cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5939992
title: KadiStudio Walkthrough

description: This record contains all necessary data to obtain the results presented in the walkthrough section of the KadiStudio paper. A description on how to execute the workflow can be found in the README file.
DOI: 10.5519/qd.q1hzjwq8
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (415 records)
DOI: 10.6084/m9.figshare.19103030
title: Supplementary Material for: New Report of a Different Clinical Presentation of <b><i>CD151</i></b> Splicing Mutation (c.351+2T&gt;C): Could <b><i>TSPAN11</i></b> be Considered as a Potential Modifier Gene for <b><i>CD151</i></b>?

description: CD151, a member of the tetraspanin family, is essential for normal development of skin and kidney. To date, only 2 pathogenic variants of the <i>CD151</i> gene have been identified in a related disorder with recessive inheritance. Here, in the third study of <i>CD151</i> mutations, we report 3 affected siblings presenting variable degrees of renal and dermal symptoms. Whole exome sequencing (WES) was performed on the proband, followed by data analysis and in silico assessments. Confirmation of the mutation in the other patients were carried out using Sanger sequencing. The consequence of the <i>CD151</i> mutation was investigated by RNA extraction and Sanger sequencing of PCR products from cDNA. Multiple computational tools were applied for protein alignment, homology modeling, and molecular interaction analysis. WES revealed the variant c.351+2T&gt;C, NM_139029 (GRCh37) in <i>CD151</i>, and this was confirmed by Sanger sequencing in all patients. This variant is the result of a substitution of nucleotide T with C that changes the position +2 of the donor splice site in intron 5, leading to total loss of exon 5 from the transcript. The mentioned variant was not found in population allele frequency databases, and prediction tools concurred in its damaging effect on the protein. Based on the criteria from ACMG guidelines, this variant is pathogenic. Interestingly, in terms of clinical findings, symptoms and severity of the disease in the patients in this study were different compared to the previous report of the mutation and the disease. In addition, in silico analysis in this study appears to suggest a candidate protein, Tetraspanin-11 (TSPAN11), that could partially modify CD151 functions. This study supports the pathogenic effect of the <i>CD151</i> variant c.351+2T&gt;C, highlights the extensive variable expressivity amongst patients, reinforces the contribution of genomic content to clinical characteristics of <i>CD151</i> mutations, and accentuates the importance of modifier genes.
DOI: 10.5281/zenodo.5940004
title: KadiStudio Walkthrough

description: This record contains all necessary data to obtain the results presented in the walkthrough section of the KadiStudio paper. A description on how to execute the workflow can be found in the README file.
DOI: 10.5281/zenodo.5939991
title: KadiStudio Walkthrough

description: This record contains all necessary data to obtain the results presented in the walkthrough section of the KadiStudio paper. A description on how to execute the workflow can be found in the README file.
DOI: 10.5281/zenodo.5906991
title: Common Dynamic Determinants Govern Quorum Quenching Activity in N-terminal Serine Hydrolases

description: (File-01) Free enzymes molecular dynamics: input parameters and topologies for aPGA, ecPGA and paPvdQ enzymes general input files for MD simulations in AMBER output restart files from minimization, equilibration and production runs output files from minimization, equilibration and production runs raw data for analysis and visualization: protein backbone RMSD evolution binding cavity dynamics analysis principal component analysis of catalytic machinery (with states' representatives in PDF format) (File-02) Ligand-enzyme complexes molecular dynamics: input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules general input files for MD simulations in AMBER output restart files from minimization, equilibration and production runs output files from minimization, equilibration and production runs raw data for analysis and visualization: protein backbone RMSD evolution near-attack-conformation (NAC) stabilization HSLs RMSD evolution MM/GBSA binding energy estimation HSLs heavy atoms RMSF (File-03) Michaelis complex ensemble generation molecular dynamics: input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules general input files for MD simulations in AMBER output restart files from ensemble generation production runs output files from ensemble generation production runs (Files-04-06) Ligand-enzyme QM/MM steered molecular dynamics: input parameters for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules ensemble of input restart files generated in stage 3 general input files for QM/MM steered MD simulations in AMBER output restart files from QM/MM MD equilibration simulations and QM/MM steered MD simulations output files and output work from QM/MM steered MD simulations (File-07) Ligand-enzyme QM/MM steered molecular dynamics data for analysis and visualization: reaction states ensembles (in PDB format) extracted from QM/MM steered MD simulations with crucial distances measured evolution of the reaction coordinate elements in the first and second step of acylation representative states of the reaction stages for visualization (in PDB format) different dynamics of the residues gating access to acyl-binding cavity at TS1 different dynamics of the residues gating overall access to active site at TS2a different system-dependent bending of the HSLs at TS1 and TS2a
DOI: 10.5281/zenodo.5722498
title: Summary statistics for association tests between human and Plasmodium falciparum genetic variants in 3,346 severe malaria cases from The Gambia and Kenya

description: This dataset contains summary statistics for association tests between human and<br> <em>Plasmodium falciparum</em> malaria parasite genetic variants, using data from 3,346 severe malaria cases from The Gambia and Kenya. These results underlie the analysis described in our paper: <strong>"Malaria protection due to sickle haemoglobin depends on parasite genotype"</strong> Gavin Band, Ellen M. Leffler, Muminatou Jallow, Fatoumatta Sisay-Joof, Carolyne M. Ndila, Alexander W. Macharia, Christina Hubbart, Anna E. Jeffreys, Kate Rowlands, Thuy Nguyen, Sónia M. Gonçalves, Cristina V. Ariani, Jim Stalker, Richard D. Pearson, Roberto Amato, Eleanor Drury, Giorgio Sirugo, Umberto d'Alessandro, Kalifa A. Bojang, Kevin Marsh, Norbert Peshu, Joseph W. Saelens, Mahamadou Diakité, Steve M. Taylor, David J. Conway, Thomas N. Williams, Kirk A. Rockett, Dominic P. Kwiatkowski Nature (2021) doi: 10.1038/s41586-021-04288-3 <strong>bioRxiv link</strong>:: doi.org/10.1101/2021.03.30.437659<br> <br> The genotype data underlying these summary statistics has also been deposited on Zenodo<br> (doi:10.5281/zenodo.4973477). The HPTEST software used to generate these results has also been deposited (doi:10.5281/zenodo.5685580). Please see the MalariaGEN website for a full list of datasets which have been released with this manuscript. <strong>Data contents.</strong> The dataset consists of a single sqlite database file containing the results, and an accompanying README file in markdown and html format. Please see the README file for full details of the data contents.
DOI: 10.5281/zenodo.5722497
title: Summary statistics for association tests between human and Plasmodium falciparum genetic variants in 3,346 severe malaria cases from The Gambia and Kenya

description: This dataset contains summary statistics for association tests between human and<br> <em>Plasmodium falciparum</em> malaria parasite genetic variants, using data from 3,346 severe malaria cases from The Gambia and Kenya. These results underlie the analysis described in our paper: <strong>"Malaria protection due to sickle haemoglobin depends on parasite genotype"</strong> Gavin Band, Ellen M. Leffler, Muminatou Jallow, Fatoumatta Sisay-Joof, Carolyne M. Ndila, Alexander W. Macharia, Christina Hubbart, Anna E. Jeffreys, Kate Rowlands, Thuy Nguyen, Sónia M. Gonçalves, Cristina V. Ariani, Jim Stalker, Richard D. Pearson, Roberto Amato, Eleanor Drury, Giorgio Sirugo, Umberto d'Alessandro, Kalifa A. Bojang, Kevin Marsh, Norbert Peshu, Joseph W. Saelens, Mahamadou Diakité, Steve M. Taylor, David J. Conway, Thomas N. Williams, Kirk A. Rockett, Dominic P. Kwiatkowski Nature (2021) doi: 10.1038/s41586-021-04288-3 <strong>bioRxiv link</strong>:: doi.org/10.1101/2021.03.30.437659<br> <br> The genotype data underlying these summary statistics has also been deposited on Zenodo<br> (doi:10.5281/zenodo.4973477). The HPTEST software used to generate these results has also been deposited (doi:10.5281/zenodo.5685580). Please see the MalariaGEN website for a full list of datasets which have been released with this manuscript. <strong>Data contents.</strong> The dataset consists of a single sqlite database file containing the results, and an accompanying README file in markdown and html format. Please see the README file for full details of the data contents.
DOI: 10.5281/zenodo.5940006
title: Dataset related to article "Hepatic and Extrahepatic Colorectal Metastases Have Discordant Responses to Systemic Therapy. Pathology Data from Patients Undergoing Simultaneous Resection of Multiple Tumor Sites"

description: This record contains raw data related to article "Hepatic and Extrahepatic Colorectal Metastases Have Discordant Responses to Systemic Therapy. Pathology Data from Patients Undergoing Simultaneous Resection of Multiple Tumor Sites" <strong>Background: </strong> Systemic therapy is the standard treatment for patients with hepatic and extrahepatic colorectal metastases. It is assumed to have the same effectiveness on all disease foci, independent of the involved organ. The present study aims to compare the response rates of hepatic and extrahepatic metastases to systemic therapy. <strong>Methods: </strong> All consecutive patients undergoing simultaneous resection of hepatic and extrahepatic metastases from colorectal cancer after oxaliplatin- and/or irinotecan-based preoperative chemotherapy were analyzed. All specimens were reviewed. Pathological response to chemotherapy was classified according to tumor regression grade (TRG). <strong>Results: </strong> We analyzed 45 patients undergoing resection of 134 hepatic and 72 extrahepatic metastases. Lung and lymph node metastases had lower response rates to chemotherapy than liver metastases (TRG 4-5 95% and 100% vs. 67%, <em>p</em> = 0.008, and <em>p</em> = 0.006). Peritoneal metastases had a higher pathological response rate than liver metastases (TRG 1-3 66% vs. 33%, <em>p</em> &lt; 0.001) and non-hepatic non-peritoneal metastases (3%, <em>p</em> &lt; 0.001). Metastases site was an independent predictor of pathological response to systemic therapy. <strong>Conclusions: </strong> Response to chemotherapy of distant metastases from colorectal cancer varies in different organs. Systemic treatment is highly effective for peritoneal metastases, more so than liver metastases, while it has a very poor impact on lung and lymph node metastases.
DOI: 10.5281/zenodo.5940005
title: Dataset related to article "Hepatic and Extrahepatic Colorectal Metastases Have Discordant Responses to Systemic Therapy. Pathology Data from Patients Undergoing Simultaneous Resection of Multiple Tumor Sites"

description: This record contains raw data related to article "Hepatic and Extrahepatic Colorectal Metastases Have Discordant Responses to Systemic Therapy. Pathology Data from Patients Undergoing Simultaneous Resection of Multiple Tumor Sites" <strong>Background: </strong> Systemic therapy is the standard treatment for patients with hepatic and extrahepatic colorectal metastases. It is assumed to have the same effectiveness on all disease foci, independent of the involved organ. The present study aims to compare the response rates of hepatic and extrahepatic metastases to systemic therapy. <strong>Methods: </strong> All consecutive patients undergoing simultaneous resection of hepatic and extrahepatic metastases from colorectal cancer after oxaliplatin- and/or irinotecan-based preoperative chemotherapy were analyzed. All specimens were reviewed. Pathological response to chemotherapy was classified according to tumor regression grade (TRG). <strong>Results: </strong> We analyzed 45 patients undergoing resection of 134 hepatic and 72 extrahepatic metastases. Lung and lymph node metastases had lower response rates to chemotherapy than liver metastases (TRG 4-5 95% and 100% vs. 67%, <em>p</em> = 0.008, and <em>p</em> = 0.006). Peritoneal metastases had a higher pathological response rate than liver metastases (TRG 1-3 66% vs. 33%, <em>p</em> &lt; 0.001) and non-hepatic non-peritoneal metastases (3%, <em>p</em> &lt; 0.001). Metastases site was an independent predictor of pathological response to systemic therapy. <strong>Conclusions: </strong> Response to chemotherapy of distant metastases from colorectal cancer varies in different organs. Systemic treatment is highly effective for peritoneal metastases, more so than liver metastases, while it has a very poor impact on lung and lymph node metastases.
DOI: 10.6084/m9.figshare.19099754
title: Data_2_Share.zip

description: Data for upper limbs (U) or lower limbs (L) cycling for each subject : - 1 Lode.csv for torque data - 1 c3d for kinematics data - 2 csv for EMG data (Wingate + experiment) <br> Codebook: In Lode.csv : - Complexe = revolution - Heure de début = Starting timing - Puissance moyenne = Mean power - TPM moyen = mean rotation per minute - Couple de pédale gauche/droit = left/right crank torque - Heure du delta = timing apparition of the sample during the revolution <br> In emg.csv : The first 4 columns concern the Quattro electrodes. For Legs, corresponding muscles are : SOL / GL / GM / TA For arms, corresponding muscles are : FDS / FCR / BR / ECRL
DOI: 10.6084/m9.figshare.19099754.v1
title: Data_2_Share.zip

description: Data for upper limbs (U) or lower limbs (L) cycling for each subject : - 1 Lode.csv for torque data - 1 c3d for kinematics data - 2 csv for EMG data (Wingate + experiment) <br> Codebook: In Lode.csv : - Complexe = revolution - Heure de début = Starting timing - Puissance moyenne = Mean power - TPM moyen = mean rotation per minute - Couple de pédale gauche/droit = left/right crank torque - Heure du delta = timing apparition of the sample during the revolution <br> In emg.csv : The first 4 columns concern the Quattro electrodes. For Legs, corresponding muscles are : SOL / GL / GM / TA For arms, corresponding muscles are : FDS / FCR / BR / ECRL
DOI: 10.17028/rd.lboro.19103060
title: Supplementary Information Files for: The gender-differential effect of financial inclusion on household financial resilience

description: Supplementary Information Files for: The gender-differential effect of financial inclusion on household financial resilience<br>This paper applies the kernel propensity score matching difference-in-differences method to examine gender-differential effects of financial inclusion on household financial resilience, using repeated cross-sectional data from two successive large-scale surveys of Ghanaian households. Applying standardised indices for financial inclusion and financial resilience, we find that financial inclusion significantly improves household financial resilience. Results from gender and locality disaggregated analyses suggest that the effect of financial inclusion on household resilience does not significantly vary by gender or locality. Results from different measures of financial inclusion show that savings and formal account ownership yield more pronounced resilience effect, with mobile money (m-money) exerting the least impact. Remittances via m-money – sending and receiving (a proxy for social capital) – provide significant financial resilience effects, with generally stronger effects in rural than in urban areas, especially for females.<br>
DOI: 10.17028/rd.lboro.19103060.v1
title: Supplementary Information Files for: The gender-differential effect of financial inclusion on household financial resilience

description: Supplementary Information Files for: The gender-differential effect of financial inclusion on household financial resilience<br>This paper applies the kernel propensity score matching difference-in-differences method to examine gender-differential effects of financial inclusion on household financial resilience, using repeated cross-sectional data from two successive large-scale surveys of Ghanaian households. Applying standardised indices for financial inclusion and financial resilience, we find that financial inclusion significantly improves household financial resilience. Results from gender and locality disaggregated analyses suggest that the effect of financial inclusion on household resilience does not significantly vary by gender or locality. Results from different measures of financial inclusion show that savings and formal account ownership yield more pronounced resilience effect, with mobile money (m-money) exerting the least impact. Remittances via m-money – sending and receiving (a proxy for social capital) – provide significant financial resilience effects, with generally stronger effects in rural than in urban areas, especially for females.<br>
DOI: 10.5066/p9iqdhit
title: Petaluma Model GIS Data

description: This data release contains 3 land use shapefiles (years 1959, 1979, and 1986) and 1 model grid shapefile for the Petaluma River Watershed in California.
DOI: 10.5066/p9nl90p8
title: Data release of Three-Dimensional Hydrogeologic Framework Model of the Petaluma Valley Watershed, Sonoma County, California

description: This digital dataset was created as part of a U.S. Geological Survey study, done in cooperation with the Sonoma County Water Agency and the City of Petaluma, to be used as the digital hydrogeologic input data for numerical simulation of the groundwater system of the Petaluma Valley Watershed, Sonoma County, California. Elevation, thickness, and extent of the hydrostratigraphic units define the geohydrologic layering of the digital framework model. The location of faults may be used to define the location of potential horizontal flow barriers in numerical simulation of the groundwater system. The intended uses of this dataset include, but are not limited to, natural resource modeling, mapping, and visualization applications. This digital dataset represents the three-dimensional hydrogeologic framework for the Petaluma Valley Watershed, Sonoma County, California. The data define the elevation, thickness, and extent of the principal hydrostratigraphic units of the region, and faults that cut these units. The digital data describe the following eight hydrostratigraphic units: Qal, Quaternary alluvial deposits; BM, Holocene Bay Mud deposits; Qmix, Quaternary mixed unit; WG, Wilson Grove Formation; PF, Petaluma Formation; SV, Sonoma Volcanics; TV, Tolay Volcanics; BSMT, Basement rocks. Most of the three-dimensional hydrogeologic framework data are contained within a single polygon feature class (HFM_300m_polys), which contains a mesh of polygons that represent model cells that have multiple attributes including X, Y, elevation, and thickness of each hydrostratigraphic unit. Faults are provided as a separate line features class (HFM_faults). Two additional ascii files contain the model output from 3D geologic framework and lithologic properties models for the Petaluma groundwater basin. An additional tabular data file contains specific capacity data calculated from well pumping tests.
DOI: 10.5281/zenodo.5940025
title: Dataset related to article "Virtual Biopsy for Diagnosis of Chemotherapy-Associated Liver Injuries and Steatohepatitis: A Combined Radiomic and Clinical Model in Patients with Colorectal Liver Metastases "

description: This record contains raw data related to article "Virtual Biopsy for Diagnosis of Chemotherapy-Associated Liver Injuries and Steatohepatitis: A Combined Radiomic and Clinical Model in Patients with Colorectal Liver Metastases " Non-invasive diagnosis of chemotherapy-associated liver injuries (CALI) is still an unmet need. The present study aims to elucidate the contribution of radiomics to the diagnosis of sinusoidal dilatation (SinDil), nodular regenerative hyperplasia (NRH), and non-alcoholic steatohepatitis (NASH). Patients undergoing hepatectomy for colorectal metastases after chemotherapy (January 2018-February 2020) were retrospectively analyzed. Radiomic features were extracted from a standardized volume of non-tumoral liver parenchyma outlined in the portal phase of preoperative post-chemotherapy computed tomography. Seventy-eight patients were analyzed: 25 had grade 2-3 SinDil, 27 NRH, and 14 NASH. Three radiomic fingerprints independently predicted SinDil: GLRLM_f3 (OR = 12.25), NGLDM_f1 (OR = 7.77), and GLZLM_f2 (OR = 0.53). Combining clinical, laboratory, and radiomic data, the predictive model had accuracy = 82%, sensitivity = 64%, and specificity = 91% (AUC = 0.87 vs. AUC = 0.77 of the model without radiomics). Three radiomic parameters predicted NRH: conventional_HUQ2 (OR = 0.76), GLZLM_f2 (OR = 0.05), and GLZLM_f3 (OR = 7.97). The combined clinical/laboratory/radiomic model had accuracy = 85%, sensitivity = 81%, and specificity = 86% (AUC = 0.91 vs. AUC = 0.85 without radiomics). NASH was predicted by conventional_HUQ2 (OR = 0.79) with accuracy = 91%, sensitivity = 86%, and specificity = 92% (AUC = 0.93 vs. AUC = 0.83 without radiomics). In the validation set, accuracy was 72%, 71%, and 91% for SinDil, NRH, and NASH. Radiomic analysis of liver parenchyma may provide a signature that, in combination with clinical and laboratory data, improves the diagnosis of CALI.
DOI: 10.5281/zenodo.5940024
title: Dataset related to article "Virtual Biopsy for Diagnosis of Chemotherapy-Associated Liver Injuries and Steatohepatitis: A Combined Radiomic and Clinical Model in Patients with Colorectal Liver Metastases "

description: This record contains raw data related to article "Virtual Biopsy for Diagnosis of Chemotherapy-Associated Liver Injuries and Steatohepatitis: A Combined Radiomic and Clinical Model in Patients with Colorectal Liver Metastases " Non-invasive diagnosis of chemotherapy-associated liver injuries (CALI) is still an unmet need. The present study aims to elucidate the contribution of radiomics to the diagnosis of sinusoidal dilatation (SinDil), nodular regenerative hyperplasia (NRH), and non-alcoholic steatohepatitis (NASH). Patients undergoing hepatectomy for colorectal metastases after chemotherapy (January 2018-February 2020) were retrospectively analyzed. Radiomic features were extracted from a standardized volume of non-tumoral liver parenchyma outlined in the portal phase of preoperative post-chemotherapy computed tomography. Seventy-eight patients were analyzed: 25 had grade 2-3 SinDil, 27 NRH, and 14 NASH. Three radiomic fingerprints independently predicted SinDil: GLRLM_f3 (OR = 12.25), NGLDM_f1 (OR = 7.77), and GLZLM_f2 (OR = 0.53). Combining clinical, laboratory, and radiomic data, the predictive model had accuracy = 82%, sensitivity = 64%, and specificity = 91% (AUC = 0.87 vs. AUC = 0.77 of the model without radiomics). Three radiomic parameters predicted NRH: conventional_HUQ2 (OR = 0.76), GLZLM_f2 (OR = 0.05), and GLZLM_f3 (OR = 7.97). The combined clinical/laboratory/radiomic model had accuracy = 85%, sensitivity = 81%, and specificity = 86% (AUC = 0.91 vs. AUC = 0.85 without radiomics). NASH was predicted by conventional_HUQ2 (OR = 0.79) with accuracy = 91%, sensitivity = 86%, and specificity = 92% (AUC = 0.93 vs. AUC = 0.83 without radiomics). In the validation set, accuracy was 72%, 71%, and 91% for SinDil, NRH, and NASH. Radiomic analysis of liver parenchyma may provide a signature that, in combination with clinical and laboratory data, improves the diagnosis of CALI.
DOI: 10.17043/andersson-2016-china-1
title: Black carbon concentrations and carbon isotope signatures for three sites in China, January 2013