cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.34691/uchile/iae3n6
title: Optimized adeno-associated vector to deliver the unfolded protein response transcription factor XBP1s into the hippocampus ameliorates Alzheimer’s disease features in mouse models

description: Proteostasis impairment at the level of the endoplasmic reticulum (ER) is a salient feature of Alzheimer’s disease (AD). The unfolded protein response (UPR) is the main adaptive pathway to cope with protein folding stress at the ER, where the expression of the transcription factor X-Box binding protein 1 (XBP1) is central to establish repair programs. To artificially enforce the adaptive capacity of the UPR in the AD brain, we recently reported the protective effects of overexpressing active XBP1 in the nervous system through the local delivery into the hippocampus of an AD mice using adeno-associated vectors (AAVs). Here we have generated a next generation vector suitable for clinical trials by (i) expressing codon optimized human XBP1s without tags, (ii) the use the synapsin promoter to restrict expression to neurons, and (iii) a novel variant of AAV2 that has greater spreading capacity (AAV-TT) in the brain because of reduced affinity to heparin (termed AAV-TT-Syn-hXBP1s or Proteostaser-1). Treatment of 5xFAD mice with AAV-TT-Syn-hXBP1s improved long-term potentiation, memory performance, and reduced amyloid plaques deposition. In addition, we validated the protective effects of AAV-TT-Syn-hXBP1s on a model of sporadic AD based on the intracerebral injection of amyloid beta oligomers. Our results further support the therapeutic potential of targeting UPR-dependent gene expression programs as a strategy to ameliorate AD features and sustain synaptic function.
DOI: 10.60520/ieda/113252
title: Sr-Nd-Pb isotope ratios for marine sediment core TN057-6 in the southeast Atlantic Ocean and cores located under the Agulhas Current over the past 150,000 years

description: Disentangling inputs of aeolian dust, ice-rafted debris (IRD), and terrigenous detritus delivered by ocean currents to marine sediment provides important insights into Earth System processes and climate. This study uses Sr-Nd-Pb isotope ratios of the lithogenic fraction in deep-sea core TN057-6/ODP1090 (42°54’S, 8°54’E, 3751 m) from the subantarctic Southern Ocean southwest of Africa to identify source areas and quantify their relative contributions over the past 150,000 years (Marine Isotope Stage 1 to 6). We additionally report Sr-Nd-Pb isotope ratios of the lithogenic fraction in four deep-sea marine sediment cores (RC11-86, RC17-69, VM14-77, VM19-214) located under the Agulhas Current.
description: Patagonian dust, Agulhas Current and Antarctic ice rafted debris contributions to the South Atlantic Ocean over the past 150,000 years. Under Review at Proceedings of the National Academy of Science
DOI: 10.15468/dl.fucx3y
title: Occurrence Download

description: A dataset containing 198 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abramites hypselonotus (Günther, 1868)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 198 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030646-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uwkzrt
title: Occurrence Download

description: A dataset containing 210 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Magnolia nilagirica (Zenker) Figlar"
 ]
}

 The dataset includes 210 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030647-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.22343906
title: Creating and confirming observable professional activities (OPAs): A brief report on the practical approach for OPA design for resident education

description: The transition of graduate medical education to competency-based education systems has resulted in exploration of the efficacy of Entrustable Professional Activities (EPAs) and related Observable Practice Activities (OPAs) as evaluation tools. EPAs were introduced to PM&R in 2017, but no OPAs have been reported for a non-procedurally based EPA. The primary aims of this study were to create and form consensus on OPAs for the Spinal Cord Injury EPA. A Modified Delphi panel of seven experts in the field was utilized to gain consensus on ten PM&R OPAs for the Spinal Cord Injury EPA. After the first round of evaluations, most OPAs were evaluated by experts as requiring modifications (30/70 votes to keep, 34/70 votes to modify) with a majority of comments focusing on the specific content of the OPAs. Edits were made, and after the second round, the OPAs were evaluated and determined to be kept (62/70 votes to keep, 6/70 votes to modify) with most edits being about semantics of the OPAs. Ultimately, there was significant difference in all three categories between round 1 and round 2 (P &lt; 0.0001) and 10 OPAs were finalized for use. This study created 10 OPAs that can potentially help provide targeted feedback to residents on their competency in caring for patients with spinal cord injury. With regular usage, OPAs are designed to provide residents with insight into how they are progressing towards independent practice. In the future, studies should aim to assess the feasibility and utility of implementing the newly developed OPAs.
DOI: 10.6084/m9.figshare.22343906.v2
title: Creating and confirming observable professional activities (OPAs): A brief report on the practical approach for OPA design for resident education

description: The transition of graduate medical education to competency-based education systems has resulted in exploration of the efficacy of Entrustable Professional Activities (EPAs) and related Observable Practice Activities (OPAs) as evaluation tools. EPAs were introduced to PM&R in 2017, but no OPAs have been reported for a non-procedurally based EPA. The primary aims of this study were to create and form consensus on OPAs for the Spinal Cord Injury EPA. A Modified Delphi panel of seven experts in the field was utilized to gain consensus on ten PM&R OPAs for the Spinal Cord Injury EPA. After the first round of evaluations, most OPAs were evaluated by experts as requiring modifications (30/70 votes to keep, 34/70 votes to modify) with a majority of comments focusing on the specific content of the OPAs. Edits were made, and after the second round, the OPAs were evaluated and determined to be kept (62/70 votes to keep, 6/70 votes to modify) with most edits being about semantics of the OPAs. Ultimately, there was significant difference in all three categories between round 1 and round 2 (P &lt; 0.0001) and 10 OPAs were finalized for use. This study created 10 OPAs that can potentially help provide targeted feedback to residents on their competency in caring for patients with spinal cord injury. With regular usage, OPAs are designed to provide residents with insight into how they are progressing towards independent practice. In the future, studies should aim to assess the feasibility and utility of implementing the newly developed OPAs.
DOI: 10.6084/m9.figshare.19317798
title: Examining long-term motivational and behavioral outcomes of two physical activity interventions

description: To examine possible impacts of two theory-based interventions – “Enhancing quality of life through exercise: A tele-rehabilitation approach (TEQ) and Active Living Lifestyles for individuals with SCI who use Wheelchair (ALLWheel)” – 12–18 months post-intervention on the satisfaction of psychological needs and motivation for leisure-time physical activity (LTPA), LTPA participation, and participation experience. A mixed-methods follow-up study. Community. Sixteen TEQ and six ALLWheel participants completed questionnaires and a semi-structured interview, 12–18 months after completing the interventions. TEQ intervention participants received a weekly LTPA counseling session with a trained kinesiologist through videoconferencing for 8 weeks. ALLWheel participants interacted with a peer mentor who provided LTPA counseling using smartphones for 10 weeks. The Psychological Need Satisfaction in Exercise, and the Treatment Self-Regulation Questionnaire were used as primary outcome measures. The LTPA barrier self-efficacy scale, the Measure of Experiential Aspects of Participation, and the 7-day LTPA Questionnaire for Adults with SCI were used as secondary outcome measures. A coding framework was created and deductive thematic analyses were used to analyze the qualitative data. Medium to large effects were found for autonomous motivation (TEQ), competence (TEQ and ALLWheel), and barrier self-efficacy (TEQ and ALLWheel). LTPA remained higher for the TEQ intervention group compared to the control group at follow-up, while an increase in moderate-to-vigorous LTPA was found in ALLWheel participants. Community-based tele-rehabilitation and virtual rehabilitation approaches, informed by theory, may assist adults with SCI in implementing LTPA over the long term.
DOI: 10.6084/m9.figshare.19317798.v1
title: Examining long-term motivational and behavioral outcomes of two physical activity interventions

description: To examine possible impacts of two theory-based interventions – “Enhancing quality of life through exercise: A tele-rehabilitation approach (TEQ) and Active Living Lifestyles for individuals with SCI who use Wheelchair (ALLWheel)” – 12–18 months post-intervention on the satisfaction of psychological needs and motivation for leisure-time physical activity (LTPA), LTPA participation, and participation experience. A mixed-methods follow-up study. Community. Sixteen TEQ and six ALLWheel participants completed questionnaires and a semi-structured interview, 12–18 months after completing the interventions. TEQ intervention participants received a weekly LTPA counseling session with a trained kinesiologist through videoconferencing for 8 weeks. ALLWheel participants interacted with a peer mentor who provided LTPA counseling using smartphones for 10 weeks. The Psychological Need Satisfaction in Exercise, and the Treatment Self-Regulation Questionnaire were used as primary outcome measures. The LTPA barrier self-efficacy scale, the Measure of Experiential Aspects of Participation, and the 7-day LTPA Questionnaire for Adults with SCI were used as secondary outcome measures. A coding framework was created and deductive thematic analyses were used to analyze the qualitative data. Medium to large effects were found for autonomous motivation (TEQ), competence (TEQ and ALLWheel), and barrier self-efficacy (TEQ and ALLWheel). LTPA remained higher for the TEQ intervention group compared to the control group at follow-up, while an increase in moderate-to-vigorous LTPA was found in ALLWheel participants. Community-based tele-rehabilitation and virtual rehabilitation approaches, informed by theory, may assist adults with SCI in implementing LTPA over the long term.
DOI: 10.6084/m9.figshare.22343906.v1
title: Creating and confirming observable professional activities (OPAs): A brief report on the practical approach for OPA design for resident education

description: The transition of graduate medical education to competency-based education systems has resulted in exploration of the efficacy of Entrustable Professional Activities (EPAs) and related Observable Practice Activities (OPAs) as evaluation tools. EPAs were introduced to PM&R in 2017, but no OPAs have been reported for a non-procedurally based EPA. The primary aims of this study were to create and form consensus on OPAs for the Spinal Cord Injury EPA. A Modified Delphi panel of seven experts in the field was utilized to gain consensus on ten PM&R OPAs for the Spinal Cord Injury EPA. After the first round of evaluations, most OPAs were evaluated by experts as requiring modifications (30/70 votes to keep, 34/70 votes to modify) with a majority of comments focusing on the specific content of the OPAs. Edits were made, and after the second round, the OPAs were evaluated and determined to be kept (62/70 votes to keep, 6/70 votes to modify) with most edits being about semantics of the OPAs. Ultimately, there was significant difference in all three categories between round 1 and round 2 (P &lt; 0.0001) and 10 OPAs were finalized for use. This study created 10 OPAs that can potentially help provide targeted feedback to residents on their competency in caring for patients with spinal cord injury. With regular usage, OPAs are designed to provide residents with insight into how they are progressing towards independent practice. In the future, studies should aim to assess the feasibility and utility of implementing the newly developed OPAs.
DOI: 10.6084/m9.figshare.19224445
title: Neuromuscular disorders in women and men with spinal cord injury are associated with changes in muscle and tendon architecture

description: The present study aimed to determine the association between neuromuscular function, motor function impairment, and muscle and tendon structures in individuals with spinal cord injury (SCI) compared to a control (non-disabled) population. A cross-sectional study with a control group. Center of Adapted Sports Training and Special Physical Education. Fifteen individuals with SCI and motor function impairments participated in the study. A paired non-disabled group was recruited for comparison. Not applicable. Muscle (biceps brachii, rectus femoris, vastus lateralis, vastus medialis, and tibialis anterior) and tendon (quadriceps and patellar tendons) structures were assessed by ultrasound imaging (thickness, pennation angle, fascicle length, and echogenicity). Neuromuscular electrophysiological disorders were also assessed using electrodiagnosis techniques (stimulus non-responsivity and chronaxie) in the same muscles. Except for the biceps brachii muscle, muscle thickness, pennation angle, and fascicle length were lower (<i>p</i> &lt; 0.01) while echogenicity and chronaxie were greater (<i>p</i> &lt; 0.01) in SCI participants. The SCI participants had a higher prevalence of neuromuscular electrophysiological disorders for all muscles, except the biceps brachii. Neuromuscular disorders occur in association with muscle and tendon maladaptation in individuals with chronic SCI. A higher prevalence of electrophysiological disorders suggests an acquired polyneuromyopathy for muscles with motor function impairment even though the muscle was innerved, in addition to widespread muscle atrophy.
DOI: 10.6084/m9.figshare.19224445.v1
title: Neuromuscular disorders in women and men with spinal cord injury are associated with changes in muscle and tendon architecture

description: The present study aimed to determine the association between neuromuscular function, motor function impairment, and muscle and tendon structures in individuals with spinal cord injury (SCI) compared to a control (non-disabled) population. A cross-sectional study with a control group. Center of Adapted Sports Training and Special Physical Education. Fifteen individuals with SCI and motor function impairments participated in the study. A paired non-disabled group was recruited for comparison. Not applicable. Muscle (biceps brachii, rectus femoris, vastus lateralis, vastus medialis, and tibialis anterior) and tendon (quadriceps and patellar tendons) structures were assessed by ultrasound imaging (thickness, pennation angle, fascicle length, and echogenicity). Neuromuscular electrophysiological disorders were also assessed using electrodiagnosis techniques (stimulus non-responsivity and chronaxie) in the same muscles. Except for the biceps brachii muscle, muscle thickness, pennation angle, and fascicle length were lower (<i>p</i> &lt; 0.01) while echogenicity and chronaxie were greater (<i>p</i> &lt; 0.01) in SCI participants. The SCI participants had a higher prevalence of neuromuscular electrophysiological disorders for all muscles, except the biceps brachii. Neuromuscular disorders occur in association with muscle and tendon maladaptation in individuals with chronic SCI. A higher prevalence of electrophysiological disorders suggests an acquired polyneuromyopathy for muscles with motor function impairment even though the muscle was innerved, in addition to widespread muscle atrophy.
DOI: 10.15468/dl.s4xqg8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"in","key":"TAXON_KEY","values":["1"],"matchCase":false},{"type":"equals","key":"HAS_COORDINATE","value":"true","matchCase":false},{"type":"in","key":"BASIS_OF_RECORD","values":["Preserved Specimen","Material Citation"],"matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030645-240626123714530/datasets/export for details.
DOI: 10.5281/zenodo.12515410
title: Processed CODEX Datasets from - Discovery and Generalization of Tissue Structures from Spatial Omics Data

description: This entry provides access to processed CODEX data files of four studies analyzed in the article "Discovery and Generalization of Tissue Structures from Spatial Omics Data". Details of datasets can be found in the STAR Methods section of the article.

For each dataset, a zip file containing multiple comma-separated values (CSV) files is included.

Each region is assigned an unique identifier (e.g., DKD_kidney_001), and its related data files are:



`{region_id}.cell_data.csv`, a table containing three columns: "CELL_ID", "X", and "Y". This table provides centroid locations for all cells segmented in this region.

`{region_id}.expression.csv`, a table containing multiple columns: "CELL_ID", "DAPI", "CD45", etc. This table provides detailed protein biomarker expression quantified for all cells in this region.

`{region_id}.scgp_annotations.csv`, a table containing two columns: "CELL_ID" and "SCGP". This table provides SCGP/SCGP-Extension annotations for all cells in this region.


Code base for SCGP is also included in this entry. Please refer to https://gitlab.com/enable-medicine-public/scgp for the latest codes, questions, and/or issues. Raw CODEX data and images will be accessible through links posted at the code base. Raw data will also be available from lead contact (A.E.T.) upon request.
DOI: 10.5281/zenodo.12682727
title: Processed CODEX Datasets from - Discovery and Generalization of Tissue Structures from Spatial Omics Data

description: This entry provides access to processed CODEX data files of four studies analyzed in the article "Discovery and Generalization of Tissue Structures from Spatial Omics Data". Details of datasets can be found in the STAR Methods section of the article.

For each dataset, a zip file containing multiple comma-separated values (CSV) files is included.

Each region is assigned an unique identifier (e.g., DKD_kidney_001), and its related data files are:



`{region_id}.cell_data.csv`, a table containing three columns: "CELL_ID", "X", and "Y". This table provides centroid locations for all cells segmented in this region.

`{region_id}.expression.csv`, a table containing multiple columns: "CELL_ID", "DAPI", "CD45", etc. This table provides detailed protein biomarker expression quantified for all cells in this region.

`{region_id}.scgp_annotations.csv`, a table containing two columns: "CELL_ID" and "SCGP". This table provides SCGP/SCGP-Extension annotations for all cells in this region.


Code base for SCGP is also included in this entry. Please refer to https://gitlab.com/enable-medicine-public/scgp for the latest codes, questions, and/or issues. Raw CODEX data and images will be accessible through links posted at the code base. Raw data will also be available from lead contact (A.E.T.) upon request.
DOI: 10.15468/dl.agsyqk
title: Occurrence Download

description: A dataset containing 198 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abramites hypselonotus (Günther, 1868)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 198 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030649-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10998456
title: Data for Huang, Luo, et al., Dopamine-mediated interactions between short- and long-term memory dynamics, Nature, 2024

description: Zip files contain voltage imaging traces and on-ball behavioral data from the five main figures in Huang, Luo, et al., Dopamine-mediated interactions between short- and long-term memory dynamics, Nature, 2024
DOI: 10.15468/dl.x9deet
title: Occurrence Download

description: A dataset containing 283 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acestrorhynchus pantaneiro Menezes, 1992",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 283 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030650-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sent4x
title: Occurrence Download

description: A dataset containing 649 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ageneiosus inermis (Linnaeus, 1766)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 649 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030651-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w2xpvm
title: Occurrence Download

description: A dataset containing 433 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aphyocharax anisitsi Eigenmann & Kennedy, 1903",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 433 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030652-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.