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  • Neuroinformatics
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Chakhoyan, Ararat; Raymond, Catalina; Chen, Jason; Goldman, Jodi; +4 Authors

    Figure S2. Comparison of arterial, venous or overlap components proportional to enhancing tumor volume at 1.5 T and 3 T. The arterial component was significantly smaller in ‘other’ group when using 1.5 T (7.59%) as compared to 3 T (17.99%, p

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    Authors: Mena, Lorena De; Smith, Michael A.; Martin, Jason; Dunton, Katie L.; +8 Authors

    Additional file 1 : Figure S1. Aβ levels in the cell culture media following pAAV transfection. pAAV-BRI2-Aβ constructs were transfected into 293 T cells using Polyethylenimine (PEI). Aβ levels secreted into the culture media were detected by Western blotting (A) with N-terminal specific 82E1 antibody and by sandwich ELISA (B) using C-terminal Aβ40 or Aβ42 specific antibody for capture and HRP-conjugated pan-Aβ antibody that recognizes Aβ1–16 epitope or 4G8 (anti Aβ17–24) as a detection.

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    Authors: Perez-Rando, Marta; Dujardin, Simon; Bennett, Rachel E.; Commins, Caitlin; +2 Authors

    Additional file 2. Synaptophysin expression in neurons without NFT. a Single focal planes of neurons not bearing an NFTs, lacking HsMAPT expression (HsMAPT-, blue arrowheads) or expressing HsMAPT (HsMAPT + , orange arrowheads). b Graphs summarizing the percentage of area covered with the synaptophysin probe. Scale bar: 12 µm.

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    Authors: Sathish Kumar; Lemere, Cynthia A.; Walter, Jochen;

    Additional file 1: Supplementary Figure 1. Specificity of phosphorylation-state specific Aβ antibodies. SDS-PAGE electrophoresis and immunoblotting of non-modified full length (Aβ1–40/42), truncated (Aβ3–40/42), phosphorylated (pSer8Aβ1–40/42, pSer26Aβ1–40, pSer8Aβ3–40/42, pSer26Aβ3–40/42), pyroglutaminated Aβ (pyroAβ3–40/42) or nitrated Aβ (NitroAβ1–42) variants with 1E4E11 (pSer8Aβ-specific) and 7H3D6 (npAβ-specific) antibodies. 1E4E11 specifically recognized phosphorylated Ser-8 full-length (1–40/42) and truncated pSer8Aβ3–40/42 variants, whereas 7H3D6 antibody demonstrated no reactivity against Aβ peptides phosphorylated at Ser-8 residue and specifically detects only full-length Aβ1–40/42 variants without N-terminal modifications. Generic 4G8-antibody (epitope 17–24) recognizes all examined Aβ variants.

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    Authors: Etsuro Nakanishi; Uemura, Norihito; Akiyama, Hisako; Kinoshita, Masato; +7 Authors

    Additional file 15: Figure S8. gba2 mRNA expression in brains measured by qRT-PCR. Measurement of asyn mRNA expression in the brains was conducted at 3 mpf. (n = 4 for each genotypes). A one-way ANOVA with Tukey's multiple comparison test was performed. n.s.: not significant.

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    Authors: David, Olivier; Lemaréchal, Jean-Didier; Jedynak, Maciej; Trebaul, Lena; +39 Authors

    F-TRACT atlas release - December 2021 ====================================== The F-TRACT atlas is provided as .csv (comma-separated values) files that can be read in any table editor. In addition, we provide a Matlab routine allowing to read the features of the atlas as Matlab variables. The atlas is provided for free use for research use only, with limited accuracy, which hopefully will improve with subsequent releases. Please cite David et al. (2013) Probabilistic functional tractography of the human cortex, NeuroImage, and Trebaul et al. (2018) Probabilistic functional tractography of the human cortex revisited, NeuroImage, Lemarechal et al. (2022) A brain atlas of axonal and synaptic delays based on modelling of cortico-cortical evoked potentials, Brain, when using the F-TRACT atlas. - f-tract_v2112 : Connectivity probability as well as features describing fibers biophysical properties, estimated from CCEP data recorded in 780 patients, in the AAL, AICHA, Brodmann, Freesurfer, Hammers, HCP-MMP1, Lausanne2008 (resolutions 33, 60, 125, 250, 500) and MarsAtlas parcellation schemes. The CCEP features are: peak and onset latency (LatStart), amplitude, duration, integral, velocity estimated from the onset latency and the fibers distance between the parcels and axonal conduction delays. Synaptic excitatory and inhibitory delays are also provided for each parcel. All features have been estimated separately for patients younger than 15 y.o. (group "0-15") and patients older than 15 y.o. (group "15-100"). - Features maps : Images representing the connectivity probability and response features for all the regions in the Lausanne2008-60 parcellation.

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    ZENODO
    Dataset . 2021
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    Dataset . 2021
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      Dataset . 2021
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      Dataset . 2021
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    Authors: Rizzardi, Lindsay F.; Hickey, Peter F.; Idrizi, Adrian; Tryggvadóttir, Rakel; +7 Authors

    Additional file 11: Table S10. List of 75 granule cell marker genes and hippocampal CpG DMRs that overlap granule cell marker genes or their promoters.

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    Dataset . 2021
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    Authors: Macrì, Simone; Di-Poï, Nicolas;

    4K movie displaying the 3D rendering of the head and both the morphological features and spatial organization of the major brain subdivisions of the Flying Dragon lizard. The brain reconstruction was obtained from a microCT scan of a iodine-stained specimen through manual segmentation using the software Amira 5.5.0. Other videos can be found here. If you are interested in reptile brain evolution and behavior, please, have a look to our recent publication: "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization" Simone Macrì, Yoland Savriama, Imran Khan & Nicolas Di-Poï Nature Communications 10, 5560 (2019) For any inquiries or additional information, please, refer to the contacts provided in the article.

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    ZENODO
    Audiovisual . 2020
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    Authors: Torrieri, G.;

    Abstract SHARE is a collection of programs designed for the statistical analysis of particle production in relativistic heavy-ion collisions. With the physical input of intensive statistical parameters, it generates the ratios of particle abundances. The program includes cascade decays of all confirmed resonances from the Particle Data Tables. The complete treatment of these resonances has been known to be a crucial factor behind the success of the statistical approach. An optional feature implemented... Title of program: SHARE, October 2004, version 1.2 Catalogue Id: ADVD_v1_0 Nature of problem Statistical analysis of particle production in relativistic heavy-ion collisions involves the formation and the subsequent decays of a large number of resonances. With the physical input of thermal parameters, such as the temperature and fugacities, and considering cascading decays, along with weak interaction feed-down corrections, the observed hadron abundances are obtained. SHARE incorporates diverse physical approaches, with a flexibility of choice of the details of the statistical hadroniza ... Versions of this program held in the CPC repository in Mendeley Data ADVD_v1_0; SHARE, October 2004, version 1.2; 10.1016/j.cpc.2005.01.004 ADVD_v2_0; SHAREv2; 10.1016/j.cpc.2006.07.010 ADVD_v3_0; SHARE with CHARM; 10.1016/j.cpc.2014.02.026 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)

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    Dataset . 2019
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    Dataset . 2019
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    Authors: Voutsa, Venetia; Battaglia, Demian; Bracken, Louise J.; Brovelli, Andrea; +21 Authors

    The relationship of network structure and dynamics is one of the most extensively investigated problems in the theory of complex systems of the last years. Understanding this relationship is of relevance to a range of disciplines—from Neuroscience to Geomorphology. A major strategy of investigating this relationship is the quantitative comparison of a representation of network architecture (structural connectivity) with a (network) representation of the dynamics (functional connectivity). Here, we show that one can distinguish two classes of functional connectivity—one based on simultaneous activity (co-activity) of nodes, the other based on sequential activity of nodes. We delineate these two classes in different categories of dynamical processes—excitations, regular and chaotic oscillators—and provide examples for SC/FC correlations of both classes in each of these models. We expand the theoretical view of the SC/FC relationships, with conceptual instances of the SC and the two classes of FC for various application scenarios in Geomorphology, Ecology, Systems Biology, Neuroscience and Socio-Ecological Systems. Seeing the organisation of dynamical processes in a network either as governed by co-activity or by sequential activity allows us to bring some order in the myriad of observations relating structure and function of complex networks.

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    Authors: Chakhoyan, Ararat; Raymond, Catalina; Chen, Jason; Goldman, Jodi; +4 Authors

    Figure S2. Comparison of arterial, venous or overlap components proportional to enhancing tumor volume at 1.5 T and 3 T. The arterial component was significantly smaller in ‘other’ group when using 1.5 T (7.59%) as compared to 3 T (17.99%, p

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    Authors: Mena, Lorena De; Smith, Michael A.; Martin, Jason; Dunton, Katie L.; +8 Authors

    Additional file 1 : Figure S1. Aβ levels in the cell culture media following pAAV transfection. pAAV-BRI2-Aβ constructs were transfected into 293 T cells using Polyethylenimine (PEI). Aβ levels secreted into the culture media were detected by Western blotting (A) with N-terminal specific 82E1 antibody and by sandwich ELISA (B) using C-terminal Aβ40 or Aβ42 specific antibody for capture and HRP-conjugated pan-Aβ antibody that recognizes Aβ1–16 epitope or 4G8 (anti Aβ17–24) as a detection.

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    Authors: Perez-Rando, Marta; Dujardin, Simon; Bennett, Rachel E.; Commins, Caitlin; +2 Authors

    Additional file 2. Synaptophysin expression in neurons without NFT. a Single focal planes of neurons not bearing an NFTs, lacking HsMAPT expression (HsMAPT-, blue arrowheads) or expressing HsMAPT (HsMAPT + , orange arrowheads). b Graphs summarizing the percentage of area covered with the synaptophysin probe. Scale bar: 12 µm.

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    Authors: Sathish Kumar; Lemere, Cynthia A.; Walter, Jochen;

    Additional file 1: Supplementary Figure 1. Specificity of phosphorylation-state specific Aβ antibodies. SDS-PAGE electrophoresis and immunoblotting of non-modified full length (Aβ1–40/42), truncated (Aβ3–40/42), phosphorylated (pSer8Aβ1–40/42, pSer26Aβ1–40, pSer8Aβ3–40/42, pSer26Aβ3–40/42), pyroglutaminated Aβ (pyroAβ3–40/42) or nitrated Aβ (NitroAβ1–42) variants with 1E4E11 (pSer8Aβ-specific) and 7H3D6 (npAβ-specific) antibodies. 1E4E11 specifically recognized phosphorylated Ser-8 full-length (1–40/42) and truncated pSer8Aβ3–40/42 variants, whereas 7H3D6 antibody demonstrated no reactivity against Aβ peptides phosphorylated at Ser-8 residue and specifically detects only full-length Aβ1–40/42 variants without N-terminal modifications. Generic 4G8-antibody (epitope 17–24) recognizes all examined Aβ variants.

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