cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35077/act-jar
title: Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819206421

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819206421', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.302', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'38', Ageunit:'years', Sex:'Male', Genotype:'culture, enhancer AAV', OrganName:'Brain', SampleLocalID:'819206421', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24080', Locations:'MTG' INSTRUMENT METADATA: MicroscopeType:'Vaa3D', MicroscopeManufacturerAndModel:'NA' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'
DOI: 10.25345/c5jm23r8d
title: MassIVE MSV000091748 - GNPS-Adding Open Spectral Data to MassBank and PubChem using Open Source Tools to Support Non-Targeted Exposomics of Mixtures
title: Title: Adding Open Spectral Data to MassBank and PubChem using Open Source Tools to Support Non-Targeted Exposomics of Mixtures Author: Anjana Elapavalore1*, Todor Kondic, Randolph R. Singh1,2, Benjamin A. Shoemaker3, Paul A. Thiessen3, Jian Zhang3, Evan E. Bolton3, Emma L. Schymanski1*
DOI: 10.35077/act-jaw
title: Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819209252

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819209252', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.302', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'40', Ageunit:'years', Sex:'Male', Genotype:'culture, enhancer AAV', OrganName:'Brain', SampleLocalID:'819209252', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24080', Locations:'MTG' INSTRUMENT METADATA: MicroscopeType:'Vaa3D', MicroscopeManufacturerAndModel:'NA' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'
DOI: 10.5281/zenodo.7828403
title: Raw data for: Structure and assembly of a bacterial gasdermin pore

description: This repository contains raw data and code related to "Structure and assembly of a bacterial gasdermin pore" by Johnson et al. Included are molecular dynamics parameter files, structure files after energy minimization and equilibration steps, production trajectories, and code used for analysis. Trajectories are subsampled with every second frame of the original raw trajectories. This results in 1 frame / 2 ns for simulations of full 52-meric pores and 1 frame / 1 ns for all other simulations. <br> Contact information:<br> Name: Stefan L. Schaefer<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: stefan.schaefer@biophys.mpg.de
description: This work was supported by the Max Planck Society and the Collaborative Research Center 1507 funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). We also thank the Max Planck Computing and Data Facility (MPCDF) for computational resources.
DOI: 10.5281/zenodo.7828402
title: Raw data for: Structure and assembly of a bacterial gasdermin pore

description: This repository contains raw data and code related to "Structure and assembly of a bacterial gasdermin pore" by Johnson et al. Included are molecular dynamics parameter files, structure files after energy minimization and equilibration steps, production trajectories, and code used for analysis. Trajectories are subsampled with every second frame of the original raw trajectories. This results in 1 frame / 2 ns for simulations of full 52-meric pores and 1 frame / 1 ns for all other simulations. <br> Contact information:<br> Name: Stefan L. Schaefer<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: stefan.schaefer@biophys.mpg.de
description: This work was supported by the Max Planck Society and the Collaborative Research Center 1507 funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). We also thank the Max Planck Computing and Data Facility (MPCDF) for computational resources.
DOI: 10.35077/act-jet
title: Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819213795

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819213795', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.302', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'41', Ageunit:'years', Sex:'Male', Genotype:'culture, enhancer AAV', OrganName:'Brain', SampleLocalID:'819213795', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24080', Locations:'MTG' INSTRUMENT METADATA: MicroscopeType:'Vaa3D', MicroscopeManufacturerAndModel:'NA' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'
DOI: 10.6084/m9.figshare.22661470
title: S1 Table_Characteristics of included studies.docx

description: The characteristics of included studies
DOI: 10.6084/m9.figshare.22661470.v1
title: S1 Table_Characteristics of included studies.docx

description: The characteristics of included studies
DOI: 10.6084/m9.figshare.22661481
title: primitives.pl from Hypothesizing an algorithm from one example: the role of specificity

description: Statistical machine learning usually achieves high-accuracy models by employing tens of thousands of examples. By contrast, both children and adult humans typically learn new concepts from either one or a small number of instances. The high data efficiency of human learning is not easily explained in terms of standard formal frameworks for machine learning, including Gold’s learning-in-the-limit framework and Valiant’s probably approximately correct (PAC) model. This paper explores ways in which this apparent disparity between human and machine learning can be reconciled by considering algorithms involving a preference for specificity combined with program minimality. It is shown how this can be efficiently enacted using hierarchical search based on identification of certificates and push-down automata to support hypothesizing compactly expressed maximal efficiency algorithms. Early results of a new system called DeepLog indicate that such approaches can support efficient top-down construction of relatively complex logic programs from a single example.This article is part of a discussion meeting issue ‘Cognitive artificial intelligence’.
DOI: 10.6084/m9.figshare.22661481.v1
title: primitives.pl from Hypothesizing an algorithm from one example: the role of specificity

description: Statistical machine learning usually achieves high-accuracy models by employing tens of thousands of examples. By contrast, both children and adult humans typically learn new concepts from either one or a small number of instances. The high data efficiency of human learning is not easily explained in terms of standard formal frameworks for machine learning, including Gold’s learning-in-the-limit framework and Valiant’s probably approximately correct (PAC) model. This paper explores ways in which this apparent disparity between human and machine learning can be reconciled by considering algorithms involving a preference for specificity combined with program minimality. It is shown how this can be efficiently enacted using hierarchical search based on identification of certificates and push-down automata to support hypothesizing compactly expressed maximal efficiency algorithms. Early results of a new system called DeepLog indicate that such approaches can support efficient top-down construction of relatively complex logic programs from a single example.This article is part of a discussion meeting issue ‘Cognitive artificial intelligence’.
DOI: 10.5281/zenodo.7696898
title: Amundsen Sea seal-tag CTD data (2014, 2019, 2020)

description: 1. Seal-tag hydrographic CTD measurements collected in the Amundsen Sea in 2014, 2019, and 2020. Columns are: Latitude [<sup>o</sup>], Longitude [<sup>o</sup>], Temperature [<sup>o</sup>C], Salinity [PSU], depth, z [m], absolute salinity, SA [g/kg], conservative temperature, CT [<sup>o</sup>C], potential temperature, PT [<sup>o</sup>C], potential density, PD [kg/m<sup>3</sup>], N<sub>2</sub>, Datetime [yyyy-mm-dd hh:mm:ss], Station/seal name. The official seal tag dataset can be found here: https://www.meop.net/database/meop-databases/. 2. Remote sensing imagery (MODIS, Landsat) dates and links.
DOI: 10.5281/zenodo.7696897
title: Amundsen Sea seal-tag CTD data (2014, 2019, 2020)

description: 1. Seal-tag hydrographic CTD measurements collected in the Amundsen Sea in 2014, 2019, and 2020. Columns are: Latitude [<sup>o</sup>], Longitude [<sup>o</sup>], Temperature [<sup>o</sup>C], Salinity [PSU], depth, z [m], absolute salinity, SA [g/kg], conservative temperature, CT [<sup>o</sup>C], potential temperature, PT [<sup>o</sup>C], potential density, PD [kg/m<sup>3</sup>], N<sub>2</sub>, Datetime [yyyy-mm-dd hh:mm:ss], Station/seal name. The official seal tag dataset can be found here: https://www.meop.net/database/meop-databases/. 2. Remote sensing imagery (MODIS, Landsat) dates and links.
DOI: 10.6084/m9.figshare.22661452
title: Appendix 1. The keywords for PHD and pathways in titles and abstracts of 27 articles published between 2017 and 2022

description: <strong>Appendix 1.</strong> The keywords for PHD and pathways in titles and abstracts of 27 articles published between 2017 and 2022
DOI: 10.6084/m9.figshare.22661452.v1
title: Appendix 1. The keywords for PHD and pathways in titles and abstracts of 27 articles published between 2017 and 2022

description: <strong>Appendix 1.</strong> The keywords for PHD and pathways in titles and abstracts of 27 articles published between 2017 and 2022
DOI: 10.35077/act-jig
title: Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819221461

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819221461', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.302', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'39', Ageunit:'years', Sex:'Male', Genotype:'culture, enhancer AAV', OrganName:'Brain', SampleLocalID:'819221461', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24080', Locations:'MTG' INSTRUMENT METADATA: MicroscopeType:'Vaa3D', MicroscopeManufacturerAndModel:'NA' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'
DOI: 10.5281/zenodo.7847383
title: IODP Expedition 374 Scanning electron microscope images

description: Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
DOI: 10.5281/zenodo.7847382
title: IODP Expedition 374 Scanning electron microscope images

description: Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
DOI: 10.5281/zenodo.7843727
title: Surf zone circulations and orange paths

description: Spectrums.zip contains two types of files. The .spt file contain the raw data from the BunkerHill buoy outside Sylt. The fourth entry is the relative PSD of the day, and in the main body of the file the coloumns represent: frequency [Hz], PSD [m^2/Hz], Main direction, directional spreading, Skew, Kurt.<br> The .txt files contains the 2D SWAN spectrums used in the paper. For further description look to: https://swanmodel.sourceforge.io/online_doc/swanuse/node50.html. radsAndCircs.txt contain data about the circulations calculated in the surf zone. Each row corresponds to one circulations, and the coloumns correspond to: <br> Number, tide [m], spreadfactor, main direction [degr], x-location [m], y-location [m], \(\sigma [m], \Gamma_{max} [m^2/s]\). Then 100 radii and then the 100 corresponding circulations. Tracers.zip contain the 6 orange paths described in the paper. They contain lon/lat coordinates for the oranges sampled at 3Hz. BOSZ_outputs contains all the data from all the runs used in the paper. The .bosz files must be opened with the load_BZ_array.py script. Of interest of the paper are the longitudes and latitudes, X.bosz and Y.bosz; averaged U and V velocites, Ubartmp.bosz and Vbartmp.bosz. The files are stored as a MxN array, where each element correspond to the value of the variable on the calcualted grid. <br> The Drifter.txt files contains all the data of the numerical drifters. They are built up as:<br> time, xDrift1, yDrift1, xDrift2, yDrift2, xDrift3, yDrift3, ... For data about the bathymetry we refer to the LKN.SH.
DOI: 10.5281/zenodo.7843726
title: Surf zone circulations and orange paths

description: Spectrums.zip contains two types of files. The .spt file contain the raw data from the BunkerHill buoy outside Sylt. The fourth entry is the relative PSD of the day, and in the main body of the file the coloumns represent: frequency [Hz], PSD [m^2/Hz], Main direction, directional spreading, Skew, Kurt.<br> The .txt files contains the 2D SWAN spectrums used in the paper. For further description look to: https://swanmodel.sourceforge.io/online_doc/swanuse/node50.html. radsAndCircs.txt contain data about the circulations calculated in the surf zone. Each row corresponds to one circulations, and the coloumns correspond to: <br> Number, tide [m], spreadfactor, main direction [degr], x-location [m], y-location [m], \(\sigma [m], \Gamma_{max} [m^2/s]\). Then 100 radii and then the 100 corresponding circulations. Tracers.zip contain the 6 orange paths described in the paper. They contain lon/lat coordinates for the oranges sampled at 3Hz. BOSZ_outputs contains all the data from all the runs used in the paper. The .bosz files must be opened with the load_BZ_array.py script. Of interest of the paper are the longitudes and latitudes, X.bosz and Y.bosz; averaged U and V velocites, Ubartmp.bosz and Vbartmp.bosz. The files are stored as a MxN array, where each element correspond to the value of the variable on the calcualted grid. <br> The Drifter.txt files contains all the data of the numerical drifters. They are built up as:<br> time, xDrift1, yDrift1, xDrift2, yDrift2, xDrift3, yDrift3, ... For data about the bathymetry we refer to the LKN.SH.
DOI: 10.35077/act-job
title: Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819770858

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819770858', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.304', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'37', Ageunit:'years', Sex:'Male', Genotype:'culture, enhancer AAV', OrganName:'Brain', SampleLocalID:'819770858', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24080', Locations:'TemL' INSTRUMENT METADATA: MicroscopeType:'Vaa3D', MicroscopeManufacturerAndModel:'NA' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'
DOI: 10.35077/act-jog
title: Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819891764

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in .swc format from Patch-seq experiments in human neocortex, Cell ID 819891764', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.304', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'36', Ageunit:'years', Sex:'Male', Genotype:'culture, enhancer AAV', OrganName:'Brain', SampleLocalID:'819891764', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24080', Locations:'TemL' INSTRUMENT METADATA: MicroscopeType:'Vaa3D', MicroscopeManufacturerAndModel:'NA' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'