cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.34945/f5jg6n
title: Contralateral sprouting in C57Bl/J6 mouse cervical spinal cord after unilateral pyramidotomy and cortical injection of RO48 8 weeks following injury: Figure 3

description: STUDY PURPOSE: The aim of the study was to test if a multitarget kinase inhibitor, RO48, when injected into the sensorimotor cortex 8 weeks following unilateral pyramidotomy, could promote sprouting of uninjured corticospinal tract (CST) axons into the denervated contralateral cervical spinal cord. There are two experimental groups: vehicle (DMSO) control, and 5mM RO48. Each animal received 5 injections (500nl at each of 5 locations), for a total of 2.5ul, into sensorimotor cortex. AAV8 viral particles were co-injected with the compound/control to label CST axons. DATA COLLECTED: The primary outcome measure for this dataset was “axon sprouting index”, which is a ratio of the density of labeled axon sprouts at 3 distances from the midline in the contralateral cervical spinal cord to the number of labeled axons counted in the uninjured pyramidal tract at the level of the medulla. The number of labeled axons in the medulla was estimated by measuring the area of the medullary pyramid, then counting labeled axons in 5 constant area rectangles (“boxes”) randomly placed within the medullary pyramid area as a measure of average axon density. The axon sprout density in the spinal cord was estimated by counting intersections of labeled axons in cross-sections of the cord with each of 3 lines drawn dorso-ventrally at 100, 400, and 700 um from the midline, respectively. The data were obtained from confocal images of histological sections taken at sacrifice, 5 weeks after cortical microinjections. DATA USAGE NOTES:
DOI: 10.34945/f5pc77
title: Cytokine expression and peripheral monocyte infiltration time course and effect of CCR2-antagonist treatment on chronic behavioral outcome in wildtype adult mice after controlled cortical impact TBI

description: STUDY PURPOSE: The study was designed to study the role of peripheral infiltrating monocytes to traumatic brain injury induced neuroinflammation and outcome. DATA COLLECTED: The dataset includes several cohorts of wildtype or CX3CR1(gfp/+)/CCR2(rfp/+) transgenic adult (6-7 mo) mice. TBI was induced using the controlled cortical impact model. (1) Transgenic mice were given sham or TBI surgery and samples were collected at 3 hours, 6 hours, 12 hours, 24 hours, 48 hours, 7 days, 14 days, or 28 days post-injury (dpi). Infiltrating monocytes (CD11b+,F4/80+, CCR2-rfp+, CX3CR1-gfp- and CD11b+,F4/80+, CCR2-rfp+, CX3CR1-gfp+) and resident microglia (CD11b+,F4/80+, CCR2-rfp-, CX3CR1-gfp+) numbers were measured by flow cytometry. 14 inflammatory markers were measured from isolated leukocytes in the injured brain via qPCR. (2) Wildtype adult mice were treated with vehicle or a CCR2-antagonist (CCX872). Infiltrating monocytes (CD11b+, CD45hi) were measured by flow cytometry and 18 inflammatory and oxidative stress molecule expression was measured by qPCR at 1 day post-injury (1 dpi). (3) Wildtype mice treated with vehicle or CCR2-antagonist were measured on radial arm water maze (RAWM) performance at 28 dpi. DATA USAGE NOTES: Analysis of the data revealed the temporal infiltration window of peripheral, infiltrating monocytes into the brain after TBI. Principal component analysis was used to identify the inflammatory responses associated with different monocyte (i.e. peripheral monocytes vs resident microglia) populations. Administration of CCR2 antagonist significantly reduced the number of infiltrating monocytes after TBI and resulted in reduced neuroinflammation and oxidative stress. CCR2 antagonism additionally reduced TBI-induced chronic cognitive deficits as measured on the radial arm water maze.
DOI: 10.34945/f5t01d
title: Contralateral axon sprouting in male and female c57Bl/6J mouse cervical spinal cord by uninjured corticospinal axons following unilateral pyramidotomy and cortical injection of kinase inhibitors

description: STUDY PURPOSE: This study was designed to test whether a multitarget kinase inhibitor called SBP926, when microinjected into sensorimotor cortex of male and female c57Bl/6J mice at the time of injury, could promote sprouting of uninjured corticospinal tract axons into denervated contralateral cervical spinal cord after unilateral pyramidotomy. A related kinase inhibitor, RO48, was used as a comparison group, since we already had evidence that RO48 can promote sprouting in this assay. DATA COLLECTED: Data collected: There were 4 experimental groups, depending on the solution microinjected into the cortex from which the uninjured corticospinal tract arose. These were vehicle (DMSO) control, 1mM SBP926, 10mM SBP926, and 10mM RO48. In each case the volume injected into the cortex was a total of 2.5ul (500 nl at 5 locations: -1.0mm anterioposterior (AP) and +1.0mm lateral, -0.25mm AP and +1.0mm lateral, +0.5mm AP and +1.5mm lateral, +1.25mm AP and +1.5mm lateral, +2.0mm AP and +1.5mm lateral (all coordinates in reference to bregma), at a depth of 0.5mm below the surface of the brain), and AAV8 viral particles were co-injected into the cortex to label the sprouting axons. PKC-gamma staining of cervical spinal cord cross-sections was performed to confirm unilateral pyramidal tract section. The primary outcome measure for this dataset was “sprouting index”, which is a ratio of the density of labeled axon sprouts at 3 different distances from the midline in the contralateral cervical spinal cord to the number of labeled axons counted in the uninjured pyramidal tract at the level of the medulla. The number of labeled axons in the medulla was estimated by measuring the area of the medullary pyramid, then counting labeled axons in 5 constant area rectangles (“boxes”) randomly placed within the medullary pyramid area as a measure of average axon density. The axon sprout density in the spinal cord was estimated by counting intersections of labeled axons in cross-sections of the cord with each of 3 lines drawn dorso-ventrally in the parasagittal plane at 100, 400, and 700 um from the midline, respectively. The data were obtained from confocal images of histological sections taken at sacrifice, 5 weeks after surgery. The data are part of a larger study on RO48 and its derivatives. DATA USAGE NOTES:
DOI: 10.34945/f5t595
title: Peripheral monocyte and resident microglia number and cytokine expression at subchronic timepoints after controlled cortical impact TBI in adult and aged mice

description: STUDY PURPOSE: The purpose of the study was to investigate the effect of age on the inflammatory response of peripheral, infiltrating monocytes after traumatic brain injury. DATA COLLECTED: The dataset includes several experiments with mice using the parietal controlled cortical impact (CCI) TBI model. A summary of experiments are as follows: (1) Amount of infiltrating monocytes (CD11b+, CD45hi) in the injured brain of wildtype adult (3-4 mo) and aged (18+ mo) mice at 4 and 7 days post-injury (dpi) measured by flow cytommetry. (2) Amount of infiltrating monocyte (CD11b+, CCR2-rfp+) in the injured brain and in the blood of adult and aged (22-24 mo) CCR2-rfp-labeled mice at 4 and 7 dpi measured by flow cytommetry. (3) Amount of newly proliferated infiltrating monocytes (CD11b+, F4/80+, CD45hi) and resident microglia (CD11b+, F4/80+, CD45lo) in the injured brain labeled with BrdU between 3-4 dpi. (4) CCL2, CCL7, CCL8, and CCL12 quantified by qPCR from adult and aged animals at 4 and 7 dpi (normalized to young sham controls). (5) IL-1B, TNFa, iNOS, Ym1, CD206, TGF-B, and IL4Ra inflammatory marker expression measured by qPCR in wildtype adult and aged, Sham and TBI mice at 7 dpi. (6) Radial arm water maze behavior (errors; RAWM) measured at 26-28 dpi in wildtype and CCR2 knockout adult and aged (16-18 mo), Sham and TBI mice. (7) Amount of newly proliferated infiltrating monocytes (CCR2-rfp+) in the blood and bone marrow of adult and aged CCR2-rfp-labeled mice at 4 dpi using EdU labeling and flow cytometry. DATA USAGE NOTES: Analysis of the data showed that age increased the amount of peripheral infiltrating monocytes present in the injured brain at subchronic timepoints (4 and 7 days post-injury). Furthermore, the infiltration rate of the peripheral monocytes was higher in aged mice at 4 dpi. There were corresponding age-associated increases CCR2 chemotactic ligand expression and circulating monocytes. Age additionally impaired the subchronic anti-inflammatory response in the monocyte population. Knocking out CCR2 to inhibit monocyte infiltration mitigated chronic TBI-induced deficits on the radial arm water maze in aged mice.
DOI: 10.34945/f5vs3d
title: CatWalk Gait parameters at 8 weeks after T10 thoracic contusion using the MASCIS impactor model III in male and female 8- to 10-week old rats

description: STUDY PURPOSE: In preclinical studies of spinal cord injury (SCI), behavioral assessment is crucial in determining the effectiveness of interventions. As an automated gait analysis system, catwalk provides a large number of objective gait parameters through the acquisition and calculation of rodent footprints and videos. However, the gait parameters may not all be suitable for assessing hindlimb locomotor function in animals with thoracic contusion SCI. The purpose of this study was to discover CatWalk gait parameters applicable to different severity ranges (sham, mild, moderate, severe) of T10 spinal cord contusion injury in rats. DATA COLLECTED: A total of 48 adult male and female Wistar rats, weighing 190-210 g and aged 8-10 weeks old, were used in this study. The thoracic spinal cord of rats was contused by MASCIS impactor model III (W. M. Keck Center, Rutgers University, United States) according to the modified Allen's method. The animals subsequently underwent T10 spinal cord contusions caused by a 10 g impactor dropped at varying heights of 12.5 mm (mild), 25.0 mm (moderate), and 50.0 mm (severe). Animals in the sham group only received laminectomy without contusion.N=12/group. Catwalk gait analysis were performed at 8 weeks post-injury. The performance of moving in one direction without stopping or turning around was recorded.The specific detection settings used in the experiment were as follows: camera gain = 17.75 dB, green intensity threshold = 0.12, red ceiling light= 17.1 V, and green walkway light = 15.4 V. Multiple groups were compared using Kruskal-Wallis test with Dunn's post-hoc test. DATA USAGE NOTES:
DOI: 10.34945/f5xs31
title: Assessment of spinal cord glutathione levels and regulatory pathways at 1- and 3-days post-injury after 60 kDyn T9 spinal-contusion using the Infinite Horizons impactor in male and female 4- and 14-month old mice and evaluating n-acetylcysteine amide as a therapy in female 4- and 14-month old mice to restore spinal cord levels of glutathione and to protect against oxidative stress and affect locomotor outcomes and thermal sensitivity by 28-days after spinal cord injury.

description: STUDY PURPOSE: The purpose of this study was to evaluate the role of advanced age at the time of spinal cord injury (SCI) on antioxidant defense, with an emphasis on glutathione synthesis and metabolism. Further, this study aimed to determine if enhancing spinal levels of glutathione using the cysteine supplement, n-acetylcysteine amide (NACA), would confer age-dependent effects on functional and histological outcomes. DATA COLLECTED: Levels of spinal glutathione were deterred in sham and injured mice at 1- and 3-days post-injury (dpi). Further, the relative protein abundance of glutathione synthetase, peroxidase, reductase, and glutamyl-cysteine ligase were determined on western blot. Activity assays were used to determine the function of glutathione peroxidase and reductase at 1- and 3-dpi. Accumulation of oxidative stress using dot blots against 3-nitrotyrosine or 4-hydroxynonenol were obtained. Mice were treated with n-acetylcysteine amide and spinal cord levels of glutathione were determined both in naive 4-month-old mice and after SCI in 4- and 14-month-old mice and 1-dpi. Next, mice were treated with NACA for 3-dpi and were allowed to recover for 28-days. Locomotor functions were assessed on the BMS and horizontal ladder, and the Hargreaves test of thermal hypersensitivity was used to determine effects on SCI-induced pain. Lesion outcomes and neuron survival were assessed in tissue sections. DATA USAGE NOTES:
DOI: 10.4246/ca_dwr_waterbalance_20220526_2018-md5965415f4e26af1804bb178bb95c51bde.zip
title: CA_DWR_WaterBalance_20220526_2018-md5965415f4e26af1804bb178bb95c51bde.zip
DOI: 10.4246/ca_dwr_waterbalance_20230208_2019-md55e194ed224d5ee3d9b939f81f0a8086f.zip
title: CA_DWR_WaterBalance_20230208_2019-md55e194ed224d5ee3d9b939f81f0a8086f.zip
DOI: 10.15468/dl.xf3rxh
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Diasemocera marginella (Fallén, 1823)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 15 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080403-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.myezxh
title: Occurrence Download

description: A dataset containing 5809 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Metellina segmentata (Clerck, 1757)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 5809 records from 269 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080402-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gpjd8e
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Brachydesmus tetevensis Strasser, 1973",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080404-240626123714530/datasets/export for details.
DOI: 10.15468/dl.fbfm7e
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Microtus tatricus Kratochvíl, 1952",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080405-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.269xnw
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Tetragnatha nitens (Audouin, 1826)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 92 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080407-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wfrdme
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Diasemocera glabricula (Fallén, 1813)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 75 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080408-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z8hjrc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Brachydesmus bosniensis Verhoeff, 1895",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080409-240626123714530/datasets/export for details.
DOI: 10.17592/002.2020100389
title: Numerical substorm data
title: REPPU

description: Ebihara, Y., T. Tanaka and N. Kamiyoshikawa (2019), New diagnosis for energy flow from solar wind to ionosphere during substorm: Global MHD simulation, J. Geophys. Res., 124, https://doi.org/10.1029/2018JA026117. Watanabe, M., T. Tanaka, and S. Fujita (2019), Magnetospheric Dynamo Driving Large-scale Birkeland Currents, J. Geophys. Res., 124, https://doi.org/10.1002/2018JA026025. Tanaka, T., Y. Ebihara, M. Watanabe, M. Den, S. Fujita, T. Kikuchi, K. K. Hashimoto, and R. Kataoka (2019), Development of magnetic topology during the growth phase of the substorm inducing the onset of near earth neutral line, J. Geophys. Res., 124, https://doi.org/10.1002/2018JA026386. Tanaka, T., Obara, T., et al. (2019), Magnetosphere-ionosphere convection under the due northward IMF, J. Geophys. Res., 124, http://doi.org/10.1002/2018JA026386. Yusuke Ebihara, Takuya Ikeda, Yoshiharu Omura, Takashi Tanaka, Mei-Ching Fok (2020), Nonlinear wave growth analysis of whistler-mode chorus generation regions based on coupled MHD and advection simulation of the inner magnetosphere, J. Geophy. Res., 125, https://doi.org/10.1029/2019JA026951 Tanaka, T., Y. Ebihara, M. Watanabe, M. Den, S. Fujita, T. Kikuchi, K. K. Hashimoto, and R. Kataoka (2020), Reproduction of ground magnetic variations during the SC and the substorm form the global simulation and Biot-Savart's law, J. Geophy. Res., 125, https://doi.org/10.1029/2019JA027172 Ebihara, Y., Lee, L. C., and Tanaka, T. (2020), Energy flow in the Region 2 field-aligned current region under quasi-steady convection. Journal of Geophysical Research: Space Physics, 125., e2019JA026998. https://doi.org/10.1029/2019JA026998
DOI: 10.18112/openneuro.ds004044.v2.0.3
title: WholebodySomatotopicMapping
DOI: 10.35111/ewkm-cg47
title: CSR-I (WSJ0) Complete

description: <h3>Introduction</h3><br>
<p>LDC93S6A - Complete CSR-I corpus <a href="http://catalog.ldc.upenn.edu/LDC93S6B" rel="nofollow">LDC93S6B</a> - CSR-I Sennheiser speech <a href="http://catalog.ldc.upenn.edu/LDC93S6C" rel="nofollow">LDC93S6C</a> - CSR-I other speech</p><br>
<p>During 1991, the DARPA Spoken Language Program initiated efforts to build a new corpus to support research on large-vocabulary Continuous Speech Recognition (CSR) systems.</p><br>
<p>The first two CSR Corpora consist primarily of read speech with texts drawn from a machine-readable corpus of Wall Street Journal news text and are thus often known as WSJ0 and WSJ1. (Later sections of the CSR set of corpora, however, will consist of read texts from other sources of North American business news and eventually from other news domains).</p><br>
<p>The texts to be read were selected to fall within either a 5,000-word or a 20,000-word subset of the WSJ text corpus. (See the documentation for details). Some spontaneous dictation is included in addition to the read speech. The dictation portion was collected using journalists who dictated hypothetical news articles.</p><br>
<p>Two microphones are used throughout: a close-talking Sennheiser HMD414 and a secondary microphone, which may vary. The corpora are thus offered in three configurations: the speech from the Sennheiser, the speech from the other microphone and the speech from both; all three sets include all transcriptions, tests, documentation, etc.</p><br>
<p>In general, transcriptions of the speech, test data from ARPA evaluations, scores achieved by various speech recognition systems and software used in scoring are included on separate discs from the waveform data.</p><br>
<h3>Samples</h3><br>
<p>Please listen to this <a href="desc/addenda/LDC93S6A.wav">audio sample</a>.</p></br>
Portions © 1987-1989 Dow Jones & Company, Inc., © 1992, 1993 Trustees of the University of Pennsylvania
DOI: 10.5281/zenodo.11062894
title: Data, code, and outputs for: groundwater-dependent ecosystem map exposes global dryland protection needs

description: Contains all data and code used to produce results for:

Rohde, M.M., C.M. Albano, X. Huggins, K.R. Klausmeyer, C. Morton, A. Sharman, E. Zaveri, L. Saito, Z. Freed, J.K. Howard, N. Job, H. Richter, K. Toderich, A. Rodella, T. Gleeson, J. Huntington, H.A. Chandanpurkar, A.J. Purdy, J.S. Famiglietti, M.B. Singer, D.A. Roberts, K. Caylor, J.C. Stella. 2024. Groundwater-dependent ecosystem map exposes global dryland protection needs. Nature, doi: 10.1038/s41586-024-07702-8.

The resultant global groundwater-dependent ecosystem interactive webmap is available at https://codefornature.projects.earthengine.app/view/global-gde.

The code is also available at https://github.com/XanderHuggins/global-gde-map.
DOI: 10.5281/zenodo.10695923
title: A Dataset of Reconstructed Carotid Bifurcation Lumen and Plaque Models with Centerline Tree and Simulated Hemodynamics

description: carotid_bifurcation_database.zip contains 79 cases of left and right-side carotid bifurcations (152 inner wall models). For each case, inner wall (lumen) and plaque models were extracted from computed tomography angiography (CTA) scans. The models were segmented, reconstructed, and a centerline tree was created for each geometry using the CarotidAnalyzer pipeline. The geometries include varying degrees of internal carotid stenosis. Bifurcations with 100% stenosis were omitted, as the vessel is not discernible in the scan.

carotid_flow_database.zip contains hemodynamic flow simulations of the above models. Fluid data (velocity, pressure) and surface data (wall shear stress) are given in seperate files for each case. For each field, a systolic and diastolic time step are provided.

Further information regarding the extraction pipeline and flow simulations can be obtained from the following publications:P. Eulzer,  F. von Deylen,  W.-C. Hsu,  R. Wickenhöfer,  C. M. Klingner,  and K. Lawonn (2023), A Fully Integrated Pipeline for Visual Carotid Morphology Analysis. Computer Graphics Forum, 42(3): 25-37. https://doi.org/10.1111/cgf.14808

Kevin Richter, Tristan Probst, Anna Hundertmark, Pepe Eulzer, and Kai Lawonn (2024), Longitudinal wall shear stress evaluation using centerline projection approach in the numerical simulations of the patient-based carotid artery. Computer Methods in Biomechanics and Biomedical Engineering, 27(3): 347-364. https://doi.org/10.1080/10255842.2023.2185478

P. Eulzer, K. Richter, A. Hundertmark, R. Wickenhöfer, C. M. Klingner, and K. Lawonn (2024), Instantaneous Visual Analysis of Blood Flow in Stenoses Using Morphological Similarity. Computer Graphics Forum 43(3): in print. https://doi.org/10.1111/cgf.15081