cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c50r9mf37
title: MassIVE MSV000093468 - Towards an ultimate solution for peptide retention time prediction: the effect of column temperature on separation selectivity
title: The effect of the column temperature on the selectivity of reversed-phase peptide separation in standard separation settings applied in bottom-up proteomics has been evaluated. Tryptic digests of A549, MCF7, Jurkat and HCT116 human cells in non-labeled and TMT-labeled formats have been analyzed by 1D LC-MS/MS at four different column temperature settings: 25, 35, 45 and 55 C. To increase the size of retention datasets available for retention time prediction modelling, 2D LC-MS/MS acquisitions were also performed on a Jurkat digest (both non-labeled and TMT-modified). The first dimension separation featured high pH RPLC separation (XTerra, 1x100 mm column, pH 10, 2 % per minute acetonitrile gradient). Fourteen (non-labeled) and eighteen (TMT) concatenated fractions were analyzed using RPLC-MS settings identical to that of the 1D experiments. The second dimension of RP chromatographic separation employed the Thermo Fisher Scientific EASY Spray column (PepMap, RSLC C18, 2mm, 100-angstrom, 75mm x 50cm), operated at four temperatures with a gradient of 1% to 50% B (A: 100% water, B: 80:20 ACN: water, both containing 0.1% formic acid) in 107 min, followed by a 1 min rapid increase to 100%B and 12 minute wash. The total acquisition time for each sample/fraction was 120 min.
DOI: 10.6084/m9.figshare.24615636
title: Binding Selectivity Analysis of AURKs Inhibitors through Molecular Dynamics Simulation Studies - Raw Data

description: Aurora kinases (AURKs) have been identified as promising biological targets for the treatment of cancer. In this study, molecular dynamics simulations were employed to investigate the binding selectivity of three inhibitors (HPM, MPY, and VX6) towards AURKA and AURKB by predicting their binding free energies. The results show that the inhibitors HPM, MPY, and VX6 have more favorable interactions with AURKB as compared to AURKA. The binding energy decomposition analysis revealed that four common residue pairs (L139, L83), (V147, V91), (L210, L154), and (L263, L207) showed significant binding energies with HPM, MPY, and VX6, hence responsible for the binding selectivity of AURKA and AURKB to the inhibitors. The MD trajectory analysis also revealed that the inhibitors affect the dynamic flexibility of protein structure, which is also responsible for the partial selectivity of HPM, MPY, and VX6 towards AURKA and AURKB. As expected, this study provides useful insights for the design of potential inhibitors with high selectivity for AURKA and AURKB.
DOI: 10.6084/m9.figshare.24615636.v1
title: Binding Selectivity Analysis of AURKs Inhibitors through Molecular Dynamics Simulation Studies - Raw Data

description: Aurora kinases (AURKs) have been identified as promising biological targets for the treatment of cancer. In this study, molecular dynamics simulations were employed to investigate the binding selectivity of three inhibitors (HPM, MPY, and VX6) towards AURKA and AURKB by predicting their binding free energies. The results show that the inhibitors HPM, MPY, and VX6 have more favorable interactions with AURKB as compared to AURKA. The binding energy decomposition analysis revealed that four common residue pairs (L139, L83), (V147, V91), (L210, L154), and (L263, L207) showed significant binding energies with HPM, MPY, and VX6, hence responsible for the binding selectivity of AURKA and AURKB to the inhibitors. The MD trajectory analysis also revealed that the inhibitors affect the dynamic flexibility of protein structure, which is also responsible for the partial selectivity of HPM, MPY, and VX6 towards AURKA and AURKB. As expected, this study provides useful insights for the design of potential inhibitors with high selectivity for AURKA and AURKB.
DOI: 10.5281/zenodo.10116671
title: Data Source file for manuscript: Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients

description: ABSTRACT
Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) are associated with excess morbidity and mortality. Despite recognition of this immediate impact on human health, essential aspects of their molecular epidemiology remain under-investigated. This includes knowledge on the potential of a particular strain to persist in a host, mutational events during colonization, and the genetic diversity in individual patients over time. To investigate long-term genetic diversity of colonizing and infecting ESBL-producing Klebsiella pneumoniae species complex and ESBL-Escherichia coli in individual patients over time, we conducted performed a ten-year longitudinal retrospective study and extracted clinical and microbiological data from electronic health records. In this investigation, 76 ESBL-K. pneumoniae species complex and 284 ESBL-E. coli isolates were recovered from 19 and 61 patients. Strain persistence was detected in all patients colonized with ESBL-K. pneumoniae species complex, and 83.6% of patients colonized with ES BL-E. coli. Antimicrobial resistance genes, plasmid replicons, and whole ESBL-plasmids were shared between isolates regardless of chromosomal relatedness. Our study suggests that patients colonized with ESBL-producers may act as durable reservoirs for ongoing transmission of ESBLs, and that they are at a prolonged risk of recurrent infection with colonizing strains.
DATA SOURCE FILE
In this Data Source file, you will find access to the raw data, metadata and results obtained during the study: "Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients". Data is organized following the structure of Figures/Tables of the manuscript and Supplementary Material. Additional figures not included in the main manuscript nor in the Supplementary Material are also available.
All sequencing and sample data from this study can be accessed at the NCBI database under the BioProject number PRJNA910977: http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977. No new software was developed during this study. Standard bioinformatics software was used and the commands used can be accessed at the Supplementary Information file.
DOI: 10.5281/zenodo.10116672
title: Data Source file for manuscript: Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients

description: ABSTRACT
Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) are associated with excess morbidity and mortality. Despite recognition of this immediate impact on human health, essential aspects of their molecular epidemiology remain under-investigated. This includes knowledge on the potential of a particular strain to persist in a host, mutational events during colonization, and the genetic diversity in individual patients over time. To investigate long-term genetic diversity of colonizing and infecting ESBL-producing Klebsiella pneumoniae species complex and ESBL-Escherichia coli in individual patients over time, we conducted performed a ten-year longitudinal retrospective study and extracted clinical and microbiological data from electronic health records. In this investigation, 76 ESBL-K. pneumoniae species complex and 284 ESBL-E. coli isolates were recovered from 19 and 61 patients. Strain persistence was detected in all patients colonized with ESBL-K. pneumoniae species complex, and 83.6% of patients colonized with ES BL-E. coli. Antimicrobial resistance genes, plasmid replicons, and whole ESBL-plasmids were shared between isolates regardless of chromosomal relatedness. Our study suggests that patients colonized with ESBL-producers may act as durable reservoirs for ongoing transmission of ESBLs, and that they are at a prolonged risk of recurrent infection with colonizing strains.
DATA SOURCE FILE
In this Data Source file, you will find access to the raw data, metadata and results obtained during the study: "Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients". Data is organized following the structure of Figures/Tables of the manuscript and Supplementary Material. Additional figures not included in the main manuscript nor in the Supplementary Material are also available.
All sequencing and sample data from this study can be accessed at the NCBI database under the BioProject number PRJNA910977: http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977. No new software was developed during this study. Standard bioinformatics software was used and the commands used can be accessed at the Supplementary Information file.
DOI: 10.21223/yudvig/6o4clu
title: 01_PTYield012018_CIPHQ_VHW_Cycle7.tab

description: :unav
DOI: 10.21223/yudvig/9m2ehh
title: 01_Data_PTYield012018_CIPHQ.txt

description: :unav
DOI: 10.21223/yudvig
title: Dataset for: Asian table potato early maturing. Observation trials

description: Evaluation of abiotic stress tolerance in advance potatoes clones of the lowland tropic virus resistant population (LTVR - Cycle 7) under heat conditions
DOI: 10.5281/zenodo.10198511
title: Algal Epiphyte Biomass from Seagrass Tissue Along the South Texas Coast (2011 - 2021)

description: Estimates of algal epiphytic biomass are made from separate leaf samples of entire shoots. Leaf samples for epiphytic biomass must be processed within three days of collection. In the laboratory, epiphytes are separated from a known leaf area using a scalpel or razor blade. Scraped material is then collected and retained on pre-weighed glass fiber filters. The collected epiphytic biomass and scraped seagrass leaves are then dried to a constant weight at 60°C for determination of dry weight biomass. Samples were taken at six sites along the Texas coast from 2011 - 2021.
DOI: 10.34740/kaggle/dsv/7029726
title: Balochi Language to English Translation Dataset
DOI: 10.5281/zenodo.10198609
title: Postura Crítica del conflicto de Israel y Palestina
DOI: 10.5281/zenodo.10198610
title: Postura Crítica del conflicto de Israel y Palestina
DOI: 10.6084/m9.figshare.24615654
title: 14386SNP.vcf

description: <b>Genomic Insights into Oxalate Content in Spinach: A Genome-Wide Association Study and Genomic Prediction Approach</b>
DOI: 10.6084/m9.figshare.23932863
title: DART-FISH (Kalhor, Chen et al) human brain motor cortex

description: This data set is associated with Kalhor, Chen et al (https://doi.org/10.1101/2023.08.16.553610). This repo contains the DART-FISH data on human brain presented in the paper.File descriptionM1C_cell_metadata.tsv: a data table containing the cell IDs, locations (xg and yg columns) and annotations (class and subclass columns)spots_table.tsv: a data table containing the information for all decoded spots, including location (xg and yg columns), gene, and the ID of the cell they were assigned to (cell_label column)brightfield.tif, DRAQ5.tif, RiboSoma_N9.tif: brightfield, nuclear stain, and RiboSoma stain for the entire imaged area, respectivelysegmentation_mask_custom.npy: Cell segmentation mask generated by a fine-tuned cellpose model<br>
DOI: 10.6084/m9.figshare.23937057
title: DART-FISH (Kalhor, Chen et al) human kidney cortex

description: This data set is associated with Kalhor, Chen et al (https://doi.org/10.1101/2023.08.16.553610). This repo contains the DART-FISH data on human kidney presented in the paper. File descriptionkidney_cell_metadata.tsv: a data table containing the cell IDs, locations (xg and yg columns) and annotations (class and subclass columns)spots_table.tsv: a data table containing the information for all decoded spots, including location (xg and yg columns), gene, and the ID of the cell they were assigned to (cell_label column)brightfield.tif, DRAQ5.tif, RiboSoma_N9.tif: brightfield, nuclear stain, and RiboSoma stain for the entire imaged area, respectivelysegmentation_mask_custom.npy: Cell segmentation mask generated by a fine-tuned cellpose model<br>
DOI: 10.5281/zenodo.10055965
title: Widespread warming of Earth's estuaries

description: Water temperature responses to climate change may vary across Earth's estuaries. To understand how climate change influences estuarine surface water temperature, we need global, long-term records of estuarine temperature. Here, we generated spatially explicit data of surface water temperature over 1,060 estuaries globally using Landsat 5, 7 and 8 from 1985 to 2022 and compared water warming rates with local air temperature warming rates. 47% of Earth's estuaries are warming, with a global average warming rate of 0.070 ± 0.004 degree Celsius/year (median = 0.060 degree Celsius/year). Estuaries at higher latitudes showed rapid warming. A 1 degree Celsius increase in air temperature could lead to a 0.81 degree Celsius increase in estuarine surface water warming, or 1.3 degrees Celsius in estuaries above 60.5 degrees North. We inferred the potential influences over estuarine warming based on distinct global spatial patterns in water and air warming, or lack of warming, and discussed implications for estuarine carbon cycling.
DOI: 10.5281/zenodo.10055966
title: Widespread warming of Earth's estuaries

description: Water temperature responses to climate change may vary across Earth's estuaries. To understand how climate change influences estuarine surface water temperature, we need global, long-term records of estuarine temperature. Here, we generated spatially explicit data of surface water temperature over 1,060 estuaries globally using Landsat 5, 7 and 8 from 1985 to 2022 and compared water warming rates with local air temperature warming rates. 47% of Earth's estuaries are warming, with a global average warming rate of 0.070 ± 0.004 degree Celsius/year (median = 0.060 degree Celsius/year). Estuaries at higher latitudes showed rapid warming. A 1 degree Celsius increase in air temperature could lead to a 0.81 degree Celsius increase in estuarine surface water warming, or 1.3 degrees Celsius in estuaries above 60.5 degrees North. We inferred the potential influences over estuarine warming based on distinct global spatial patterns in water and air warming, or lack of warming, and discussed implications for estuarine carbon cycling.
DOI: 10.5281/zenodo.8356236
title: The winter subset of the Saildrone 2021-2022 Mission to the Gulf Stream used for the publication  "The importance of contemporaneous measurements for regional air-sea CO2 flux estimates"

description: Data from the Saildrone 2021-2022 observational mission to the Gulf Stream. These data are published to accompany the publication "The importance of contemporaneous measurements for regional air-sea CO2 flux estimates." Included in this dataset are the primary and processed variables used throughout the paper. The data associated with each saildrone is named by the drone number. Additionally, included in the structure for each drone are the gas transfer velocities for each scenario, MBL atmospheric CO2 interpolated to the time and location of the drone, and ERA-5 wind speed, sea level pressure, significant wave height, and drag coefficient interpolated to the time and location of the drone. These variables are used to calculate CO2 fluxes for each scenario and are named as follows: "F" + gas transfer velocity equation used (DM18 or W14) + drone ID + scenario. Scenario A-D correspond to those outlined in the paper. Scenarios E and F correspond to the calculation of air-sea fluxes using all saildrone observed variables except for atmospheric CO2 (from MBL product) and significant wave height (from ERA-5), respectively.
DOI: 10.5281/zenodo.8356237
title: The winter subset of the Saildrone 2021-2022 Mission to the Gulf Stream used for the publication  "The importance of contemporaneous measurements for regional air-sea CO2 flux estimates"

description: Data from the Saildrone 2021-2022 observational mission to the Gulf Stream. These data are published to accompany the publication "The importance of contemporaneous measurements for regional air-sea CO2 flux estimates." Included in this dataset are the primary and processed variables used throughout the paper. The data associated with each saildrone is named by the drone number. Additionally, included in the structure for each drone are the gas transfer velocities for each scenario, MBL atmospheric CO2 interpolated to the time and location of the drone, and ERA-5 wind speed, sea level pressure, significant wave height, and drag coefficient interpolated to the time and location of the drone. These variables are used to calculate CO2 fluxes for each scenario and are named as follows: "F" + gas transfer velocity equation used (DM18 or W14) + drone ID + scenario. Scenario A-D correspond to those outlined in the paper. Scenarios E and F correspond to the calculation of air-sea fluxes using all saildrone observed variables except for atmospheric CO2 (from MBL product) and significant wave height (from ERA-5), respectively.
DOI: 10.21223/hztmzi/obsd7r
title: 01_PTAbiotic stress112018_Majes_VHW_Cycle 7.tab

description: :unav
DOI: 10.21223/hztmzi/27gf81
title: 02_LTVR_LM_2020_VHW_Cycle 7.tab

description: :unav
DOI: 10.21223/hztmzi
title: Dataset for: Asian table potato early maturing. Preliminary trials

description: Evaluation of abiotic stress tolerance in advance potatoes clones of the lowland tropic virus resistant population (LTVR - Cycle 7) under heat conditions in 2018 and 2020. 1) In 2018 a field trial of 1585 potato genotypes, among 1542 LVTR C7 genotypes, 41 parentals and 2 checks, were planted using an Incomplete block design (Alpha design) of 264 blocks of 12 genotipes each, at Majes - Arequipa during the months of November 2018 to February 2019. Two irrigation treatments were applied: normal irrigation (NI), Deficit Irrigation (DI)). 2). In 2020 a field trial of 2554 potato genotypes, among 2237 LVTR C7 genotypes, 41 parentals and 7 checks, were planted using an row an colum design at La Molina - Lima during the months of November 2020 to February 2021. Two irrigation treatments were applied: normal irrigation (NI), Deficit Irrigation (DI)).
DOI: 10.6084/m9.figshare.24592674
title: Dataset for "Seasonal dynamics and spatial patterns of soil moisture in a loess catchment"

description: In this study, volumetric soil moisture was monitored monthly for 5.5 years (April 2016 to October 2021) at 20 cm intervals between the surface and 5 m depth at 89 sites across a small (0.43 km<sup>2</sup>) catchment on the Chinese Loess Plateau. The median soil moisture was computed for each month and depth for each monitoring site as a measure of the typical soil moisture conditions. Here is the dataset for median soil moisture which can support our main finding:monthly_median_volumetric_soil_moisture_pct: the median soil moisture for each month and depth for each monitoring site during the measurement period,monthly_average_p_q_pet: the average monthly precipitation, average monthly potential evapotranspiration during the soil moisture measurement period, and the monthly streamflow from June 2016 to May 2017,monthly_average_solar_radiation_Wm2: the average solar radiation for each month and for each site over the soil moisture measurement period,topographic_attributes: the slope aspect and the topographic wetness index for each site.<br>
DOI: 10.6084/m9.figshare.19709485
title: Data for positions within roosts

description: Here we provide the data collected in the field for each date and separate groups, which show which bats (pit tags) were positioned where within the roost.<br>The raw data shows all data collected, and the file position by group and date only provides the data for groups with a sufficient large number of samples and is organized by group and position.<br>We also provide the code and data needed for statistical analyses and associated graphs.
DOI: 10.6084/m9.figshare.19709485.v4
title: Data for positions within roosts

description: Here we provide the data collected in the field for each date and separate groups, which show which bats (pit tags) were positioned where within the roost. <br> The raw data shows all data collected, and the file position by group and date only provides the data for groups with a sufficient large number of samples and is organized by group and position. <br> We also provide the code and data needed for the Bayesian analysis and associated graphs.
DOI: 10.6075/j09z9545
title: Data from: QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

description: 1. SEEKR2 : https://github.com/seekrcentral/seekr2 2. qmrebind: https://github.com/seekrcentral/qmrebind
description: The data set contains the files necessary to recalculate/reproduce the unbinding rates of ligands for the model host-guest systems and Hsp90-inhibitor complexes in the paper "QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations." The data contains the Simulation Enabled Estimation of Kinetic Rates v.2 (SEEKR2) and QMrebind-reparameterized SEEKR2 simulations for model host-guest systems and Hsp90-inhibitor complexes with instructions to compute the drug-target unbinding rates in these complexes.
DOI: 10.34740/kaggle/ds/4043438
title: Chemicals in Cosmetics
DOI: 10.21223/pnchjp/swtlgz
title: 01_LTVR_Majes_2022_Cycle 7.tab

description: :unav
DOI: 10.21223/pnchjp/0fqrdj
title: 01_LTVR_LM_2020_VHW_Cycle 7.tab

description: :unav
DOI: 10.21223/pnchjp/u2uafr
title: 01_PTAbiotic stress112018_Majes_VHW_Cycle 7.tab

description: :unav
DOI: 10.21223/pnchjp
title: Dataset for: Asian table potato early maturing. Preliminary trials

description: Evaluation of abiotic stress tolerance in advance potato clones of the lowland tropic virus resistant population (LTVR - Cycle 7) under drought conditions. 1) Arequipa, Majes -2018. A field trial of 1585 potato genotypes, among 1542 LVTR C7 genotypes, 41 parentals, and 2 checks, was planted using an Incomplete block design (Alpha design) of 264 blocks of 12 genotypes each, at Majes - Arequipa during the months of November 2018 to February 2019. Two irrigation treatments were applied: normal irrigation (NI) and deficit Irrigation (DI)). 2) Lima, La Molina - 2020. A field trial of 2554 potato genotypes, among 2237 LVTR C7 genotypes, 41 parentals, and 7 checks, were planted using a row and column design at La Molina - Lima during the months of November 2020 to February 2021. Two irrigation treatments were applied: normal irrigation (NI) and deficit Irrigation (DI)). 3) Arequipa, Santa Rita de Siguas - 2022. A field trial of 676 potato genotypes, among 522 LVTR C7 genotypes, 13 LTVR C5 genotypes; 67 LTVR C6 genotypes; 31 LDM genotypes; 26 LTLB genotypes and 17 varieties, were planted using a row and column design at Arequipa Majes during the months of December 2022 to February 2023. Two irrigation treatments were applied: normal irrigation (NI) and deficit Irrigation (DI)).
DOI: 10.6084/m9.figshare.24615657
title: iAT2_3D

description: iAT2 ATAC Seq BigWig
DOI: 10.6084/m9.figshare.24615657.v1
title: iAT2_3D

description: iAT2 ATAC Seq BigWig
DOI: 10.6084/m9.figshare.24615753
title: iAT2_3D

description: iAT2 ATAC Seq BigWig re-upload
DOI: 10.6084/m9.figshare.24615753.v1
title: iAT2_3D

description: iAT2 ATAC Seq BigWig re-upload
DOI: 10.5281/zenodo.10198620
title: Sequence/simulation data for Direct Prediction of Intrinsically Disordered Protein Conformational Properties From Sequence

description: This is a DOI-linked deposition of sequence/biophysical properties pairs used in the associated paper by Lotthammer et al:
Lotthammer, J. M.*, Ginell, G. M.*, Griffith, D.*, Emenecker, R. J. & Holehouse, A. S. Direct Prediction of Intrinsically Disordered Protein Conformational Properties From Sequence.Nature Methods (in press), (2023).