cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25470232
title: Supplementary Material for: Cerebral tau deposition in co-morbid progressive supranuclear palsy and amyotrophic lateral sclerosis: a [18F]-flortaucipir and 7T MRI study

description: Introduction
Progressive supranuclear palsy (PSP) is a four-repeat tauopathy characterized by multiple clinicopathologic subtypes. Advanced neuroimaging techniques have shown an early ability to distinguish PSP subtypes non-invasively for improved diagnosis. This study utilized tau-PET imaging and MRI techniques at 7 Tesla (7T) to determine the neuroimaging profile of a participant with comorbid PSP and amyotrophic lateral sclerosis (ALS).

Method
[18F]-flortaucipir PET imaging was performed on one participant with PSP-ALS, one participant with typical PSP (Richardson’s syndrome; PSP-RS), and 15 healthy control volunteers. Standardized uptake value ratio (SUVR) in each brain region was compared between PSP participants and controls. Quantitative susceptibility mapping (QSM) and inflow-based vascular-space occupancy (iVASO) MRI at 7T were performed on the two PSP participants and on two age-matched healthy controls to evaluate for differences in regional brain iron content and arteriolar cerebral blood volume (CBVa), respectively. 

Results
In the participant with PSP-ALS, the precentral gyrus demonstrated the highest [18F]-flortaucipir uptake of all brain regions relative to controls (z-score 1.94). In the participant with PSP-RS, [18F]-flortaucipir uptake relative to controls was highest in subcortical regions, including the pallidum, thalamus, hippocampus, and brainstem (z-scores 1.08, 1.41, 1.49, 1.32, respectively). Susceptibility values as a measure of brain iron content were higher in the globus pallidus and substantia nigra than in the midbrain and pons in each participant, regardless of group. CBVa values tended to be higher in the subcortical gray matter in PSP participants than in controls, although large measurement variability was noted in controls across multiple regions. 

Conclusion
In vivo tau PET imaging of an individual with PSP-ALS overlap demonstrated increased tau burden in the motor cortex that was not observed in PSP-RS or control participants. Consistent with prior PET studies, tau burden in PSP-RS was mainly observed in subcortical regions, including the brainstem and basal ganglia. QSM data suggest that off-target binding to iron may account for some but not all of the increased [18F]-flortaucipir uptake in the basal ganglia in PSP-RS. These findings support existing evidence that tau PET imaging can distinguish among PSP subtypes by detecting distinct regional patterns of tau deposition in the brain. Larger studies are needed to determine whether CBVa is sensitive to changes in brain microvasculature in PSP.
DOI: 10.6084/m9.figshare.25470232.v1
title: Supplementary Material for: Cerebral tau deposition in co-morbid progressive supranuclear palsy and amyotrophic lateral sclerosis: a [18F]-flortaucipir and 7T MRI study

description: Introduction
Progressive supranuclear palsy (PSP) is a four-repeat tauopathy characterized by multiple clinicopathologic subtypes. Advanced neuroimaging techniques have shown an early ability to distinguish PSP subtypes non-invasively for improved diagnosis. This study utilized tau-PET imaging and MRI techniques at 7 Tesla (7T) to determine the neuroimaging profile of a participant with comorbid PSP and amyotrophic lateral sclerosis (ALS).

Method
[18F]-flortaucipir PET imaging was performed on one participant with PSP-ALS, one participant with typical PSP (Richardson’s syndrome; PSP-RS), and 15 healthy control volunteers. Standardized uptake value ratio (SUVR) in each brain region was compared between PSP participants and controls. Quantitative susceptibility mapping (QSM) and inflow-based vascular-space occupancy (iVASO) MRI at 7T were performed on the two PSP participants and on two age-matched healthy controls to evaluate for differences in regional brain iron content and arteriolar cerebral blood volume (CBVa), respectively. 

Results
In the participant with PSP-ALS, the precentral gyrus demonstrated the highest [18F]-flortaucipir uptake of all brain regions relative to controls (z-score 1.94). In the participant with PSP-RS, [18F]-flortaucipir uptake relative to controls was highest in subcortical regions, including the pallidum, thalamus, hippocampus, and brainstem (z-scores 1.08, 1.41, 1.49, 1.32, respectively). Susceptibility values as a measure of brain iron content were higher in the globus pallidus and substantia nigra than in the midbrain and pons in each participant, regardless of group. CBVa values tended to be higher in the subcortical gray matter in PSP participants than in controls, although large measurement variability was noted in controls across multiple regions. 

Conclusion
In vivo tau PET imaging of an individual with PSP-ALS overlap demonstrated increased tau burden in the motor cortex that was not observed in PSP-RS or control participants. Consistent with prior PET studies, tau burden in PSP-RS was mainly observed in subcortical regions, including the brainstem and basal ganglia. QSM data suggest that off-target binding to iron may account for some but not all of the increased [18F]-flortaucipir uptake in the basal ganglia in PSP-RS. These findings support existing evidence that tau PET imaging can distinguish among PSP subtypes by detecting distinct regional patterns of tau deposition in the brain. Larger studies are needed to determine whether CBVa is sensitive to changes in brain microvasculature in PSP.
DOI: 10.60566/rjrhf-7wv24
title: ARBOCARTO-v2 Input data

description: Satellite

SPOT6/7
Sentinel-2
Other

Land-use data: Urban Atlas, land-use produced by CES OSO, IGN (OCS GE)
Open data: OpenStreetMap
IRIS breakdown (INSEE – IGN)
Meteorological data: daily rainfall and temperatures (Météo France)
DOI: 10.5281/zenodo.10868345
title: Quantitative Study Group: Fat Fraction

description: Fat Fraction============

In this directory there are Fat Fraction datasets recorded using the Dixon 3-point method on a Siemens Prisma 3T MRI scanner. There are three time points: 3.45 ms, 4.60 ms, 5.75 ms. There is a magnitude mode image (35, 38, 41) and a phase image (36, 39, 42) for each time point, for each of 5 slices through the phantom.
DOI: 10.5281/zenodo.10868346
title: Quantitative Study Group: Fat Fraction

description: Fat Fraction============

In this directory there are Fat Fraction datasets recorded using the Dixon 3-point method on a Siemens Prisma 3T MRI scanner. There are three time points: 3.45 ms, 4.60 ms, 5.75 ms. There is a magnitude mode image (35, 38, 41) and a phase image (36, 39, 42) for each time point, for each of 5 slices through the phantom.
DOI: 10.5519/qd.gl89x3nw
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (43 records)
DOI: 10.5281/zenodo.10868280
title: Data for: Arbutus unedo L. fractions exhibit chemotherapeutic properties for the treatment of gastrointestinal stromal tumors

description: FID files of the 1H NMR spectra of Arbutus unedo fractions.
DOI: 10.5281/zenodo.10868281
title: Data for: Arbutus unedo L. fractions exhibit chemotherapeutic properties for the treatment of gastrointestinal stromal tumors

description: FID files of the 1H NMR spectra of Arbutus unedo fractions.
DOI: 10.5281/zenodo.10868349
title: Quantitative Study Group: T_1

description: In this directory there are T_1 inversion recovery datasets recorded in magnitude mode at 10 inversion times using a Siemens Prisma 3T MRI scanner. Each image contains a phantom with 12 vials, each with a different SI traceable concentration of MnCl_2 or NiCl_2.
DOI: 10.5281/zenodo.10868350
title: Quantitative Study Group: T_1

description: In this directory there are T_1 inversion recovery datasets recorded in magnitude mode at 10 inversion times using a Siemens Prisma 3T MRI scanner. Each image contains a phantom with 12 vials, each with a different SI traceable concentration of MnCl_2 or NiCl_2.
DOI: 10.5281/zenodo.10868360
title: Quantitative Study Group: T_2^*

description: In this directory there are T2star GRE datasets recorded in magnitude mode at 11 echo times using a Siemens Prisma 3T MRI scanner. Each image contains a phantom with 12 vials, each with a different SI traceable concentration of NiCl2 or FeCl3.
DOI: 10.5281/zenodo.10868361
title: Quantitative Study Group: T_2^*

description: In this directory there are T2star GRE datasets recorded in magnitude mode at 11 echo times using a Siemens Prisma 3T MRI scanner. Each image contains a phantom with 12 vials, each with a different SI traceable concentration of NiCl2 or FeCl3.
DOI: 10.6084/m9.figshare.25470136
title: PeltierRocker_CAD

description: CAD files for the 3D printable biofilm incubator with temperature and flow control.
DOI: 10.6084/m9.figshare.25470136.v1
title: PeltierRocker_CAD

description: CAD files for the 3D printable biofilm incubator with temperature and flow control.
DOI: 10.5281/zenodo.10868354
title: Fish fauna of the Khoper pondscapes
DOI: 10.6084/m9.figshare.25470292
title: Supplementary Material for: ERRγ1 and Aromatase Expression in Human Placental Tissues from Term Deliveries of Large for Gestational Age (LGA) Newborns

description: Introduction: Being born either large (LGA) or small for gestational age (SGA) has been associated with an increased risk of developing metabolic syndrome in adulthood. However, the mechanism underlying this early programming remained unclear. 
Estrogen-related receptor gamma (ERRγ) is an orphan nuclear receptor with a high expression in human placenta, particularly ERRγ1. ERRγ has been proposed to play a central role in controlling genes involved in energy metabolism. In placenta, ERRγ1 acts as an oxygen-responsive transcription factor regulating aromatase (Aro) expression during trophoblast differentiation. Aromatase is an enzyme that catalyzes the synthesis of estrogens from androgens and is located in the syncytiotrophoblast. An adequate estrogen-androgen balance is required for normal pregnancy progression. Our aim was to analyze ERRγ1 and Aro mRNA in human placenta from term LGA newborns. We propose that ERRγ1 and CYP19A1 expressions in human placenta from LGA newborns are impaired, which would modify fetal programming of LGA newborns, since an imbalance in intrauterine estrogen-androgen ratio would be occurred
Methods: Total RNA was obtained from placental tissues of LGA (GA: 39-41 weeks, n=8) and adequate for gestational age (AGA; 39-40 weeks, n=10) newborns. ERRγ1 and Aro mRNA variants were analyzed by RT2-PCR. Primers for Aro analysis were specific for Total aromatase (TotalAro) binding in exons 2-3 and for Active aromatase (ActAro) in exons 9-10. Aro protein was analyzed by Western-blot.
Results: ERRγ1 mRNA was significantly higher in LGA compare to AGA. TotalAro mRNA was significantly lower in LGA in comparison with AGA control. Similar results with Aro protein. In contrast ActAro/TotalAro ratio was higher in LGA compared to the AGA control. 
Conclusions: High expression of ERRγ1 as well as ActAro/TotalAro ratio in LGA suggests that ERRγ1 is involved in ActAro variant expression and hence disrupted estrogen-androgen balance in the intrauterine environment. 
We propose that dysregulation of ERRγ1 in placenta might modify the estrogen-androgen balance in the intrauterine environment in LGA newborns, possibly representing one of the key factors in the regulation of fetal programming.
DOI: 10.6084/m9.figshare.25470292.v1
title: Supplementary Material for: ERRγ1 and Aromatase Expression in Human Placental Tissues from Term Deliveries of Large for Gestational Age (LGA) Newborns

description: Introduction: Being born either large (LGA) or small for gestational age (SGA) has been associated with an increased risk of developing metabolic syndrome in adulthood. However, the mechanism underlying this early programming remained unclear. 
Estrogen-related receptor gamma (ERRγ) is an orphan nuclear receptor with a high expression in human placenta, particularly ERRγ1. ERRγ has been proposed to play a central role in controlling genes involved in energy metabolism. In placenta, ERRγ1 acts as an oxygen-responsive transcription factor regulating aromatase (Aro) expression during trophoblast differentiation. Aromatase is an enzyme that catalyzes the synthesis of estrogens from androgens and is located in the syncytiotrophoblast. An adequate estrogen-androgen balance is required for normal pregnancy progression. Our aim was to analyze ERRγ1 and Aro mRNA in human placenta from term LGA newborns. We propose that ERRγ1 and CYP19A1 expressions in human placenta from LGA newborns are impaired, which would modify fetal programming of LGA newborns, since an imbalance in intrauterine estrogen-androgen ratio would be occurred
Methods: Total RNA was obtained from placental tissues of LGA (GA: 39-41 weeks, n=8) and adequate for gestational age (AGA; 39-40 weeks, n=10) newborns. ERRγ1 and Aro mRNA variants were analyzed by RT2-PCR. Primers for Aro analysis were specific for Total aromatase (TotalAro) binding in exons 2-3 and for Active aromatase (ActAro) in exons 9-10. Aro protein was analyzed by Western-blot.
Results: ERRγ1 mRNA was significantly higher in LGA compare to AGA. TotalAro mRNA was significantly lower in LGA in comparison with AGA control. Similar results with Aro protein. In contrast ActAro/TotalAro ratio was higher in LGA compared to the AGA control. 
Conclusions: High expression of ERRγ1 as well as ActAro/TotalAro ratio in LGA suggests that ERRγ1 is involved in ActAro variant expression and hence disrupted estrogen-androgen balance in the intrauterine environment. 
We propose that dysregulation of ERRγ1 in placenta might modify the estrogen-androgen balance in the intrauterine environment in LGA newborns, possibly representing one of the key factors in the regulation of fetal programming.
DOI: 10.6084/m9.figshare.25470238
title: water voles r code.pdf

description: This study investigated microhabitat preferences of reintroduced European water voles (Arvicola amphibius) at Trelusback Farm, Cornwall, UK, aiming to provide insights into habitat suitability for future reintroduction efforts. Water voles, emblematic of declining species facing extinction threats, were reintroduced to Trelusback Farm as part of rewilding conservation strategies. Utilizing post-release monitoring, I assessed abiotic (bank height, water depth) and biotic (vegetation abundance, alpha species richness, vegetation height) characteristics of microhabitats to delineate present (water vole-occupied) and absent (non-occupied) sites. Voles exhibited a preference for an abundance of herbaceous vegetation as well as elevated banks, and controversially swathes of shorter vegetation at riparian edges. These findings underscore the importance of multifaceted habitat attributes in guiding reintroduction success.
DOI: 10.6084/m9.figshare.25470238.v1
title: water voles r code.pdf

description: This study investigated microhabitat preferences of reintroduced European water voles (Arvicola amphibius) at Trelusback Farm, Cornwall, UK, aiming to provide insights into habitat suitability for future reintroduction efforts. Water voles, emblematic of declining species facing extinction threats, were reintroduced to Trelusback Farm as part of rewilding conservation strategies. Utilizing post-release monitoring, I assessed abiotic (bank height, water depth) and biotic (vegetation abundance, alpha species richness, vegetation height) characteristics of microhabitats to delineate present (water vole-occupied) and absent (non-occupied) sites. Voles exhibited a preference for an abundance of herbaceous vegetation as well as elevated banks, and controversially swathes of shorter vegetation at riparian edges. These findings underscore the importance of multifaceted habitat attributes in guiding reintroduction success.
DOI: 10.5281/zenodo.10523321
title: Supplementary data to Frasson et al. 2023

description: Supplementary data for Frasson et al. 2023 submitted to Solid Earth. The data consist of full snapshots of the geoids, topography, CMB heat flux, and composition at the CMB for the six cases of the study; the PCA outputs for the six cases; and movies showing the time evolutions of the outputs in the mantle convection models.

 

The full snapshots are given in HDF5 format, with one file per time step. They can be found in the archives MF.zip and MC.zip for the MF model and the MC model respectively. The files contain:



The fields in the physical space. The first coordinate is the latitude, the second coordinate is the longitude (dataset "data").

The latitudes and longitudes associated with the fields (datasets "latitude" and "longitude").

Some information regarding the snapshots (attributes "Time (Myr)", "Model", "Case", "Correction", and "Unit").


The files are called "name_xxxx.h5", where xxxx stands for the time in Myr before the end of the simulation.The names of the files are:



qcmb: CMB heat flux

geoid: Total geoid

geoid_nolvv: No LVVs geoid

topo: Topography

prim: Composition at the CMB


 

The PCA outputs are given in HDF5 format. Each file has an "outputs" and a "grid" group. The "outputs" section gives:



The average heat flux pattern. The first coordinate is the latitude, the second coordinate is the longitude (dataset "average").

The list of patterns for each PCA component in physical space. The first coordinate is the latitude, the second coordinate is the longitude (dataset "pattern").

The time-dependent weight of the components. The first coordinate is the time, the second coordinate is the component number (dataset "weights").

The singular values of the components  (dataset "singular values").

The time in Myr (dataset "Time").

The component numbers (dataset "components").


The "grid" group gives the latitudes (dataset "latitude") and the longitudes (dataset "longitude") associated with the patterns.

 

Description of the movies:



outputs_MF: As in Fig. 2 in Frasson et al. 2023.

outputs_MC: As in Fig. 3 in Frasson et al. 2023.

qcmb_MF: CMB heat flux in cases MF0, MF1, MF2, and MF* in a Mollweide projection. Black lines delineate the edges of basal chemical piles.

qcmb_MC: CMB heat flux in cases MC0 and MC1 in a Mollweide projection. Black lines delineate the edges of basal chemical piles.
DOI: 10.5281/zenodo.10868304
title: Supplementary data to Frasson et al. 2024

description: Supplementary data and code for Frasson et al. 2024  accepted for publication in Solid Earth. The data consist of full snapshots of the geoids, topography, CMB heat flux, and composition at the CMB for the six cases of the study; the PCA outputs for the six cases; and movies showing the time evolutions of the outputs in the mantle convection models. The scripts can be ran on the snapshots to compute the principal component analysis (PCA) and the true polar wander (TPW).

 

The full snapshots are given in HDF5 format, with one file per time step. They can be found in the archives MF.zip and MC.zip for the MF model and the MC model respectively. The files contain:



The fields in the physical space. The first coordinate is the latitude, the second coordinate is the longitude (dataset "data").

The latitudes and longitudes associated with the fields (datasets "latitude" and "longitude").

Some information regarding the snapshots (attributes "Time (Myr)", "Model", "Case", "Correction", and "Unit").


The files are called "name_xxxx.h5", where xxxx stands for the time in Myr before the end of the simulation.The names of the files are:



qcmb: CMB heat flux

geoid: Total geoid

geoid_nolvv: No LVVs geoid

topo: Topography

prim: Composition at the CMB


 

The PCA outputs are given in HDF5 format. Each file has an "outputs" and a "grid" group. The "outputs" section gives:



The average heat flux pattern. The first coordinate is the latitude, the second coordinate is the longitude (dataset "average").

The list of patterns for each PCA component in physical space. The first coordinate is the latitude, the second coordinate is the longitude (dataset "pattern").

The time-dependent weight of the components. The first coordinate is the time, the second coordinate is the component number (dataset "weights").

The singular values of the components  (dataset "singular values").

The time in Myr (dataset "Time").

The component numbers (dataset "components").


The "grid" group gives the latitudes (dataset "latitude") and the longitudes (dataset "longitude") associated with the patterns.

 

Description of the movies:



outputs_MF: As in Fig. 2 in Frasson et al. 2024.

outputs_MC: As in Fig. 3 in Frasson et al. 2024.

qcmb_MF: CMB heat flux in cases MF0, MF1, MF2, and MF* in a Mollweide projection. Black lines delineate the edges of basal chemical piles.

qcmb_MC: CMB heat flux in cases MC0 and MC1 in a Mollweide projection. Black lines delineate the edges of basal chemical piles.


 

Description of the scripts



PCA.py: Computes the PCA of the field stored in the path provided as argument for the given model.

inertia.py: Computes the successive positions of the inertia axis. This script includes functions to rotate the outputs according to the positions of the inertia axis.
DOI: 10.5281/zenodo.8205152
title: Supplementary data to Frasson et al. 2024

description: Supplementary data and code for Frasson et al. 2024  accepted for publication in Solid Earth. The data consist of full snapshots of the geoids, topography, CMB heat flux, and composition at the CMB for the six cases of the study; the PCA outputs for the six cases; and movies showing the time evolutions of the outputs in the mantle convection models. The scripts can be ran on the snapshots to compute the principal component analysis (PCA) and the true polar wander (TPW).

 

The full snapshots are given in HDF5 format, with one file per time step. They can be found in the archives MF.zip and MC.zip for the MF model and the MC model respectively. The files contain:



The fields in the physical space. The first coordinate is the latitude, the second coordinate is the longitude (dataset "data").

The latitudes and longitudes associated with the fields (datasets "latitude" and "longitude").

Some information regarding the snapshots (attributes "Time (Myr)", "Model", "Case", "Correction", and "Unit").


The files are called "name_xxxx.h5", where xxxx stands for the time in Myr before the end of the simulation.The names of the files are:



qcmb: CMB heat flux

geoid: Total geoid

geoid_nolvv: No LVVs geoid

topo: Topography

prim: Composition at the CMB


 

The PCA outputs are given in HDF5 format. Each file has an "outputs" and a "grid" group. The "outputs" section gives:



The average heat flux pattern. The first coordinate is the latitude, the second coordinate is the longitude (dataset "average").

The list of patterns for each PCA component in physical space. The first coordinate is the latitude, the second coordinate is the longitude (dataset "pattern").

The time-dependent weight of the components. The first coordinate is the time, the second coordinate is the component number (dataset "weights").

The singular values of the components  (dataset "singular values").

The time in Myr (dataset "Time").

The component numbers (dataset "components").


The "grid" group gives the latitudes (dataset "latitude") and the longitudes (dataset "longitude") associated with the patterns.

 

Description of the movies:



outputs_MF: As in Fig. 2 in Frasson et al. 2024.

outputs_MC: As in Fig. 3 in Frasson et al. 2024.

qcmb_MF: CMB heat flux in cases MF0, MF1, MF2, and MF* in a Mollweide projection. Black lines delineate the edges of basal chemical piles.

qcmb_MC: CMB heat flux in cases MC0 and MC1 in a Mollweide projection. Black lines delineate the edges of basal chemical piles.


 

Description of the scripts



PCA.py: Computes the PCA of the field stored in the path provided as argument for the given model.

inertia.py: Computes the successive positions of the inertia axis. This script includes functions to rotate the outputs according to the positions of the inertia axis.