cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8146689
title: otoole et al (2023) apobec3 published data

description: Contents Data<br> - 3 XML files (epoch model, exponential model and skygrid model with 2 APOBEC3 partitions defined).<br> - 4 phylogenies (B.1 and Clade IIb, Clade I and Clade IIa, outgroup pruned)<br> - 4 state reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 branch SNP reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 amino acid reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 snp count files (B.1 and Clade IIb, Clade I and Clade IIa) <br> - 2 heptamer count files for Clade IIb (internal and all branches)<br> - 4 root-to-tip data files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 1 mutation count file including data from Clade IIb and B.1<br> <br> Scripts<br> - all_in_one notebook (notebook of most work from the paper- reconstructs the branch snps from the state files, generates tree figures, calculates amino acid information, calculates root-to-tip data for regression, code for generating figures present in the manuscript, sliding window calculations)<br> - analysis_until_roottotip (stand alone notebook to get root-to-tip data)<br> - cleaner_apobec_work (earlier version of analysis, including sankey diagram code)<br> - get_ml_tree_with_reconstruction (shell commands for aligning, generating ml tree, reconstructing states and pruning off outgroup)<br> - make_partitions (extraction of code for generating the two partitions of the alignment, apobec3 and non-apobec3)<br> - roottotip.R (regression analysis using roottotip data)<br> - synonprob.R (probability of getting x synonymous mutations given the data)
DOI: 10.5281/zenodo.8146688
title: otoole et al (2023) apobec3 published data

description: Contents Data<br> - 3 XML files (epoch model, exponential model and skygrid model with 2 APOBEC3 partitions defined).<br> - 4 phylogenies (B.1 and Clade IIb, Clade I and Clade IIa, outgroup pruned)<br> - 4 state reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 branch SNP reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 amino acid reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 snp count files (B.1 and Clade IIb, Clade I and Clade IIa) <br> - 2 heptamer count files for Clade IIb (internal and all branches)<br> - 4 root-to-tip data files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 1 mutation count file including data from Clade IIb and B.1<br> <br> Scripts<br> - all_in_one notebook (notebook of most work from the paper- reconstructs the branch snps from the state files, generates tree figures, calculates amino acid information, calculates root-to-tip data for regression, code for generating figures present in the manuscript, sliding window calculations)<br> - analysis_until_roottotip (stand alone notebook to get root-to-tip data)<br> - cleaner_apobec_work (earlier version of analysis, including sankey diagram code)<br> - get_ml_tree_with_reconstruction (shell commands for aligning, generating ml tree, reconstructing states and pruning off outgroup)<br> - make_partitions (extraction of code for generating the two partitions of the alignment, apobec3 and non-apobec3)<br> - roottotip.R (regression analysis using roottotip data)<br> - synonprob.R (probability of getting x synonymous mutations given the data)
DOI: 10.6084/m9.figshare.23636793
title: Lifespan_data.csv from Sex bias in mortality risk changes over the lifespan of bottlenose dolphins

description: Lifespan and sighting data
DOI: 10.6084/m9.figshare.23636799
title: BaSTA_data.csv from Sex bias in mortality risk changes over the lifespan of bottlenose dolphins

description: Data formatted for BaSTA analysis
DOI: 10.6084/m9.figshare.23636799.v1
title: BaSTA_data.csv from Sex bias in mortality risk changes over the lifespan of bottlenose dolphins

description: Data formatted for BaSTA analysis
DOI: 10.6084/m9.figshare.23636802
title: R code from Sex bias in mortality risk changes over the lifespan of bottlenose dolphins

description: Code to reproduce models and figures
DOI: 10.6084/m9.figshare.23636802.v1
title: R code from Sex bias in mortality risk changes over the lifespan of bottlenose dolphins

description: Code to reproduce models and figures
DOI: 10.34731/pbn7-8g89
title: DATA: Combining deep learning and automated feature extraction to analyze minirhizotron images development and validation of a new pipeline

description: This repository contains data that are supplementary to the publication "Combining deep learning and automated feature extraction to analyze minirhizotron images development and validation of a new pipeline". The workflow presented in the publication can be retraced with this data. Furthermore, root length data from the Selhausen minirhizotrons from 2017 and 2018 is published here.
DOI: 10.34740/kaggle/dsv/6134271
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.5281/zenodo.8146400
title: Eurasian beaver – A semi-aquatic ecosystem engineer rearranges the assemblage of terrestrial mammals in winter - dataset

description: Dataset to paper of Fedyń, I., Przepióra, F., Sobociński, W., Wyka, J., & Ciach, M. (2022). Eurasian beaver–A semi-aquatic ecosystem engineer rearranges the assemblage of terrestrial mammals in winter. <em>Science of The Total Environment</em>, <em>831</em>, 154919 (https://doi.org/10.1016/j.scitotenv.2022.154919).
description: This study was financially supported by the National Science Centre, Poland (grant no. 2021/41/N/NZ8/02423).
DOI: 10.5281/zenodo.8146399
title: Eurasian beaver – A semi-aquatic ecosystem engineer rearranges the assemblage of terrestrial mammals in winter - dataset

description: Dataset to paper of Fedyń, I., Przepióra, F., Sobociński, W., Wyka, J., & Ciach, M. (2022). Eurasian beaver–A semi-aquatic ecosystem engineer rearranges the assemblage of terrestrial mammals in winter. <em>Science of The Total Environment</em>, <em>831</em>, 154919 (https://doi.org/10.1016/j.scitotenv.2022.154919).
description: This study was financially supported by the National Science Centre, Poland (grant no. 2021/41/N/NZ8/02423).
DOI: 10.34740/kaggle/dsv/6134281
title: Egypt Gold Prices | Daily Updated
DOI: 10.5517/ccdc.csd.cc2fq0ry
title: CCDC 2255490: Experimental Crystal Structure Determination

description: Related Article: Zhen Zhang, Jie Zhou, Xue Chen, Tong Yan, Hanxu Sun, Lin Du, Qihua Zhao|2023|Inorg.Chem.Front.|10|4117|doi:10.1039/D3QI00731F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.18712/nsd-nsd0507-v4
title: Consumer Expenditure Survey 1982

description: "The Consumer Expenditure Survey 1982" is the ninth in the series of annual surveys conducted by Statistics Norway. The data is organized in several sections and contains background information on the household (collected through an initial interview that maps the household composition), detailed consumption in terms of value and quantity (recorded by diary keeping, respectively for household and individuals), the households purchases of durable consumer goods (tangible capital goods, collected by a comprehensive exit interview), consumption of own products and income and taxes. In this survey the log part is especially well documented. This leads to an extensive amount of information on houshold cosumption patterns. The information presented is also used as the basis for calculating the CPI. Through the data collection the households are treated as independent respondents. For this purpose, a household was defined as persons living permanently in common housing with shared costs.
This study is the third, and last, of the panel period between 1980-1982.
DOI: 10.18712/nsd-nsd0518-v4
title: Consumer Expenditure Survey 1993

description: Statistics Norway has used periodic consumption surveys as a basis for preparing and updating the weight basis for the consumer price index. Detailed overviews of consumption in private households have also formed an important basis for the living conditions statistics, and for research on income, living conditions and e.g. effects of the tax system's use of direct and indirect taxes. The material is also so detailed that it provides an interesting basis for dietary analyses. Data can also be used for demand studies, in economic planning models or for specification of private consumption in the national accounts.

Up to and including 1973, Statistics Norway carried out consumption surveys at intervals of several years, in 1974 Statistics Norway switched to a system of annual surveys, with a somewhat smaller sample. From 1974-1976, data is published for 3 years at a time, and the annual gross sample is approximately 1,500 households, net sample 1,100-1,200 households. The aim was still to build up a detailed overview of consumption in private households, as a basis for updating the weight basis in the consumer price index. One also wants to survey consumption in different types of households. The households are classified according to characteristics such as household type, income, main employee's occupational status and age, area of residence, size of total consumption expenditure, etc. Data is organized in several parts and contains background information about the household (collected through an introductory interview that maps the household composition), detailed consumption measured in value and quantity (registered by keeping a diary, respectively for the household and individuals), the household's purchase of durable consumer goods (durable capital goods, collected at a comprehensive closing interview), consumption of self-produced goods and income and tax

Gross sample: 6,518 households for the 3-year period 1992-1994
A household has shared housing and shared meals
Net sample: 1993: 1308 households Somewhat variable for different parts of the data collection
For the 3-year period 1992-1994, the net sample is 4,032 households (Response rate 61.9%)
DOI: 10.5281/zenodo.8146605
title: mESC m2i and m15 data

description: This repository contains the mESC data needed to recreate the analysis presented in the manuscript.
DOI: 10.5281/zenodo.8146604
title: mESC m2i and m15 data

description: This repository contains the mESC data needed to recreate the analysis presented in the manuscript.
DOI: 10.25345/c5qn5zn50
title: MassIVE MSV000092442 - The hGID GID4 E3 ubiquitin ligase complex targets ARHGAP11A to regulate cell migration
title: The human GID (hGID) complex is a key E3 ligase regulating multiple cellular processes, including cell cycle progression and metabolic activity. However, the biological functions controlled by hGID remain poorly investigated. Here, we show that the hGID substrate receptor GID4 regulates cell migration and growth. Biochemical and cellular assays combined with proximity-dependent biotinylation (BioID2) uncovered that GID4 targets ARHGAP11A for degradation. Knockdown of GID4 or inhibition of the GID4 substrate binding pocket impairs motility and directed cell movement, whereas abrogation of ARHGAP11A significantly rescues this cell migration defect. GID4 inhibits cell migration by degrading ARHGAP11A thereby preventing its accumulation at the cell periphery where it turns off RhoA activity. Moreover, our BioID2-GID4 screens revealed a variety of substrate profiles beyond Pro/N-degron motifs with functions in microtubule binding, cytoskeletal dynamics and other biological processes. Overall, we identified cellular functions and a wide range of physiological hGID degradation substrates, which paves the way for deciphering molecular pathways regulated by hGID E3 ligase activity through its GID4 substrate receptor.
DOI: 10.5517/ccdc.csd.cc28hcrx
title: CCDC 2100149: Experimental Crystal Structure Determination

description: Related Article: Lang Qu|2021|CSD Communication|||
description: Related Article: Lang Qu, Hui Xiao, Bao Zhang, Qingping Yang, Jintong Song, Xiangge Zhou, Zong-Xiang Xu, Haifeng Xiang|2023|Chem.Eng.Journal|471|144709|doi:10.1016/j.cej.2023.144709
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.8146694
title: LMI data

description: LMI data is used to analyze the response characteristics of LMI and the flash properties observed by LMI.
DOI: 10.5281/zenodo.8146693
title: LMI data

description: LMI data is used to analyze the response characteristics of LMI and the flash properties observed by LMI.
DOI: 10.5281/zenodo.7966308
title: Simulations for: The Energetics and Ion Coupling of Cholesterol Transport Through Patched1

description: <strong>Free energy profiles:</strong> Coarse-grained (CG) potential of mean force (PMF) free energy and histogram outputs, obtained via the gromacs weighted-histogram analysis method (WHAM). PMF profile numbers match those described in the accompanying manuscript for cholesterol movement between the: - PTCH1-molA ECD base and the sterol binding domain (SBD) (PMF_1a_PTCH1_molA-SHH_cholesterol) - PTCH1-molB ECD base and the SBD (PMF_1a_PTCH1_molB-free_cholesterol) - PTCH1-molA ECD base and the sterol sensing domain (SSD) (PMF_1b_PTCH1_molA-SHH_cholesterol) - PTCH1-molA SSD and the membrane (PMF_2_PTCH1_molA-SSD_cholesterol_OHup) - PTCH1-molB SSD and the membrane (PMF_2_PTCH1_molB-SSD_cholesterol_OHup) - PTCH1-molB SSD and the membrane in a flipped conformation (PMF_2_PTCH1_molB-SSD_cholesterol_OHdown) - Membrane and solvent (PMF_3_Membrane_cholesterol) - PTCH1-molA SBD and the solvent (PMF_4_PTCH1_molA-SSH_cholesterol) - PTCH1-molB SBD and the solvent (PMF_4_PTCH1_molB-free_cholesterol) 2000 rounds of Bayesian Bootstrapping were performed. <strong>File description for each system:</strong> - histo.xvg: umbrella window histograms - bsres.xvg: Average free energy profile and computed bootstrapping error. <strong>Atomistic simulations:</strong> Subset of atomistic molecular dynamics simulations of wild-type (WT) Patched1 (PTCH1) and Dispatched1 (DISP1) in distinct ion-bound states: - PTCH1 with Na+ bound at Site 1 initially (PTCH1_WT_Na_Site1) - PTCH1 apo in 0.15 M NaCl (PTCH1_WT_apo_inNaCl) - PTCH1 apo in 0.15 M KCl (PTCH1_WT_apo_inKCl) - PTCH1 with 3 x Na+ ions bound to anionic triad residues (PTCH1_WT_3xNa) - PTCH1 with 3 x K+ ions bound to anionic triad residues (PTCH1_WT_3xK) - DISP1 apo in 0.15 M NaCl (DISP1_WT_apo) - DISP1 with 3 x Na+ ions bound to anionic triad residues (DISP1_WT_3xNa) - DISP1 with 2 x Na+ ions bound, generated by sequential ion removal from the end of DISP1_WT_3xNa simulations (DISP1_WT_2xNa) - DISP1 with 1 x Na+ ion bound, generated by sequential ion removal from the end of DISP1_WT_2xNa simulations (DISP1_WT_1xNa) - DISP1 without Na+ bound, generated by sequential ion removal from the end of DISP1_WT_1xNa simulations (DISP1_WT_0xNa) All simulations were run for 3 x 100 ns except for PTCH1_WT_apo_inNaCl which was run for 3 x 50 ns. The PTCH1 and DISP1 conformations were obtained from the Protein Data Bank (PDB IDs: 6DMY, 7RPH). <strong>File description for each system:</strong> - md_fit_firstframe.pdb : Initial frame used for atomistic simulations (replicate 1, each replicate equilibrated independently). - md_fit_<em>X</em>.xtc : Gromacs trajectory file for each replicate (X=replicate number).
DOI: 10.5281/zenodo.7966307
title: Simulations for: The Energetics and Ion Coupling of Cholesterol Transport Through Patched1

description: <strong>Free energy profiles:</strong> Coarse-grained (CG) potential of mean force (PMF) free energy and histogram outputs, obtained via the gromacs weighted-histogram analysis method (WHAM). PMF profile numbers match those described in the accompanying manuscript for cholesterol movement between the: - PTCH1-molA ECD base and the sterol binding domain (SBD) (PMF_1a_PTCH1_molA-SHH_cholesterol) - PTCH1-molB ECD base and the SBD (PMF_1a_PTCH1_molB-free_cholesterol) - PTCH1-molA ECD base and the sterol sensing domain (SSD) (PMF_1b_PTCH1_molA-SHH_cholesterol) - PTCH1-molA SSD and the membrane (PMF_2_PTCH1_molA-SSD_cholesterol_OHup) - PTCH1-molB SSD and the membrane (PMF_2_PTCH1_molB-SSD_cholesterol_OHup) - PTCH1-molB SSD and the membrane in a flipped conformation (PMF_2_PTCH1_molB-SSD_cholesterol_OHdown) - Membrane and solvent (PMF_3_Membrane_cholesterol) - PTCH1-molA SBD and the solvent (PMF_4_PTCH1_molA-SSH_cholesterol) - PTCH1-molB SBD and the solvent (PMF_4_PTCH1_molB-free_cholesterol) 2000 rounds of Bayesian Bootstrapping were performed. <strong>File description for each system:</strong> - histo.xvg: umbrella window histograms - bsres.xvg: Average free energy profile and computed bootstrapping error. <strong>Atomistic simulations:</strong> Subset of atomistic molecular dynamics simulations of wild-type (WT) Patched1 (PTCH1) and Dispatched1 (DISP1) in distinct ion-bound states: - PTCH1 with Na+ bound at Site 1 initially (PTCH1_WT_Na_Site1) - PTCH1 apo in 0.15 M NaCl (PTCH1_WT_apo_inNaCl) - PTCH1 apo in 0.15 M KCl (PTCH1_WT_apo_inKCl) - PTCH1 with 3 x Na+ ions bound to anionic triad residues (PTCH1_WT_3xNa) - PTCH1 with 3 x K+ ions bound to anionic triad residues (PTCH1_WT_3xK) - DISP1 apo in 0.15 M NaCl (DISP1_WT_apo) - DISP1 with 3 x Na+ ions bound to anionic triad residues (DISP1_WT_3xNa) - DISP1 with 2 x Na+ ions bound, generated by sequential ion removal from the end of DISP1_WT_3xNa simulations (DISP1_WT_2xNa) - DISP1 with 1 x Na+ ion bound, generated by sequential ion removal from the end of DISP1_WT_2xNa simulations (DISP1_WT_1xNa) - DISP1 without Na+ bound, generated by sequential ion removal from the end of DISP1_WT_1xNa simulations (DISP1_WT_0xNa) All simulations were run for 3 x 100 ns except for PTCH1_WT_apo_inNaCl which was run for 3 x 50 ns. The PTCH1 and DISP1 conformations were obtained from the Protein Data Bank (PDB IDs: 6DMY, 7RPH). <strong>File description for each system:</strong> - md_fit_firstframe.pdb : Initial frame used for atomistic simulations (replicate 1, each replicate equilibrated independently). - md_fit_<em>X</em>.xtc : Gromacs trajectory file for each replicate (X=replicate number).
DOI: 10.5281/zenodo.8146006
title: Dominance of Auger excitation in beam heating in transmission electron microscopy: Irradiation experiments and quantitative thermal analysis of α-Al2O3

description: The collection of uploaded files constitutes a dataset supporting our findings, titled Dominance of Auger excitation in beam heating in transmission electron microscopy: Irradiation experiments and quantitative thermal analysis of α-Al<sub>2</sub>O<sub>3</sub>, to be submitted to a scientific journal. The co-authors are Jihye Kwon and Hyoung Seop Kim, both at Pohang University of Science and Technology (POSTECH), Republic of Korea
DOI: 10.5281/zenodo.8146005
title: Dominance of Auger excitation in beam heating in transmission electron microscopy: Irradiation experiments and quantitative thermal analysis of α-Al2O3

description: The collection of uploaded files constitutes a dataset supporting our findings, titled Dominance of Auger excitation in beam heating in transmission electron microscopy: Irradiation experiments and quantitative thermal analysis of α-Al<sub>2</sub>O<sub>3</sub>, to be submitted to a scientific journal. The co-authors are Jihye Kwon and Hyoung Seop Kim, both at Pohang University of Science and Technology (POSTECH), Republic of Korea
DOI: 10.5281/zenodo.8146770
title: Dataset for combined influences of sources and atmospheric bleaching on light absorption of water-soluble brown carbon aerosols

description: This dataset provides the mass-absorption cross section at 365 nm and the corresponding absorption Ångström exponent, carbon isotope (13C and 14C) signature of water-soluble organic carbon, and OC, EC and WS-BrC concentration for aerosol samples collected in East Asia. The PM2.5 samples were collected simultaneously during the winter period (January 2014) from the representative hotspot regions of BrC emissions in E. Asia, including in the Beijing-Tianjin-Hebei (BTH) area, Yangtze River Delta (YRD), Pearl River Delta (PRD), Sichuan (SC) province and SE Yellow Sea regional receptor site — the Korea Climate Observatory at Gosan (KCOG). The earlier published data in E. and S. Asia, such as KCOG, urban city Delhi, Bangladesh Climate Observatory at Bhola Island (BCOB) in the outflow region of the Indo-Gangetic Plain and Maldives Climate Observatory at Hanimaadhoo Island (MCOH) in the Indian Ocean are from corresponding references (see the annotation in each sheet). Please cite Wenzheng Fang, August Andersson, Meehye Lee, Mei Zheng, Ke Du, Sang-Woo Kim, Henry Holmstrand and Örjan Gustafsson (2023): Combined influences of sources and atmospheric bleaching on light absorption of water-soluble brown carbon aerosols. npj Climate and Atmospheric Science.
DOI: 10.5281/zenodo.8146769
title: Dataset for combined influences of sources and atmospheric bleaching on light absorption of water-soluble brown carbon aerosols

description: This dataset provides the mass-absorption cross section at 365 nm and the corresponding absorption Ångström exponent, carbon isotope (13C and 14C) signature of water-soluble organic carbon, and OC, EC and WS-BrC concentration for aerosol samples collected in East Asia. The PM2.5 samples were collected simultaneously during the winter period (January 2014) from the representative hotspot regions of BrC emissions in E. Asia, including in the Beijing-Tianjin-Hebei (BTH) area, Yangtze River Delta (YRD), Pearl River Delta (PRD), Sichuan (SC) province and SE Yellow Sea regional receptor site — the Korea Climate Observatory at Gosan (KCOG). The earlier published data in E. and S. Asia, such as KCOG, urban city Delhi, Bangladesh Climate Observatory at Bhola Island (BCOB) in the outflow region of the Indo-Gangetic Plain and Maldives Climate Observatory at Hanimaadhoo Island (MCOH) in the Indian Ocean are from corresponding references (see the annotation in each sheet). Please cite Wenzheng Fang, August Andersson, Meehye Lee, Mei Zheng, Ke Du, Sang-Woo Kim, Henry Holmstrand and Örjan Gustafsson (2023): Combined influences of sources and atmospheric bleaching on light absorption of water-soluble brown carbon aerosols. npj Climate and Atmospheric Science.
DOI: 10.5517/ccdc.csd.cc221y47
title: CCDC 1908488: Experimental Crystal Structure Determination

description: Related Article: Yu Ge, Guoqing Wang, Yahong Li|2023|Polyhedron|242|116515|doi:10.1016/j.poly.2023.116515
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bc899
title: CCDC 2155780: Experimental Crystal Structure Determination

description: Related Article: Dan Luo, Fei Wang, Chen-Hui Liu, San-Tai Wang, Ya-Yong Sun, Wei-Hui Fang, Jian Zhang|2022|Inorg.Chem.Front.|9|4506|doi:10.1039/D2QI01108E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.