cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8479268
title: Data and code for Genus paper

description: All data and code for 2019 Genus paper (Bruckner, Ima, Nguyen, Noymer). All input data for the paper and all code for the Lee-Carter analysis, including "helper files" (sub-programs, etc.). See the file README for a catalog of what's what.<br>
DOI: 10.6084/m9.figshare.8479274.v1
title: Dataset for: Individualized Quantification of the Benefit from Reperfusion Therapy using Stroke Predictive Models

description: Purpose: Recent imaging developments have shown the potential of voxel-based models in assessing infarct growth after stroke. Many models have been proposed but their relevance in predicting the benefit of a reperfusion therapy remains unclear. We searched for a predictive model whose volumetric predictions would identify stroke patients who are to benefit from tissue Plasminogen Activator (t-PA)-induced reperfusion. Material and Methods: Forty-five cases were used to study retrospectively stroke progression from admission to end of follow-up. Predictive approaches based on various statistical models, predictive variables, and spatial filtering methods were compared. The optimal approach was chosen according to the area under the precision-recall curve (AUPRC). The final lesion volume was then predicted assuming that the patient would or would not reperfuse. Patients with an acute lesion of ≤50 mL and a predicted reduction in presence of reperfusion &gt;6 mL, and &gt;25% of the acute lesion were classified as responders. Results: The optimal model was a logistic regression using the voxel distance to the acute lesion, the volume of the acute lesion, and Gaussian-filtered MRI contrast parameters as predictive variables. The predictions gave a median AUPRC of 0.655, a median AUC of 0.976, and a median volumetric error of 8.29mL. Nineteen patients matched the responder profile. A non-significant trend of improved reduction in NIHSS score (-42.8%, p=0.09) and in lesion volume (-78.1%, p=0.21) following reperfusion was observed for responder patients. Conclusion: Despite limited volumetric accuracy, predictive stroke models can be used to quantify the benefit of reperfusion therapies.
DOI: 10.6084/m9.figshare.8479268.v1
title: Data and code for Genus paper

description: All data and code for 2019 Genus paper (Bruckner, Ima, Nguyen, Noymer). All input data for the paper and all code for the Lee-Carter analysis, including "helper files" (sub-programs, etc.). See the file README for a catalog of what's what.<br>
DOI: 10.6084/m9.figshare.8479079
title: DATA (figshare).xlsx

description: The objective of this study was to evaluate the <i>in vitro</i> antioxidant properties of sodium alginate bioactive films containing resveratrol<i> </i>and <i>Z. multiflora</i> essential oil as well as their potential synergistic effects.
DOI: 10.6084/m9.figshare.8479079.v1
title: DATA (figshare).xlsx

description: The objective of this study was to evaluate the <i>in vitro</i> antioxidant properties of sodium alginate bioactive films containing resveratrol<i> </i>and <i>Z. multiflora</i> essential oil as well as their potential synergistic effects.
DOI: 10.6084/m9.figshare.8479055
title: training set for lcquad 2.0

description: training set for lcquad 2.0
DOI: 10.6084/m9.figshare.8479052
title: test set for lcquad 2.0

description: test set for lcquad 2.0
DOI: 10.6084/m9.figshare.8476025
title: Frog decision times

description: response times in frogs to whines and whine-chucks
DOI: 10.6084/m9.figshare.8476025.v1
title: frog decision times

description: response times in frogs to whines and whine-chucks
DOI: 10.6084/m9.figshare.8475533
title: Bat decision times

description: Response times in bats with whines and whine-chucks
DOI: 10.6084/m9.figshare.8475533.v1
title: Bat_decisionTime_data_noW_Wc.csv

description: Response times in bats with whines and whine-chucks
DOI: 10.6084/m9.figshare.8438048
title: XLEAP spectra measurements

description: Calibrated spectra with photon energy labels for 650 eV and 905 eV experimental runs
DOI: 10.6084/m9.figshare.8438048.v1
title: XLEAP spectra measurements

description: Calibrated spectra with photon energy labels for 650 eV and 905 eV experimental runs
DOI: 10.6084/m9.figshare.8429231
title: Raw Data: The attenuation surface for contrast sensitivity has the form of a witch’s hat within the central visual field

description: Data from: Baldwin, A. S., Meese, T. S. & Baker, D. H. The attenuation surface for contrast sensitivity has the form of a witch’s hat within the central visual field. Journal of Vision 12(11), 1–17 (2012).
DOI: 10.6084/m9.figshare.8429111
title: Frequency of behaviors.xlsx

description: <br>Todos os comportamentos foram observados em burros e são mostrados antes de serem submetidos aos testes estatísticos.<br>
DOI: 10.6084/m9.figshare.8429111.v1
title: Frequency of behaviors.xlsx

description: <br>Todos os comportamentos foram observados em burros e são mostrados antes de serem submetidos aos testes estatísticos.<br>
DOI: 10.6084/m9.figshare.8428958
title: Ch3_SupplementaryTables

description: Supplementary tables for Chapter 3 of my PhD thesis.
DOI: 10.6084/m9.figshare.8428958.v3
title: Ch3_SupplementaryTables

description: Supplementary tables for Chapter 3 of my PhD thesis.
DOI: 10.6084/m9.figshare.8428895
title: Normative Data Dutch Oxford Cognitive Screen (OCS-NL)

description: These files contain all data files of the OCS-NL normative study.<br>
DOI: 10.6084/m9.figshare.8428910
title: Metadata Dutch Oxford Cognitive Screen (OCS-NL)

description: These files contain metadata about the raw datafiles of the normative dataset of the Dutch Oxford Cognitive Screen.<br>
DOI: 10.6084/m9.figshare.8428892
title: Table S2. Muscle perfusion and oxygenation heterogeneities.

description: Temporal evolution of local skeletal muscle (cremaster) blood flow and PO<sub>2</sub> heterogeneities in normovolemic and hemorrhagic shock rats.
DOI: 10.6084/m9.figshare.8428910.v1
title: Metadata Dutch Oxford Cognitive Screen (OCS-NL)

description: These files contain metadata about the raw datafiles of the normative dataset of the Dutch Oxford Cognitive Screen.<br>
DOI: 10.6084/m9.figshare.8428892.v1
title: Table S2. Muscle perfusion and oxygenation heterogeneities.

description: Temporal evolution of local skeletal muscle (cremaster) blood flow and PO<sub>2</sub> heterogeneities in normovolemic and hemorrhagic shock rats.
DOI: 10.6084/m9.figshare.8428877
title: A genome-wide association study implicates that the <i>TTC39C</i> gene is associated with diabetic maculopathy with decreased visual acuity

description: <b>Background</b>: Diabetic maculopathy is a form of diabetic retinopathy. The visual acuity of one third of patients with diabetic maculopathy will be affected. The purpose of this study was to identify genetic contributors of diabetic maculopathy with decreased visual acuity based on a genome-wide association approach using a well-defined Scottish diabetic cohort. <b>Methods</b>: We used linked e-health records of diabetic patients to define our cases and controls. The cases in this study were defined as type 2 diabetic patients who had ever been recorded in the linked e-health records as having maculopathy (observable or referable) in at least one eye and whose visual acuity of the eye was recorded to have decreased between the first and the last visual acuity record of that eye in the longitudinal e-health records. The controls were defined as a type 2 diabetic individual who had never been diagnosed with maculopathy or retinopathy in the linked e-health records. Anyone who had laser photocoagulation treatment was also excluded from the controls. A standard genome-wide association approach was applied. <b>Results</b>: Overall, we identified 469 cases and 1,374 controls within the Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS) dataset. We found that the <i>P</i> value of rs9966620 in the <i>TTC39C</i> gene was 4.13x10<sup>−8</sup>, which reached genome-wide significance. <b>Conclusions</b>: We suggest that the <i>TTC39C</i> gene is associated with diabetic maculopathy with decreased visual acuity. This needs to be confirmed by further replication studies and functional studies.
DOI: 10.6084/m9.figshare.8428874
title: Data-analysis scripts

description: These files contain all scripts used for analyzing the data of the norms of the Dutch Oxford Cognitive Screen.
DOI: 10.6084/m9.figshare.8428877.v1
title: A genome-wide association study implicates that the <i>TTC39C</i> gene is associated with diabetic maculopathy with decreased visual acuity

description: <b>Background</b>: Diabetic maculopathy is a form of diabetic retinopathy. The visual acuity of one third of patients with diabetic maculopathy will be affected. The purpose of this study was to identify genetic contributors of diabetic maculopathy with decreased visual acuity based on a genome-wide association approach using a well-defined Scottish diabetic cohort. <b>Methods</b>: We used linked e-health records of diabetic patients to define our cases and controls. The cases in this study were defined as type 2 diabetic patients who had ever been recorded in the linked e-health records as having maculopathy (observable or referable) in at least one eye and whose visual acuity of the eye was recorded to have decreased between the first and the last visual acuity record of that eye in the longitudinal e-health records. The controls were defined as a type 2 diabetic individual who had never been diagnosed with maculopathy or retinopathy in the linked e-health records. Anyone who had laser photocoagulation treatment was also excluded from the controls. A standard genome-wide association approach was applied. <b>Results</b>: Overall, we identified 469 cases and 1,374 controls within the Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS) dataset. We found that the <i>P</i> value of rs9966620 in the <i>TTC39C</i> gene was 4.13x10<sup>−8</sup>, which reached genome-wide significance. <b>Conclusions</b>: We suggest that the <i>TTC39C</i> gene is associated with diabetic maculopathy with decreased visual acuity. This needs to be confirmed by further replication studies and functional studies.
DOI: 10.6084/m9.figshare.8428736
title: Ch2_SupplementaryTables

description: Supplementary table for Chapter 2.
DOI: 10.6084/m9.figshare.8428874.v1
title: Data-analysis scripts

description: These files contain all scripts used for analyzing the data of the norms of the Dutch Oxford Cognitive Screen.
DOI: 10.6084/m9.figshare.8428868
title: Table S1 - Muscle perfusion and oxygenation.

description: <br>Local skeletal muscle perfusion (blood flow) and oxygenation (PO<sub>2</sub>) in normovolemic and hemorrhagic shock rats.
DOI: 10.6084/m9.figshare.8428736.v1
title: Supplementary Tables

description: Supplementary table for Chapter 2.
DOI: 10.6084/m9.figshare.8428184
title: Aerosol extraction and the direct laser ablation ICP-MS analysis of the fine and ultrafine fractions of regolith

description: Aerosol digital data. Run = indicates which session analysis was undertaken. Sample = analytical medium. Regolith = broad regolith type based on regolith mapping and chemistry of the 0.45 − 2 mm fraction (Morris <i>et al.</i> 1997). Impactor = diameter of impactor (µm) used in individual run. Duration = run time in minutes. Negative concentration = value &lt; designated lower level of detection (LLD). All concentrations in ppm (parts per million).
DOI: 10.6084/m9.figshare.8428736.v3
title: Ch2_SupplementaryTables

description: Supplementary table for Chapter 2.
DOI: 10.6084/m9.figshare.8428184.v1
title: Aerosol extraction and the direct laser ablation ICP-MS analysis of the fine and ultrafine fractions of regolith

description: Aerosol digital data. Run = indicates which session analysis was undertaken. Sample = analytical medium. Regolith = broad regolith type based on regolith mapping and chemistry of the 0.45 − 2 mm fraction (Morris <i>et al.</i> 1997). Impactor = diameter of impactor (µm) used in individual run. Duration = run time in minutes. Negative concentration = value &lt; designated lower level of detection (LLD). All concentrations in ppm (parts per million).
DOI: 10.6084/m9.figshare.8428736.v2
title: Supplementary Tables

description: Supplementary table for Chapter 2.
DOI: 10.6084/m9.figshare.8427998
title: Reconciling the contribution of niche and stochastic structuring of tropical forest diversity through the lens of imaging spectroscopy

description: Supplementary data for the article of Bongalov et al. "Reconciling the contribution of niche and stochastic structuring of tropical forest diversity through the lens of imaging spectroscopy" (2019) Ecology Letters (in press).<br>Please refer to the paper for description of the methods. Note that the Airborne data is available via the CEDA archive (project code MA14/21); plot data is archived on forestplots.net (codes SEP-03, 04, 05, 07, 08, 09, 10, 11, 12).<br>Environmental_description.csv stores information on the ALS-derived environmental variables;Spectral_clusters.csv stores information on the abundance of spectral clusters in each cell over the landscape;Simulations.csv.gz stores the modelled communities; its unzipped size is ca. 2GB<br>
DOI: 10.6084/m9.figshare.8427998.v1
title: Reconciling the contribution of niche and stochastic structuring of tropical forest diversity through the lens of imaging spectroscopy

description: Supplementary data for the article of Bongalov et al. "Reconciling the contribution of niche and stochastic structuring of tropical forest diversity through the lens of imaging spectroscopy" (2019) Ecology Letters (in press).<br>Please refer to the paper for description of the methods. Note that the Airborne data is available via the CEDA archive (project code MA14/21); plot data is archived on forestplots.net (codes SEP-03, 04, 05, 07, 08, 09, 10, 11, 12).<br>Environmental_description.csv stores information on the ALS-derived environmental variables;Spectral_clusters.csv stores information on the abundance of spectral clusters in each cell over the landscape;Simulations.csv.gz stores the modelled communities; its unzipped size is ca. 2GB<br>
DOI: 10.6084/m9.figshare.8427746
title: Tenofovir resistance in HBV

description: These files are the supporting data for a project to identify mutations in Hepatitis B Virus (HBV) that have been reported in association with resistance to tenofovir.<br><b>Suppl Fig 1: </b>Schematic view of Pharmacodynamics of TDF, TAF and ADV.<b><br></b><b>Suppl Fig 2: </b>PRISMA flow diagram to illustrate the identification of studies for inclusion in a systematic review of tenofovir resistance in HBV infection (provided in pdf format).<br> <b>Suppl Table 1: </b>Metadata for 15 studies reporting TDF resistance in HBV infection identified from a systematic literature review.<b><br></b><b>Suppl Table 2: </b>Quality assessment for 15 studies reporting TDF resistance in HBV infection. Studies identified from a systematic literature review.<b><br></b><b>Suppl Table 3: </b>List of 37 tenofovir RAMs in HBV Reverse Transcriptase (RT) reported in 15 studies identified through a systematic literature review (provided in xls format).<b><br></b><b>Suppl Table 4: </b>List of TFV RAMs in HBV, showing consensus residue at each position according to HBV genotype, and genotype-specific resistance where this has been reported. List of RAMs obtained from 12 studies included in the review. HBV reference sequences used are the same as for Fig 1. Grey colour highlights the sites that differ from majority consensus. Ticks represent RAMs situated in sites where there is a difference (at consensus level) between genotype sequences. RAMs are listed with the wild-type amino acid first, followed by the numbered position in RT sequence, and the amino acid substitution that is associated with resistance. TFV = tenofovir, RAMs = resistance associated mutations, HBV = hepatitis B virus.<b><br></b><b>Suppl Table 5: </b>Reference sequence alignment of HBV RT and HIV RT. Sequences downloaded from HIV sequence database online at https://www.hiv.lanl.gov/ and Hepatitis B Virus Database online at https://hbvdb.ibcp.fr/HBVdb/. Alignment undertaken using MAFFT version 7. HIV subtype B reference sequence is shown in light green (accession number K03455). HBV reference sequences (Geno-A: FJ692557; Geno-B: GU815637; Geno-C: GQ377617; Geno-D: KC875277; Geno-: GQ161817 shown in light yellow. TFV RAMs are highlighted in red. HIV TFV RAMs were obtained from Stanford Database (https://hivdb.stanford.edu/dr-summary/resistance-notes/NRTI/). HBV TFV RAMs were obtained from 12 studies included in the review. Sites with the same amino acid at homologous sites are indicated with asterisks (*); among these sites, those that are also shared TVF RAMs are shaded in light blue.<br><b>Suppl Table 6:</b> Mapping of RAMs to the HIV RT structure. RAMs were mapped onto the high-resolution structure of HIV RT to infer their possible functional consequences in terms of structure.<br> <br><b>PRISMA checklist:</b> criteria for a systematic review
DOI: 10.6084/m9.figshare.8427746.v1
title: Tenofovir resistance in HBV

description: These files are the supporting data for a project to identify mutations in Hepatitis B Virus (HBV) that have been reported in association with resistance to tenofovir.<br><b>Suppl Fig 1: </b>Schematic view of Pharmacodynamics of TDF, TAF and ADV.<b><br></b><b>Suppl Fig 2: </b>PRISMA flow diagram to illustrate the identification of studies for inclusion in a systematic review of tenofovir resistance in HBV infection (provided in pdf format).<br> <b>Suppl Table 1: </b>Metadata for 15 studies reporting TDF resistance in HBV infection identified from a systematic literature review.<b><br></b><b>Suppl Table 2: </b>Quality assessment for 15 studies reporting TDF resistance in HBV infection. Studies identified from a systematic literature review.<b><br></b><b>Suppl Table 3: </b>List of 37 tenofovir RAMs in HBV Reverse Transcriptase (RT) reported in 15 studies identified through a systematic literature review (provided in xls format).<b><br></b><b>Suppl Table 4: </b>List of TFV RAMs in HBV, showing consensus residue at each position according to HBV genotype, and genotype-specific resistance where this has been reported. List of RAMs obtained from 12 studies included in the review. HBV reference sequences used are the same as for Fig 1. Grey colour highlights the sites that differ from majority consensus. Ticks represent RAMs situated in sites where there is a difference (at consensus level) between genotype sequences. RAMs are listed with the wild-type amino acid first, followed by the numbered position in RT sequence, and the amino acid substitution that is associated with resistance. TFV = tenofovir, RAMs = resistance associated mutations, HBV = hepatitis B virus.<b><br></b><b>Suppl Table 5: </b>Reference sequence alignment of HBV RT and HIV RT. Sequences downloaded from HIV sequence database online at https://www.hiv.lanl.gov/ and Hepatitis B Virus Database online at https://hbvdb.ibcp.fr/HBVdb/. Alignment undertaken using MAFFT version 7. HIV subtype B reference sequence is shown in light green (accession number K03455). HBV reference sequences (Geno-A: FJ692557; Geno-B: GU815637; Geno-C: GQ377617; Geno-D: KC875277; Geno-: GQ161817 shown in light yellow. TFV RAMs are highlighted in red. HIV TFV RAMs were obtained from Stanford Database (https://hivdb.stanford.edu/dr-summary/resistance-notes/NRTI/). HBV TFV RAMs were obtained from 12 studies included in the review. Sites with the same amino acid at homologous sites are indicated with asterisks (*); among these sites, those that are also shared TVF RAMs are shaded in light blue.<br><b>Suppl Table 6:</b> Mapping of RAMs to the HIV RT structure. RAMs were mapped onto the high-resolution structure of HIV RT to infer their possible functional consequences in terms of structure.<br> <br>
DOI: 10.6084/m9.figshare.8427608
title: Resource allocation to growth or luxury consumption drives mycorrhizal responses

description: Growth and functional trait data for Brachypodium distachyon grown under variable nitrogen and phosphorus supply rates and in the presence or absence of arbuscular mycorrhizal (AM) fungi.<br>ID.Tag = unique plant identifierGenotype = Genotype of B. distachyonSalt = Salinity treatment (not manipulated here)Nutrient = Nutrient addition treatmentMycorrhizal = AM fungi added or notlane, position = pot location in glasshousePSA.fd = projected shoot area on final day (in pixels)<br>HA.fd = hue angle on final dayAGRmax = maximum absolute growth rate (pixels/day)<br>Dry.Shoot.Weights = dry mass of shoot (g)Dry.Root.Weights = dry mass of root (g)Fresh.Shoot.Weights = mass of shoot before drying (g)P.concentration = tissue phosphorus concentration (mg/g)<br>N.concentration = tissue nitrogen concentration (mg/g)<br>C.concentration = tissue carbon concentration (mg/g)Tissue.C.N.ratio = mass ratio of C to N in tissueTissue.N.P.ratio = mass ratio of N to P in tissueSupply.NP.ratio = mass ratio of available N to available P in soil <br>SAMR = shoot area to mass ratio (pixels/g)<br>Total.Shoot.P = total mass of phosphorus in tissue (mg)<br>Total.Shoot.N = total mass of nitrogen in tissue (mg)RMF = root mass fraction<br>percent.colonisation = <br>PC1 = ordination of plant functional traits, loadings on first axis<br>PC2 = ordination of plant functional traits, loadings on second axis<br>PC1.response = ordination of plant functional traits excluding N and P concentrations, loadings on first axis<br>MGR = mycorrhizal growth response calculated from PSA on final day<br><br>For more details, see publication (<i>to be included</i>).<br><br>
DOI: 10.6084/m9.figshare.8427608.v2
title: Resource allocation to growth or luxury consumption drives mycorrhizal responses

description: Growth and functional trait data for Brachypodium distachyon grown under variable nitrogen and phosphorus supply rates and in the presence or absence of arbuscular mycorrhizal (AM) fungi.<br>ID.Tag = unique plant identifierGenotype = Genotype of B. distachyonSalt = Salinity treatment (not manipulated here)Nutrient = Nutrient addition treatmentMycorrhizal = AM fungi added or notlane, position = pot location in glasshousePSA.fd = projected shoot area on final day (in pixels)<br>HA.fd = hue angle on final dayAGRmax = maximum absolute growth rate (pixels/day)<br>Dry.Shoot.Weights = dry mass of shoot (g)Dry.Root.Weights = dry mass of root (g)Fresh.Shoot.Weights = mass of shoot before drying (g)P.concentration = tissue phosphorus concentration (mg/g)<br>N.concentration = tissue nitrogen concentration (mg/g)<br>C.concentration = tissue carbon concentration (mg/g)Tissue.C.N.ratio = mass ratio of C to N in tissueTissue.N.P.ratio = mass ratio of N to P in tissueSupply.NP.ratio = mass ratio of available N to available P in soil <br>SAMR = shoot area to mass ratio (pixels/g)<br>Total.Shoot.P = total mass of phosphorus in tissue (mg)<br>Total.Shoot.N = total mass of nitrogen in tissue (mg)RMF = root mass fraction<br>percent.colonisation = <br>PC1 = ordination of plant functional traits, loadings on first axis<br>PC2 = ordination of plant functional traits, loadings on second axis<br>PC1.response = ordination of plant functional traits excluding N and P concentrations, loadings on first axis<br>MGR = mycorrhizal growth response calculated from PSA on final day<br><br>For more details, see publication (<i>to be included</i>).<br><br>