cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25493/d2cw-jr
title: 3D cyto- and receptor architectonic map of macaque area PFG of the inferior parietal lobe

description: A multimodal analysis of the macaque inferior parietal lobule was carried out to create a 3D atlas integrating and reconciling discrepancies between previously published maps. This involved a quantitative and statistically testable approach to the analysis of cytoarchitecture in the macaque monkey inferior parietal lobe, in combination with an in vitro quantitative receptor autoradiographic analysis of the regional and laminar distribution patterns of 15 different neurotransmitter receptors. The borders of the identified areas were traced onto a reference macaque monkey brain in stereotaxic space. We provide here for the first time a map of area PFG of the macaque monkey brain integrating cyto- and receptor architectonic features in stereotaxic space. It constitutes a valuable resource for the analysis of functional experiments with non-human primates, and provides crucial data for modeling approaches with realistic synaptic dynamics.
DOI: 10.25493/bt52-9ct
title: Spike time dependent plasticity (STDP) data from neonate neuroligin-3 knock-out mice, positive pairing

description: Spike-time dependent plasticity (STDP is a particular form of Hebbian type of learning which consists in bidirectional modifications of synaptic strength according to the temporal order of pre- and postsynaptic spiking (*Dan Y1, Poo MM (2006) Spike timing-dependent plasticity: from synapse to perception. Physiol Rev 86:1033-1048*). Thus, positively correlated pre- and postsynaptic spiking (pre before post) within a critical window leads to long term potentiation (LTP), whereas a negative correlation (post before pre) leads to long term depression (LTD). At the neonatal stage, the hippocampal mossy fiber (MF)-CA3 is GABAergic and exhibits STDP. Our data demonstrate that, at the same age, positive pairing fails to induce STD-LTP at MF-CA3 synapses in hippocampal slices obtained from neuroligin-3 (NL3) knock-in (NL3<sup>R451C</sup>KI) and NL3 knock-out (KO) mice. Similarly, in NLR<sup>R451C</sup> KI mice, negative pairing failed to cause STD-LTD. In contrast, STD-LTP and STD-LTD can be readily produced in control age-matched WT littermates. In NLR<sup>R451C</sup> KI mice, the impairment in STD-LTP is maintained in adulthood when MF are glutamatergic. This set of data refers to the neonate, NL3 knock-out, positive pairing condition.
DOI: 10.25493/exet-xnd
title: E15.5 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain Atlas

description: 3D imaging necessitates corresponding 3D anatomical atlases, but generating such atlases is time consuming and challenging. Substantial efforts have generated such atlases including the Allen Developing Mouse Brain Atlas (ADMBA) but are typically limited by the process of serial 2D annotation for 3D reconstruction leading to artifacts. We have developed an automated, edge-aware atlas refinement method to curate existing atlases in a topologically consistent, 3D manner. Applying this approach to the E15.5 atlas in the ADMBA, we inferred labels for incompletely labeled areas, smoothed the labels in 3D, and realigned the labels to the underlying anatomical edges. As required, we also rotated images in 3D for midline symmetry and used the completed labels to strip regions outside of the central nervous system.
DOI: 10.25493/wjjg-zmm
title: Whole-cell recording and labelling of hippocampal neurons in vivo

description: This study has provided both intracellular recordings from single neurons and LFP recordings from the hippocampal CA1 region in head-restrained, behaving mice, along with morphological reconstructions of some of the recorded cells. This dataset complements our larger database of hippocampal neurons recorded and filled in hippocampal slices, mainly by characterizing the spontaneous and evoked physiological behavior of the cells under in vivo conditions.
DOI: 10.25493/kakx-tgk
title: Probabilistic cytoarchitectonic map of Area PFm (IPL) (v11.0)

description: This dataset contains the distinct architectonic Area PFm (IPL) in the individual, single subject template of the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. As part of the Julich-Brain cytoarchitectonic atlas, the area was identified using cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of Düsseldorf. The results of the cytoarchitectonic analysis were then mapped to both reference spaces, where each voxel was assigned the probability to belong to Area PFm (IPL). The probability map of Area PFm (IPL) is provided in the NifTi format for each brain reference space and hemisphere. The Julich-Brain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets. Other available data versions of Area PFm (IPL): Caspers et al. (2018) [Data set, v9.2] [DOI: 10.25493/AJGE-PNH](https://doi.org/10.25493%2FAJGE-PNH) Caspers et al. (2019) [Data set, v9.4] [DOI: 10.25493/TB94-HRK](https://doi.org/10.25493%2FTB94-HRK) The most probable delineation of Area PFm (IPL) derived from the calculation of a maximum probability map of all currently released Julich-Brain brain structures can be found here: Amunts et al. (2019) [Data set, v1.13] [DOI: 10.25493/Q3ZS-NV6](https://doi.org/10.25493%2FQ3ZS-NV6) Amunts et al. (2019) [Data set, v1.18] [DOI: 10.25493/8EGG-ZAR](https://doi.org/10.25493%2F8EGG-ZAR) Amunts et al. (2020) [Data set, v2.2] [DOI: 10.25493/TAKY-64D](https://doi.org/10.25493%2FTAKY-64D) Amunts et al. (2020) [Data set, v2.4] [DOI: 10.25493/A7Y0-NX9](https://doi.org/10.25493%2FA7Y0-NX9) Amunts et al. (2020) [Data set, v2.5] [DOI: 10.25493/8JKE-M53](https://doi.org/10.25493/8JKE-M53)
DOI: 10.5281/zenodo.5069598
title: Seismic wave propagation in partially saturated rocks with a fractal distribution of fluid-patch size

description: Laboratory experiments on partially saturated rocks show that seismic attenuation can be significant, where the main mechanism is wave-induced local fluid flow (WILFF) due to patchy saturation at different spatial scales. We propose a theory to obtain the seismic properties of partially saturated rocks based on fractal (self-similar) patches, leading to an effective frequency-dependent fluid modulus. The model combines the differential effective medium (DEM) and Biot-Rayleigh theories, where the patches are inclusions incrementally added, such that the effective fluid is assumed the host for the next addition. The analysis shows that the seismic properties are independent on the number of iterations, but depend on the scale range (radius) of the inclusions, fractal dimension <em>D<sub>f</sub></em> of the self-similar distribution, parameter \(\theta\) of the exponential distribution, mean radius <em>r</em><sub>0</sub> and variance \({\sigma_r}^2\) of the Gaussian distribution. Forced-oscillation experiments are performed on a limestone sample under partial water-saturation conditions at seismic frequencies (2-500 Hz), to obtain the velocity dispersion and extensional attenuation. The proposed theory provides a reasonable description of the experimental data and other existing measurements on Berea sandstone and tight carbonates.
DOI: 10.25493/mr1v-bj3
title: Probabilistic cytoarchitectonic map of Area 45 (IFG) (v7.4)

description: This dataset contains the distinct architectonic Area 45 (IFG) in the individual, single subject template of the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. As part of the Julich-Brain cytoarchitectonic atlas, the area was identified using cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of Düsseldorf. The results of the cytoarchitectonic analysis were then mapped to both reference spaces, where each voxel was assigned the probability to belong to Area 45 (IFG). The probability map of Area 45 (IFG) are provided in the NifTi format for each brain reference space and hemisphere. The Julich-Brain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets. Other available data versions of Area 45 (IFG): Amunts et al. (2018) [Data set, v7.2] [DOI: 10.25493/J2KZ-AZW](https://doi.org/10.25493%2FJ2KZ-AZW) The most probable delineation of Area 45 (IFG) derived from the calculation of a maximum probability map of all currently released Julich-Brain brain structures can be found here: Amunts et al. (2019) [Data set, v1.13] [DOI: 10.25493/Q3ZS-NV6](https://doi.org/10.25493%2FQ3ZS-NV6) Amunts et al. (2019) [Data set, v1.18] [DOI: 10.25493/8EGG-ZAR](https://doi.org/10.25493%2F8EGG-ZAR) Amunts et al. (2020) [Data set, v2.2] [DOI: 10.25493/TAKY-64D](https://doi.org/10.25493%2FTAKY-64D)
DOI: 10.25493/1ah7-t1a
title: Pituitary homeobox 3 tetracycline-transactivator expression: horizontal sections (case 6513)

description: Bright-field microscopy images of serial horizontal brain sections showing Pituitary homeobox 3 (Pitx3) promoter expression in a bigenic Pitx3-tetracycline-transactivator (tTA) mouse brain case (6513, adult male), using a driver-reporter construct in which the Pitx3-tTA promoter regulates the expression of the E. coli derived LacZ reporter gene encoding β-galactosidase, which is visualized histologically using X-gal (5-Bromo-4-chloro-3-indolyl β-d-galactopyranoside) as a substrate. Our data show that the Pitx3-tTA promoter is spatially restricted to the substantia nigra, ventral tegmental area, and a few other regions.
DOI: 10.25493/a2eg-vpr
title: Purkinje cell protein 2 tetracycline-transactivator expression: coronal sections (case 1261)

description: Bright-field microscopy images of serial coronal brain sections showing Purkinje cell protein 2 (Pcp2) promoter expression in a bigenic Pcp2-tetracycline-transactivator (tTA) mouse brain (case 1261, adult male), generated using a driver-reporter construct in which the Pcp2-tTA promoter regulates the expression of the E. coli derived LacZ reporter gene encoding β-galactosidase, which is visualized histologically using X-gal (5-Bromo-4-chloro-3-indolyl β-d-galactopyranoside) as a substrate. Our data confirm earlier reports that Pcp2-tTA promoter expression is restricted to cerebellar Purkinje cells.
DOI: 10.25493/6c6v-bq2
title: Probabilistic cytoarchitectonic map of Area FG1 (FusG) (v3.0)

description: This dataset contains the distinct architectonic Area FG1 (FusG) in the individual, single subject template of the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. As part of the Julich-Brain cytoarchitectonic atlas, the area was identified using cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of Düsseldorf. The results of the cytoarchitectonic analysis were then mapped to both reference spaces, where each voxel was assigned the probability to belong to Area FG1 (FusG). The probability map of Area FG1 (FusG) is provided in the NifTi format for each brain reference space and hemisphere. The Julich-Brain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets. Other available data versions of Area FG1 (FusG): Caspers et al. (2018) [Data set, v1.2] [DOI: 10.25493/534D-V55](https://doi.org/10.25493%2F534D-V55) Caspers et al. (2019) [Data set, v1.4] [DOI: 10.25493/5ZVQ-R8R](https://doi.org/10.25493%2F5ZVQ-R8R) The most probable delineation of Area FG1 (FusG) derived from the calculation of a maximum probability map of all currently released Julich-Brain brain structures can be found here: Amunts et al. (2019) [Data set, v1.13] [DOI: 10.25493/Q3ZS-NV6](https://doi.org/10.25493%2FQ3ZS-NV6) Amunts et al. (2019) [Data set, v1.18] [DOI: 10.25493/8EGG-ZAR](https://doi.org/10.25493%2F8EGG-ZAR) Amunts et al. (2020) [Data set, v2.2] [DOI: 10.25493/TAKY-64D](https://doi.org/10.25493%2FTAKY-64D) Amunts et al. (2020) [Data set, v2.4] [DOI: 10.25493/A7Y0-NX9](https://doi.org/10.25493%2FA7Y0-NX9) Amunts et al. (2020) [Data set, v2.5] [DOI: 10.25493/8JKE-M53](https://doi.org/10.25493/8JKE-M53)
DOI: 10.25493/8ecv-tjj
title: 3D cyto- and receptor architectonic map of macaque lateral premotor area F5v

description: A multimodal analysis of the macaque motor cortex was carried out to create a 3D atlas integrating and reconciling discrepancies between previously published maps. This involved a quantitative and statistically testable approach to the analysis of cytoarchitecture in the macaque monkey frontal agranular cortex, in combination with an in vitro quantitative receptor autoradiographic analysis of the regional and laminar distribution patterns of 13 different neurotransmitter receptors. The borders of the identified areas were traced onto a reference macaque monkey brain in stereotaxic space. We provide here for the first time a map of lateral premotor area F5v of the macaque monkey brain integrating cyto- and receptor architectonic features in stereotaxic space. It constitutes a valuable resource for the analysis of functional experiments with non-human primates, and provides crucial data for modeling approaches with realistic synaptic dynamics.
DOI: 10.25493/hfpf-6az
title: Density measurements of different receptors for Area ifs2 (IFS) [human, v1.0]

description: This dataset contains the densities (in fmol/mg protein) of 17 receptors for classical neurotransmitters in Area ifs2 (IFS) obtained by means of quantitative in vitro autoradiography. The receptor densities are visualized as fingerprints (fp), which provide the mean density and standard deviation for each of the analyzed receptor types, averaged across samples. For exemplary samples, we also provide color-coded laminar autoradiography images (ar). The autoradiography images show an exemplary density distribution of a single receptor for one laminar cross-section in a single tissue sample. Information on the used tissue samples and corresponding subjects for the receptor fingerprints and autoradiographs as well as a list of analyzed receptors accompanies the provided dataset.
DOI: 10.25493/e28g-24u
title: Probability map of bundle rh_MOF-ST_0 (atlas of superficial white matter fibre bundles, version 2018)

description: This data contains the probability map of a short fibre bundle connecting the right hemisphere Middle Orbitofrontal and Superior Temporal regions of the Desikan-Killiany atlas, in the MNI ICBM152 reference brain. This bundle was identified using a hybrid approach, incorporating anatomical information (from cortical regions of interest) and fibre shape (fibre clustering), from the tractography datasets of 78 subjects in the Neurospin’s ARCHI database. The map shows the probability of finding a fibre belonging to the bundle in each voxel of the reference brain. The maximum probability corresponds to the voxels with the highest number of putative fibres going through.
DOI: 10.25493/mypd-qb8
title: P56 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain Atlas

description: 3D imaging necessitates corresponding 3D anatomical atlases, but generating such atlases is time consuming and challenging. Substantial efforts have generated such atlases including the Allen Developing Mouse Brain Atlas (ADMBA) but are typically limited by the process of serial 2D annotation for 3D reconstruction leading to artifacts. We have developed an automated, edge-aware atlas refinement method to curate existing atlases in a topologically consistent, 3D manner. Applying this approach to the P56 atlas in the ADMBA, we inferred labels for incompletely labeled areas, smoothed the labels in 3D, and realigned the labels to the underlying anatomical edges.
DOI: 10.25493/gptq-6bh
title: Probability map of bundle rh_Op-Tr_0 (atlas of superficial white matter fibre bundles, version 2018)

description: This data contains the probability map of a short fibre bundle connecting the right hemisphere Pars Opercularis and Pars Triangularis regions of the Desikan-Killiany atlas, in the MNI ICBM152 reference brain. This bundle was identified using a hybrid approach, incorporating anatomical information (from cortical regions of interest) and fibre shape (fibre clustering), from the tractography datasets of 78 subjects in the Neurospin’s ARCHI database. The map shows the probability of finding a fibre belonging to the bundle in each voxel of the reference brain. The maximum probability corresponds to the voxels with the highest number of putative fibres going through.
DOI: 10.25493/ahx0-9pu
title: Density measurements of different receptors for Area TE 1.0 (HESCHL) [human, v1.0]

description: This dataset contains the densities (in fmol/mg protein) of receptors for classical neurotransmitters in Area TE 1.0 (HESCHL) obtained by means of quantitative _in vitro_ autoradiography. The receptor densities are visualized as _fingerprints_ (**fp**), which provide the mean density and standard deviation for each of the analyzed receptor types, averaged across samples. Overview of available measurements [ **receptor** \| **_neurotransmitter_** \| _labeling agent_ ]: **AMPA** \| **_glutamate_** \| _[³H]AMPA_ **kainate** \| **_glutamate_** \| _[³H]kainate_ **NMDA** \| **_glutamate_** \| _[³H]MK-801_ **mGluR2/3** \| **_glutamate_** \| _[³H]LY341495_ **GABA<sub>A</sub>** \| **_GABA_** \| _[³H]muscimol_ **GABA<sub>B</sub>** \| **_GABA_** \| _[³H]CGP54626_ **GABA<sub>A</sub>/BZ** \| **_GABA_** \| _[³H]flumazenil_ **muscarinic M<sub>1</sub>** \| **_acetylcholine_** \| _[³H]pirenzepine_ **muscarinic M<sub>2</sub>** \| **_acetylcholine_** \| _[³H]oxotremorine-M_ **muscarinic M<sub>3</sub>** \| **_acetylcholine_** \| _[³H]4-DAMP_ **nicotinic α<sub>4</sub>β<sub>2</sub>** \| **_acetylcholine_** \| _[³H]epibatidine_ **α<sub>1</sub>** \| **_noradrenalin/norepinephrine_** \| _[³H]prazosin_ **α<sub>2</sub>** \| **_noradrenalin/norepinephrine_** \| _[³H]UK-14,304_ **5-HT<sub>1A</sub>** \| **_serotonin_** \| _[³H]8-OH-DPAT_ **5-HT<sub>2</sub>** \| **_serotonin_** \| _[³H]ketanserin_ **D<sub>1</sub>** \| **_dopamine_** \| _[³H]SCH23390_ Information on the used tissue samples and corresponding subjects, as well as analyzed receptors accompanies the provided dataset. **For methodological details, see:** Zilles, K. et al. (2002). Quantitative analysis of cyto- and receptorarchitecture of the human brain, pp. 573-602. In: Brain Mapping: The Methods, 2nd edition (A.W. Toga and J.C. Mazziotta, eds.). San Diego, Academic Press. Palomero-Gallagher N, Zilles K. (2018) Cyto- and receptorarchitectonic mapping of the human brain. In: Handbook of Clinical Neurology 150: 355-387 **The receptor density data of this area were also published in:** Morosan P, Rademacher J, Palomero-Gallagher N, and Zilles K (2005) Anatomical organization of the human auditory cortex: Cytoarchitecture and transmitter receptors. In Heil P, Scheich H, Bundinger E, and König R (Eds), The Auditory Cortex - Towards a Synthesis of Human and Animal Research. (pp. 27-50) [Mahwah, New Jersey, USA: Lawrence Erlbaum Associates](https://www.taylorfrancis.com/books/e/9781135613365/chapters/10.4324%2F9781410613066-9)
DOI: 10.25493/mbh3-5h0
title: Probabilistic map of the right temporal cingulate fibres (atlas of deep white matter fibre bundles, version 2018)

description: This data contains the probability map of the right temporal cingulate fibres (atlas of deep white matter fibre bundles, version 2018), in the MNI ICBM152 reference brain. This bundle was identified by fibre clustering, from the tractography datasets of 78 subjects in Neurospin’s ARCHI database. The map shows the probability of finding a fibre belonging to the bundle in each voxel of the reference brain. The maximum probability corresponds to the voxels with the highest number of putative fibres going through.
DOI: 10.25493/bweh-qrr
title: Probability map of bundle rh_PoC-SP_1 (atlas of superficial white matter fibre bundles, version 2018)

description: This data contains the probability map of a short fibre bundle connecting the right hemisphere Postcentral and Supramarginal regions of the Desikan-Killiany atlas, in the MNI ICBM152 reference brain. This bundle was identified using a hybrid approach, incorporating anatomical information (from cortical regions of interest) and fibre shape (fibre clustering), from the tractography datasets of 78 subjects in the Neurospin’s ARCHI database. The map shows the probability of finding a fibre belonging to the bundle in each voxel of the reference brain. The maximum probability corresponds to the voxels with the highest number of putative fibres going through.
DOI: 10.25493/3jx0-7e5
title: Probabilistic cytoarchitectonic map of Area p32 (pACC) (v16.1)

description: This dataset contains the distinct architectonic Area p32 (pACC) in the individual, single subject template of the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. As part of the Julich-Brain cytoarchitectonic atlas, the area was identified using cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of Düsseldorf. The results of the cytoarchitectonic analysis were then mapped to both reference spaces, where each voxel was assigned the probability to belong to Area p32 (pACC). The probability map of Area p32 (pACC) is provided in the NifTi format for each brain reference space and hemisphere. The Julich-Brain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets. Other available data versions of Area p32 (pACC): Palomero-Gallagher et al. (2019) [Data set, v16.0] [DOI: 10.25493/FZXB-M6S](https://doi.org/10.25493%2FFZXB-M6S) The most probable delineation of Area p32 (pACC) derived from the calculation of a maximum probability map of all currently released Julich-Brain brain structures can be found here: Amunts et al. (2019) [Data set, v1.18] [DOI: 10.25493/8EGG-ZAR](https://doi.org/10.25493%2F8EGG-ZAR) Amunts et al. (2020) [Data set, v2.2] [DOI: 10.25493/TAKY-64D](https://doi.org/10.25493%2FTAKY-64D)
DOI: 10.34810/data72/376
title: 01CO_1.MR.0004.0194.2016.02.04.15.44.11.109375.67141670.IMA
DOI: 10.25493/wejk-xvh
title: Characterization of prefrontal cortex responses to cerebellar nuclei stimulation in vivo

description: This project investigates the functional connectivity between the cerebellum and the prefrontal cortex. It is known that the cerebellum is indirectly connected to the prefrontal cortex through two main pathways, making synapses in the thalamus and in the ventral tegmental area. In this project, we electrically stimulated the cerebellar dentate nucleus and we recorded single-unit activity in the prelimbic region (PrL) of the medial prefrontal cortex (mPFC). This connection has been described recently (Watson et al., 2014), though not still fully investigated. In this project, extracellular recordings of the spiking activity of single-units in the PrL are performed using extracellular electrodes. The cerebellar dentate nucleus is stimulated using a tungsten bipolar electrode delivering 100Hz pulses for 200ms.