cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/kw0mt-7df62
title: Legionella IcmQ71::TevS 42C_On

description: Legionella IcmQ71::TevS 42C_On (HS004 E)
description: <strong>Tilt Series Date:</strong> 2019-05-31</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-51.0°, 51.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 42000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Howard Shuman (University of Chicago). Data collected by Debnath Ghosal and Yuxi Liu.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-31-50/rawdata/</p>HS004E-area3-tomo0003.mrc,  Tilt Series (Pixel Size 0.26 nm), 996.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-31-50/rawdata/HS004E-area3-tomo0003.mrc"
        > <i class="download icon"></i> Download </a></p>

        HS004E-area3-tomo0003_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-31-50/3dimage_103738/HS004E-area3-tomo0003_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/44c7r-mcc43
title: Legionella IcmQ71::TevS 42C_On

description: Legionella IcmQ71::TevS 42C_On (HS004 E)
description: <strong>Tilt Series Date:</strong> 2019-05-31</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-51.0°, 51.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 42000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Howard Shuman (University of Chicago). Data collected by Debnath Ghosal and Yuxi Liu.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-31-24/rawdata/</p>HS004E-area1-tomo0011.mrc,  Tilt Series (Pixel Size 0.26 nm), 996.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-31-24/rawdata/HS004E-area1-tomo0011.mrc"
        > <i class="download icon"></i> Download </a></p>

        HS004E-area1-tomo0011_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-31-24/3dimage_103669/HS004E-area1-tomo0011_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.6ctum7
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ctenopharyngodon idella (Valenciennes, 1844)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.7576 -24.3688,20.529 -24.0715,20.509 -24.0715,20.509 -28.5786,25.5395 -28.5786,25.5395 -24.0715,25.1306 -24.0715,24.9333 -24.4571,23.8962 -24.2467,22.8065 -24.295,22.3719 -24.7207,22.2323 -25.547,22.0387 -25.7188,21.7833 -25.7784,21.5388 -25.7113,21.3553 -25.5415,20.7576 -24.3688))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022929-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5pfvkk
title: Occurrence Download

description: A dataset containing 7451 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "OccurrenceStatus is Present",
 "TaxonKey is Stemodia L."
 ]
}

 The dataset includes 7451 records from 225 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022928-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ud4k4d
title: Occurrence Download

description: A dataset containing 3304609 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scarabaeidae"
 ]
}

 The dataset includes 3304609 records from 3815 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022796-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25403/upresearchdata.29910596
title: The examination of the current ethics topics in physiotherapy curricula and transformational needs

description: This study was motivated by the ethical transgressions of registered physiotherapists who were found guilty of unprofessional behavior by the Health Professions Council of South Africa (HPCSA), for misconduct that ranged from fraudulent conduct, performance of procedures without obtaining informed consent, and causing harm to patients. This led to an inquiry as to whether ethics are sufficiently covered in the undergraduate physiotherapy education curriculum in South Africa to curb the unprofessional behaviour. A convergent parallel mixed-methods design was employed to gather different yet complementary data when evaluating the HPCSA documents, university curricula, and conducting semi-structured interviews of the ethics educators from the respective universities. Using the triangulation method, the qualitative data from the HPCSA transgressions and the qualitative data from the document analysis of the university curricula and the interviews were converged using a mixed method to obtain the results of the study. The findings of the study demonstrated that the most frequently committed transgression was charging for services not rendered, followed by inaccurately drafted and false claims submitted to the medical aid. The core professional complaints included failure to establish the identity of a patient before treatment and not obtaining informed consent. The document analysis undertaken demonstrated that the undergraduate university curricula do cover a variety of ethics topics that prepare the students to provide quality patient care as well as ensure ethical behaviours that emphasise care and moral regulation in line with the HPCSA ethical guidelines. The interviews demonstrated curriculum transformation as a response to socio-political context changes in clinical practice. However, a lack of social media and technology ethics was identified, and the universities need to reform their curriculum to include these in the face of the fourth industrial revolution. The interviews revealed that the allocation of ethics topics within the curriculum, teaching approaches, the amount of time dedicated to ethics, and the assessment methods are highly variable across the university programs. The educators also employed various teaching approaches, ethics integration into clinical practice, and it is not taught as a cross-cutting theme through the curriculum. The recommendations are that the transgression case studies are to be used in the curriculum design to develop ethics topics that will assist in curbing poor ethical behaviours. The universities are to include business ethics in the curriculum. Ethics is to be taught in all years of training, and it is to be assessed to emphasise its importance. The HPCSA is to develop minimum standards for ethics hours and the assessment thereof. The curriculum needs to be transformed to reflect Ubuntu/African perspectives, culture, and diversity of the communities served.
DOI: 10.25403/upresearchdata.29910596.v1
title: The examination of the current ethics topics in physiotherapy curricula and transformational needs

description: This study was motivated by the ethical transgressions of registered physiotherapists who were found guilty of unprofessional behavior by the Health Professions Council of South Africa (HPCSA), for misconduct that ranged from fraudulent conduct, performance of procedures without obtaining informed consent, and causing harm to patients. This led to an inquiry as to whether ethics are sufficiently covered in the undergraduate physiotherapy education curriculum in South Africa to curb the unprofessional behaviour. A convergent parallel mixed-methods design was employed to gather different yet complementary data when evaluating the HPCSA documents, university curricula, and conducting semi-structured interviews of the ethics educators from the respective universities. Using the triangulation method, the qualitative data from the HPCSA transgressions and the qualitative data from the document analysis of the university curricula and the interviews were converged using a mixed method to obtain the results of the study. The findings of the study demonstrated that the most frequently committed transgression was charging for services not rendered, followed by inaccurately drafted and false claims submitted to the medical aid. The core professional complaints included failure to establish the identity of a patient before treatment and not obtaining informed consent. The document analysis undertaken demonstrated that the undergraduate university curricula do cover a variety of ethics topics that prepare the students to provide quality patient care as well as ensure ethical behaviours that emphasise care and moral regulation in line with the HPCSA ethical guidelines. The interviews demonstrated curriculum transformation as a response to socio-political context changes in clinical practice. However, a lack of social media and technology ethics was identified, and the universities need to reform their curriculum to include these in the face of the fourth industrial revolution. The interviews revealed that the allocation of ethics topics within the curriculum, teaching approaches, the amount of time dedicated to ethics, and the assessment methods are highly variable across the university programs. The educators also employed various teaching approaches, ethics integration into clinical practice, and it is not taught as a cross-cutting theme through the curriculum. The recommendations are that the transgression case studies are to be used in the curriculum design to develop ethics topics that will assist in curbing poor ethical behaviours. The universities are to include business ethics in the curriculum. Ethics is to be taught in all years of training, and it is to be assessed to emphasise its importance. The HPCSA is to develop minimum standards for ethics hours and the assessment thereof. The curriculum needs to be transformed to reflect Ubuntu/African perspectives, culture, and diversity of the communities served.
DOI: 10.15468/dl.3m3zvd
title: Occurrence Download

description: A dataset containing 15937 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quercus rubra",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 15937 records from 130 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000107-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fcew2m
title: Occurrence Download

description: A dataset containing 12004 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is South Africa",
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Gadiformes, Perciformes, Clupeiformes, Scorpaeniformes, Myctophiformes, Lophiiformes, Zeiformes, Lampriformes, Beryciformes, Ophidiiformes, Anguilliformes, Aulopiformes, Gasterosteiformes, Pleuronectiformes, Siluriformes, Tetraodontiformes, Mugiliformes, Osteoglossiformes, Elopiformes, Albuliformes, Notacanthiformes, Gonorynchiformes, Siluriformes, Osmeriformes, Ateleopodiformes, Percopsiformes, Zeidae, Polymixiiformes, Batrachoidiformes, Syngnathiformes, Synbranchiformes, Atheriniformes, Beloniformes, Blennioidei, Gobiesociformes)"
 ]
}

 The dataset includes 12004 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000052-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16965124
title: Dentate gyrus encodes prediction errors during learning of perceptual predictions

description: The hippocampus is involved in learning predictive associations, responding to prediction errors as well as representing predictions of future inputs. Recent work has shown that the balance of errors and predictions in the hippocampus changes over the course of learning, with errors dominating early on and predictions dominating once associations are learnt. However, the hippocampal-cortical circuit that underlies these dynamics is unknown. Here, we used ultra-high resolution 7T fMRI to investigate hippocampal subfield-specific learning dynamics, as well as layer-specific representations in the medial temporal lobe. In line with previous work, we found that hippocampal signals reversed from error signals to predictions during learning. This reversal was present in the dentate gyrus (DG), a hippocampal subfield known to emphasise differences between similar signals through pattern separation. Additionally, error-to-prediction reversals were observed in the parahippocampal cortex (PHC), as well as the lateral occipital cortex and primary visual cortex. Informational connectivity during error signalling was particularly strong between superficial layers of PHC and DG, in line with DG generating error signals by upregulating unexpected sensory signals from cortex. These findings shed light on the hippocampal-cortical circuit underlying the learning of perceptual predictions, increasing our understanding of the interaction between memory and perception.
description: System requirements

Running these analysis scripts requires Matlab (version R2021b or later), and the SPM toolbox (freely available at https://www.fil.ion.ucl.ac.uk/spm/). These scripts have been tested using Matlab versions R2021b and R2024b and SPM12. No non-standard hardware is required.

Installation guide

The Matlab scripts and data files can simply be copied to a folder of your choice. The most relevant scripts are:



Analyse_behaviour.m

Decode_predictions_withinExp_predTemplate_shuffledLabels.m

InformationalConnectivity_nonTimeResolved_predTemplate.m

InformationalConnectivity_timeResolved_predTemplate.m


Please change the path to the SPM folder at the top of these scripts to the path to SPM on your machine. When running one of the scripts, please make sure the folder containing the script is the current Matlab folder (e.g. by selecting 'Change Folder' when prompted).

Instructions for use

Simple run the scripts listed above to reproduce all the graphs and statistical analyses described in the manuscript. The scripts will automatically load the fMRI time courses for the regions of interest for all participants, and run the analyses described in the Methods section of the manuscript.
DOI: 10.5281/zenodo.16965123
title: Dentate gyrus encodes prediction errors during learning of perceptual predictions

description: The hippocampus is involved in learning predictive associations, responding to prediction errors as well as representing predictions of future inputs. Recent work has shown that the balance of errors and predictions in the hippocampus changes over the course of learning, with errors dominating early on and predictions dominating once associations are learnt. However, the hippocampal-cortical circuit that underlies these dynamics is unknown. Here, we used ultra-high resolution 7T fMRI to investigate hippocampal subfield-specific learning dynamics, as well as layer-specific representations in the medial temporal lobe. In line with previous work, we found that hippocampal signals reversed from error signals to predictions during learning. This reversal was present in the dentate gyrus (DG), a hippocampal subfield known to emphasise differences between similar signals through pattern separation. Additionally, error-to-prediction reversals were observed in the parahippocampal cortex (PHC), as well as the lateral occipital cortex and primary visual cortex. Informational connectivity during error signalling was particularly strong between superficial layers of PHC and DG, in line with DG generating error signals by upregulating unexpected sensory signals from cortex. These findings shed light on the hippocampal-cortical circuit underlying the learning of perceptual predictions, increasing our understanding of the interaction between memory and perception.
description: System requirements

Running these analysis scripts requires Matlab (version R2021b or later), and the SPM toolbox (freely available at https://www.fil.ion.ucl.ac.uk/spm/). These scripts have been tested using Matlab versions R2021b and R2024b and SPM12. No non-standard hardware is required.

Installation guide

The Matlab scripts and data files can simply be copied to a folder of your choice. The most relevant scripts are:



Analyse_behaviour.m

Decode_predictions_withinExp_predTemplate_shuffledLabels.m

InformationalConnectivity_nonTimeResolved_predTemplate.m

InformationalConnectivity_timeResolved_predTemplate.m


Please change the path to the SPM folder at the top of these scripts to the path to SPM on your machine. When running one of the scripts, please make sure the folder containing the script is the current Matlab folder (e.g. by selecting 'Change Folder' when prompted).

Instructions for use

Simple run the scripts listed above to reproduce all the graphs and statistical analyses described in the manuscript. The scripts will automatically load the fMRI time courses for the regions of interest for all participants, and run the analyses described in the Methods section of the manuscript.
DOI: 10.15468/dl.pf2wd5
title: Occurrence Download

description: A dataset containing 3254 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Etlingera elatior (Jack) R.M.Sm."
 ]
}

 The dataset includes 3254 records from 134 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023040-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/5bb5m7mnxf
title: Thermal (non)stability of multication and high-entropy layered double hydroxides

description: This is the data from the article "Multication and high-entropy layered double hydroxides: thermal (non)stability and rehydration structure (non)recovery". The dataset contains XRD, TGA, EDX.
DOI: 10.17632/5bb5m7mnxf.1
title: Thermal (non)stability of multication and high-entropy layered double hydroxides

description: This is the data from the article "Multication and high-entropy layered double hydroxides: thermal (non)stability and rehydration structure (non)recovery". The dataset contains XRD, TGA, EDX.
DOI: 10.17632/t8z6ckyr33
title: renewable energy data

description: This is data and code of wavelet quantile correlation.
DOI: 10.17632/t8z6ckyr33.1
title: renewable energy data

description: This is data and code of wavelet quantile correlation.
DOI: 10.25549/usctheses-ouc11399kinz
title: STRUCTURAL INVESTIGATIONS OF INTRINSICALLY DISORDERED REGIONS IN Î±-SYNUCLEIN VIA SITE-SELECTIVE 2H-NMR
DOI: 10.15468/dl.k96429
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Enteromius annectens (Gilchrist & Thompson, 1917)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.7576 -24.3688,20.529 -24.0715,20.509 -24.0715,20.509 -28.5786,25.5395 -28.5786,25.5395 -24.0715,25.1306 -24.0715,24.9333 -24.4571,23.8962 -24.2467,22.8065 -24.295,22.3719 -24.7207,22.2323 -25.547,22.0387 -25.7188,21.7833 -25.7784,21.5388 -25.7113,21.3553 -25.5415,20.7576 -24.3688))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023145-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/h4zwc-nb015
title: TRIM5-21R delSpry

description: TRIM5-21R delSpry 2D lattice prepared by Barbie Ganser-Pornillos and  Viswanathan Chandrasekaran
description: <strong>Tilt Series Date:</strong> 2012-11-23</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Unspecified</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: None μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Viswanathan Chandrasekarangrids purified the protein, Barbie Ganser-Pornillos assembled protein into 2D lattice. The sample was was plunge frozen and imaged at Caltech by Cora Woodward</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-11-23-2/rawdata/</p>12nov22_TRIM5_21R_delSpry_grid1_AT6BT10003.mrc,  Tilt Series (Pixel Size 0.45 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-11-23-2/rawdata/12nov22_TRIM5_21R_delSpry_grid1_AT6BT10003.mrc"
        > <i class="download icon"></i> Download </a></p>

        12nov22_TRIM5_21R_delSpry_grid1_AT6BT10003_full.rec,  Reconstruction (Pixel Size 1.8 nm), 353.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-11-23-2/3dimage_23841/12nov22_TRIM5_21R_delSpry_grid1_AT6BT10003_full.rec"
        > <i class="download icon"></i> Download </a></p>