showing list of genes and protein levels detected in complex with PSD95 in the CA1, CA3, CL6, and ST conditional lines 15 Figure 2: Synaptic proteome expression levels across the seven integral regions of the mouse brain 28 Figure 3: Heat-maps of synapse densities and synapse types coded by different colours across the 5 mouse brain sections 28 Figure 4: 3D reconstruction of dendritic shaft of CA1 pyramidal cells with immunogold labelling for SK2 29 Figure 5: 2D mapping of glutamate receptors in CA1 pyramidal cells by SDS-digested freeze-fracture replica labelling 30 Figure 6: Fine tuning of the segmentation algorithm for cell detection 34 Figure 7: PSD95 labelling of a layer III pyramidal neuron in the somatosensory cortex of a PSD95 EGFP mouse 37 Figure 8: Synaptic maps of Identified Neurons 38 Figure 9: Pyramidal Cell Explorer 39 Figure 10: 3D Quantification Methodology 42 Figure 11: Imaging Processing 42 Figure 12: Synaptic Map of the Hippocampus 43 Figure 13: Example of a correlative optical and FIB/SEM synaptic map 44 Figure 14: Ontology 63 Figure 15: Simple PDS xxxxx Kappa nmda 64
List of Figures and Tables. Figure 1: OPA network topology of XXXXX 7 Figure 2: Schematic view on the JURON compute node architecture 8 Figure 3: Pilot systems XXXXX (left) and XXXXX (right). The racks in the middle host the shared storage 9 Figure 4: DSS software stack architecture 11 Figure 5: Weak scaling of RTNeuron on JURON using pseudo-cylinders. 13 Figure 6: Weak scaling of RTNeuron on JURON using meshes. 13 Figure 7: Strong scaling of RTNeuron on JURON for 1,000 neurons using cylinders. 14 Figure 8: Strong scaling of RTNeuron on JURON for 2,000 neurons using cylinders. 15 Figure 9: Strong scaling of RTNeuron on JURON for 3,000 neurons using cylinders. 15 Figure 10: Strong scaling of RTNeuron on JURON for 200 neurons using meshes. 15 Figure 11: Strong scaling of RTNeuron on JURON for 500 neurons using meshes. 16 Figure 12: Strong scaling of RTNeuron on JURON for 1,000 neurons using meshes. 16 Table 1: Timeline of the HBP PCP 6
List of Figures and Tables. Figures Figure 1.1 The Awaji-shima diagnosis criteria (xx Xxxxxxxx et al., 2008) 24 Figure 1.2 Pathological protein aggregates in sporadic and familial ALS 28 Figure 1.3 Schematic representation of VAPB structure showing protein domains and the localization of ALS-associated pathogenic mutations within the MSP domain 37 Figure 1.4 The vertebrate UPR 57 Figure 3.1 siRNA knockdown of VAPB or PTPIP51 114 Figure 3.2 siRNA knockdown of VAPB or PTPIP51 reduces ER-mitochondria associations 115 Figure 3.3 FACS post-sorting analyses demonstrating high purity of ECFP/AcGFP positive samples 116 Figure 3.4 Confirmation of cell sorting purification of ECFP-VAPB and PTPIP51-HA expressing cells 118 Figure 3.5 Overexpression of VAPB and/or PTPIP51 increases ER-mitochondria associations 119 Figure 3.6 siRNA knockdown of VAPB or PTPIP51 reduces co-localization of ER and mitochondria 121 Figure 3.7 Overexpression of VAPB, PTPIP51 and VAPB with PTPIP51 all increase co-localization of ER and mitochondria 122 Figure 4.1 FACS post-sorting analyses demonstrating purification of EGFP positive samples 137 Figure 4.2 Expression of wild type and ALS mutant TDP-43 reduce ER-mitochondria associations 138 Figure 4.3 Expression of wild type or ALS mutant TDP-43 reduce ER-mitochondria co- localization 139 Figure 4.4 Overexpression of wild-type or ALS associated mutant TDP-43 do not alter expression of VAPB, PTPIP51 or mitofusin-2 (MFN2) 140 Figure 4.5 Specificity of the Duolink proximity ligation assay for VAPB and PTPIP51
List of Figures and Tables. Chapter I
