cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6546076
title: Data from: Phylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis

description: <pre>Data from: Phylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis Author information Shizuka Koshimizu1, Naoki Minamino2, Tomoaki Nishiyama3, Emiko Yoro4, Mayuko Sato5, Mayumi Wakazaki5, Kiminori Toyooka5, Kazuo Ebine2,6, Keiko Sakakibara4, Takashi Ueda2,6, and Kentaro Yano1 1 School of Agriculture, Meiji University, Kawasaki 214-8571, Japan 2 Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki 444-8585, Japan 3 Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa 920-0934, Japan 4 Department of Life Science, Rikkyo University, Tokyo 171‐8501, Japan 5 RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan 6 Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan This directory contains 0_README (this file) 1_Marchantia_FL_data 2_Physcomitrella_FL_data 3_Physcomitrella_TEM_images 4_PAML 1_Marchantia_FL_data Raw image data using quantification of spermatid phenotypes in Marchantia. quantification.xlsx: Summary of quantification data. 211111 and 211210: Observation date. ∟Mpbld10-1, Mpbld10-2, and Tak-1: Observed lines. ∟raw data: *.lsm files are raw image data. ∟binary image: *.tif files are binarization images of the Hoechst33342 data. ∟DIC: *.tif files are maximum intensity projection images of the C2 channels (detection of DIC images) of the raw data. ∟Hoechst33342: *.tif files are maximum intensity projection images of the C1 channels (detection of Hoechst33342 signals) of the raw data. 2_Physcomitrella_FL_data Merged data of DIC and Hoechst33342 signal images using quantification of spermatid phenotypes in Physcomitrella. line22-*.png: The images of Ppbld10-22 mutant. line30-*.png: The images of Ppbld10-30 mutant. wt.png: The images of wild type. Number in the images 1: With flagella 2: Without flagella 3_Physcomitrella_TEM_images TEM images of spermatids in the Ppbld10-30 mutant, except for images shown in Supporting Information Fig. S11. 4_PAML Files using analysis by PALM. input.fasta: Input multi fasta file. species_tree.nwk: The gene tree file for the global clock model (rooted using chlorophytes as an outgroup). species_tree_marked.nwk: A gene tree file with marks specifying land plant stem and crown branches as category #1 (for a local clock model). clock1: A directory containing output files of a PAML run with the global clock model (clock = 1) clock2: A directory containing output files of a PAML run with a local clock model (clock = 2). The branches assumed to have a different rate (r1) than the default rate r0 are specified with #1 in species_tree_marked.nwk.</pre>
description: {"references": ["Koshimizu S, Minamino N, Nishiyama T, Yoro E, Ebine K, Sakakibara K, Ueda T, Yano K. 2021. bioRxiv: 2021.07.25.453666."]}
DOI: 10.5281/zenodo.8106016
title: chlorellidium_tetrabotrys_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8106015
title: chlorellidium_tetrabotrys_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7886148
title: Dataset for the Paper: "Security Defect Detection via Code Review: A Study of the OpenStack and Qt Communities"

description: This is the dataset for the paper: "Security Defect Detection via Code Review: A Study of the OpenStack and Qt Communities ", including the extracted data and results. The dataset contains the following three folders: <strong>1. RQ1</strong>: <strong>Security defect in Nova.xlsx</strong> <strong>Security defect in Neutron.xlsx</strong> <strong>Security defect in Qt Base.xlsx</strong> <strong>Security defect in Qt Creator.xlsx;</strong> The RQ1 folder contains four files corresponding to the four projects (i.e., Nova and Neutron from OpenStack, Qt Base and Qt Creator from Qt), including 539 security-related review comments, in which security defects were identified by the reviewers. These instances were obtained from manual labelling after keyword-based search. The security defect type of these instances are presented to answer RQ1. <strong>How to Read the MS Excel files in RQ1:</strong> Each of the four MS Excel files in this folder contains 6 sheets for six years from 2017 to 2022. Each sheet has 10 columns for recoding 10 data items, among which the last four data items are used in our study to answer the RQs. We list the data items in the following table. <strong>Data Item</strong> <strong>Description</strong> <strong>Source</strong> Keyword The corresponding keyword of the comment. Keyword-based Search Code_change_id The code_change_id of the comment. Gerrit File The file in which the comment is added. Gerrit Patchset The patchset of the comment within the code change. Gerrit Line The line number in the file at which the comment is added. Gerrit Message The text of the review comment. Gerrit Security-related Whether the review comment is security-related (i.e., Yes or No). Labelling Security defect type The type of the security defect identified in the comment. Labelling Consequence The Consequence of the security defect. Extraction Resolution Evidence The information about where the identified security defect was resolved in the code Extraction <strong>2. RQ2</strong>: <strong>Extracted data for RQ2.mx22</strong> The RQ2 folder contains the extracted data of 539 security-related review comments in <strong>Extracted data for RQ2.mx22</strong>, which was encoded and analyzed by the MAXQDA tool, investigating the treatment of security defects by developers and reviewers to answer RQ2. <strong>3. RQ3</strong>: <strong>Extracted data for RQ3.mx22</strong> The RQ3 folder contains the extracted data of 161 review comments in which identified security defects were not resolved by developers in <strong>Extracted data for RQ3.mx22</strong>. which was also encoded and analyzed by the MAXQDA tool, exploring the causes of not resolving security defects to answer RQ3. <strong>Note</strong>: The mx22 can be opened by MAXQDA 22, which are available at https://www.maxqda.com/ for download. You may also use the free trial version of MAXQDA 2022, which is available at https://www.maxqda.com/trial for download.
DOI: 10.5281/zenodo.7886149
title: Dataset for the Paper: "Security Defect Detection via Code Review: A Study of the OpenStack and Qt Communities"

description: This is the dataset for the paper: "Security Defect Detection via Code Review: A Study of the OpenStack and Qt Communities ", including the extracted data and results. The dataset contains the following three folders: <strong>1. RQ1</strong>: <strong>Security defect in Nova.xlsx</strong> <strong>Security defect in Neutron.xlsx</strong> <strong>Security defect in Qt Base.xlsx</strong> <strong>Security defect in Qt Creator.xlsx;</strong> The RQ1 folder contains four files corresponding to the four projects (i.e., Nova and Neutron from OpenStack, Qt Base and Qt Creator from Qt), including 539 security-related review comments, in which security defects were identified by the reviewers. These instances were obtained from manual labelling after keyword-based search. The security defect type of these instances are presented to answer RQ1. <strong>How to Read the MS Excel files in RQ1:</strong> Each of the four MS Excel files in this folder contains 6 sheets for six years from 2017 to 2022. Each sheet has 10 columns for recoding 10 data items, among which the last four data items are used in our study to answer the RQs. We list the data items in the following table. <strong>Data Item</strong> <strong>Description</strong> <strong>Source</strong> Keyword The corresponding keyword of the comment. Keyword-based Search Code_change_id The code_change_id of the comment. Gerrit File The file in which the comment is added. Gerrit Patchset The patchset of the comment within the code change. Gerrit Line The line number in the file at which the comment is added. Gerrit Message The text of the review comment. Gerrit Security-related Whether the review comment is security-related (i.e., Yes or No). Labelling Security defect type The type of the security defect identified in the comment. Labelling Consequence The Consequence of the security defect. Extraction Resolution Evidence The information about where the identified security defect was resolved in the code Extraction <strong>2. RQ2</strong>: <strong>Extracted data for RQ2.mx22</strong> The RQ2 folder contains the extracted data of 539 security-related review comments in <strong>Extracted data for RQ2.mx22</strong>, which was encoded and analyzed by the MAXQDA tool, investigating the treatment of security defects by developers and reviewers to answer RQ2. <strong>3. RQ3</strong>: <strong>Extracted data for RQ3.mx22</strong> The RQ3 folder contains the extracted data of 161 review comments in which identified security defects were not resolved by developers in <strong>Extracted data for RQ3.mx22</strong>. which was also encoded and analyzed by the MAXQDA tool, exploring the causes of not resolving security defects to answer RQ3. <strong>Note</strong>: The mx22 can be opened by MAXQDA 22, which are available at https://www.maxqda.com/ for download. You may also use the free trial version of MAXQDA 2022, which is available at https://www.maxqda.com/trial for download.
DOI: 10.14473/csda/7cqgkp/0mhpto
title: PR017_V1811.pdf

description: :unav
DOI: 10.14473/csda/7cqgkp/z0cirf
title: PR010_V1811.pdf

description: Veřejnost o svých obavách a bezpečnostních rizicích pro Českou republiku – listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/aajygp
title: PR015_V1811.pdf

description: Postoje obyvatel České republiky k politickým stranám - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/qxegft
title: NS_1811_DataFile-FINAL_bezjmen.tab

description: Data
DOI: 10.14473/csda/7cqgkp/akbru4
title: PR09_V1811.pdf

description: Hodnocení bezpečnostní situace v Evropě - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/dcv5vi
title: PR04_V1811.pdf

description: Češi a spoření na důchod - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/gd4w5v
title: OM_V1811.pdf

description: :unav
DOI: 10.14473/csda/7cqgkp/c0t1ir
title: PR01_V1811.pdf

description: Voliči a strany a politická orientace občanů - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/5agczg
title: PR14_V1811.pdf

description: Volební model v listopadu 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/ma5eog
title: TI_V1811.pdf

description: Technická informace
DOI: 10.14473/csda/7cqgkp/lssul8
title: PR03_V1811.pdf

description: Názory občanů na úroveň sociálního zabezpečení v ČR a alokaci veřejných prostředků - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/mxugna
title: PR07_V1811.pdf

description: Daně z pohledu veřejného mínění - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/lbmmoy
title: PR02_V1811.pdf

description: Priority ve financování jednotlivých oblastí sociální politiky - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/jxckt7
title: K_V1811.pdf

description: Karty
DOI: 10.14473/csda/7cqgkp/4czptz
title: PR12_V1811.pdf

description: Důvěra stranickým představitelům - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/uzrwjh
title: PR05_V1811.pdf

description: Občané o důchodovém systému - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/zya4tb
title: PR13_V1811.pdf

description: Důvěra k vybraným institucím veřejného života - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/nv7bac
title: PR06_V1811.pdf

description: Názory české veřejnosti na stav důchodového systému ČR - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/9ghjwd
title: PR11_V1811.pdf

description: Důvěra ústavním institucím v listopadu 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/iqxl5r
title: PR016_V1811.pdf

description: Názory veřejnosti na důvody vstupu do politické strany - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/zumfmd
title: PR08_V1811.pdf

description: Veřejnost o svých obavách, pocitu bezpečí a spokojenosti s policií - listopad 2018 Tisková zpráva CVVM
DOI: 10.14473/csda/7cqgkp/iksub9
title: D_V1811.pdf

description: Dotazník
DOI: 10.34740/kaggle/dsv/6067821
title: Trump_Indictment_on_Twitter(March-2023)
DOI: 10.5281/zenodo.8106069
title: microctenopoma_lineatum_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8106068
title: microctenopoma_lineatum_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8106088
title: ophiopholis_aculeata_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8106087
title: ophiopholis_aculeata_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23615117
title: Biological stability of DNA methylation measurements over varying intervals of time and in the presence of acute stress

description: Identifying factors that influence the stability of DNA methylation measurements across biological replicates is of critical importance in basic and clinical research. Using a within-person between-group experimental design (<i>n</i> = 31, number of observations = 192), we report the stability of biological replicates over a variety of unique temporal scenarios, both in the absence and presence of acute psychosocial stress, and between individuals who have experienced early life adversity (ELA) and non-exposed individuals. We found that varying time intervals, acute stress, and ELA exposure influenced the stability of repeated DNA methylation measurements. In the absence of acute stress, probes were less stable as time passed; however, stress exerted a stabilizing influence on probes over longer time intervals. Compared to non-exposed individuals, ELA-exposed individuals had significantly lower probe stability immediately following acute stress. Additionally, we found that across all scenarios, probes used in most epigenetic-based algorithms for estimating epigenetic age or immune cell proportions had average or below-average stability, except for the Principal Component and DunedinPACE epigenetic ageing clocks, which were enriched for more stable probes. Finally, using highly stable probes in the absence of stress, we identified multiple probes that were hypomethylated in the presence of acute stress, regardless of ELA status. Two hypomethylated probes are located near the transcription start site of the glutathione-disulfide reductase gene (<i>GSR</i>), which has previously been shown to be an integral part of the stress response to environmental toxins. We discuss implications for future studies concerning the reliability and reproducibility of DNA methylation measurements. <b>Abbreviations:</b> DNAm – DNA methylation, CpG − 5’-cytosine-phosphate-guanine-3,’ ICC – Interclass correlation coefficient, ELA – Early-life adversity, PBMCs – Peripheral blood mononuclear cells, mQTL – Methylation quantitative trait loci, TSS – Transcription start site, GSR – Glutathione-disulfide reductase gene, TSST – Trier social stress test, PC – Principal component.
DOI: 10.6084/m9.figshare.23615117.v1
title: Biological stability of DNA methylation measurements over varying intervals of time and in the presence of acute stress

description: Identifying factors that influence the stability of DNA methylation measurements across biological replicates is of critical importance in basic and clinical research. Using a within-person between-group experimental design (<i>n</i> = 31, number of observations = 192), we report the stability of biological replicates over a variety of unique temporal scenarios, both in the absence and presence of acute psychosocial stress, and between individuals who have experienced early life adversity (ELA) and non-exposed individuals. We found that varying time intervals, acute stress, and ELA exposure influenced the stability of repeated DNA methylation measurements. In the absence of acute stress, probes were less stable as time passed; however, stress exerted a stabilizing influence on probes over longer time intervals. Compared to non-exposed individuals, ELA-exposed individuals had significantly lower probe stability immediately following acute stress. Additionally, we found that across all scenarios, probes used in most epigenetic-based algorithms for estimating epigenetic age or immune cell proportions had average or below-average stability, except for the Principal Component and DunedinPACE epigenetic ageing clocks, which were enriched for more stable probes. Finally, using highly stable probes in the absence of stress, we identified multiple probes that were hypomethylated in the presence of acute stress, regardless of ELA status. Two hypomethylated probes are located near the transcription start site of the glutathione-disulfide reductase gene (<i>GSR</i>), which has previously been shown to be an integral part of the stress response to environmental toxins. We discuss implications for future studies concerning the reliability and reproducibility of DNA methylation measurements. <b>Abbreviations:</b> DNAm – DNA methylation, CpG − 5’-cytosine-phosphate-guanine-3,’ ICC – Interclass correlation coefficient, ELA – Early-life adversity, PBMCs – Peripheral blood mononuclear cells, mQTL – Methylation quantitative trait loci, TSS – Transcription start site, GSR – Glutathione-disulfide reductase gene, TSST – Trier social stress test, PC – Principal component.
DOI: 10.5281/zenodo.8106101
title: enteromius_paludinosus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8106100
title: enteromius_paludinosus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8106121
title: enteromius_fasciolatus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8106120
title: enteromius_fasciolatus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8106119
title: Example of a survey for discovering passenger preferences

description: This dataset serves as a representative sample derived from a passenger preference survey, integral to my dissertation research. The compact nature of the dataset is intentional, focusing on three crucial variables: total travel time (C1), number of transfers (C2), and the experience of walking time (C3). Participants rated each variable on a scale of 1 (not important at all) to 5 (extremely important). For the walking time, participants could further specify whether it represented a discomfort or a benefit to their overall travel time, citing reasons such as fitness and health. These outcome data have been utilized in a preference discovery model. For additional details or inquiries, feel free to reach out directly.
DOI: 10.5281/zenodo.8106118
title: Example of a survey for discovering passenger preferences

description: This dataset serves as a representative sample derived from a passenger preference survey, integral to my dissertation research. The compact nature of the dataset is intentional, focusing on three crucial variables: total travel time (C1), number of transfers (C2), and the experience of walking time (C3). Participants rated each variable on a scale of 1 (not important at all) to 5 (extremely important). For the walking time, participants could further specify whether it represented a discomfort or a benefit to their overall travel time, citing reasons such as fitness and health. These outcome data have been utilized in a preference discovery model. For additional details or inquiries, feel free to reach out directly.
DOI: 10.6084/m9.figshare.22567318
title: AlphaFold predictions for Nasmyth et al., 2023

description: AlphaFold predictions as described in Nasmyth et al., 2023.
DOI: 10.6084/m9.figshare.22567318.v1
title: AlphaFold predictions for Nasmyth et al., 2023

description: AlphaFold predictions as described in Nasmyth et al., 2023.
DOI: 10.6084/m9.figshare.23615121.v1
title: This repository includes relevent data for economic study on WECC and NPCC systems. This dataset can be found at Github as well. See https://github.com/enliten/ENLITEN-Grid-Econ-Data/.

description: This data set will be of interest to you if you conduct electricity economic simulation studies, such as economic dispatch and LMP calculation. We provide a comprehensive economic data set for WECC and NPCC systems based on real-world grid operational data. Users can access the developed data set for generator aggregation, fuel cost, generator capacity, and line rating. This dataset can be found at Github as well. See https://github.com/enliten/ENLITEN-Grid-Econ-Data/.
DOI: 10.34740/kaggle/dsv/2664831
title: Periapical X-rays
DOI: 10.5281/zenodo.8106149
title: nanomia_bijuga_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8106148
title: nanomia_bijuga_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23615121
title: Economic Data for WECC and NPCC Electricity Markets_old

description: This repository includes relevent economic data for the Western Electricity Coordinating Council (WECC) and Northeast Power Coordinating Council (NPCC) systems, developed by the research team of Dr. Fangxing Fran Li at The University of Tennessee and his PhD student Qiwei Zhang during 2021-2022. This data set will be of interest to you if you conduct electricity economic simulation studies, such as economic dispatch and LMP calculation. We provide a comprehensive economic data set for WECC and NPCC systems based on real-world grid operational data. Users can access the developed data set for generator aggregation, fuel cost, generator capacity, and line rating. This dataset can be found at Github as well. See https://github.com/enliten/ENLITEN-Grid-Econ-Data/.
DOI: 10.6084/m9.figshare.23615121.v3
title: Economic Data for WECC and NPCC Electricity Markets_old

description: This repository includes relevent economic data for the Western Electricity Coordinating Council (WECC) and Northeast Power Coordinating Council (NPCC) systems, developed by the research team of Dr. Fangxing Fran Li at The University of Tennessee and his PhD student Qiwei Zhang during 2021-2022. This data set will be of interest to you if you conduct electricity economic simulation studies, such as economic dispatch and LMP calculation. We provide a comprehensive economic data set for WECC and NPCC systems based on real-world grid operational data. Users can access the developed data set for generator aggregation, fuel cost, generator capacity, and line rating. This dataset can be found at Github as well. See https://github.com/enliten/ENLITEN-Grid-Econ-Data/.
DOI: 10.6084/m9.figshare.23615121.v2
title: Economic Data for WECC and NPCC Electricity Markets

description: This repository includes relevent economic data for the Western Electricity Coordinating Council (WECC) and Northeast Power Coordinating Council (NPCC) systems, developed by the research team of Dr. Fangxing Fran Li at The University of Tennessee and his PhD student Qiwei Zhang during 2021-2022. This data set will be of interest to you if you conduct electricity economic simulation studies, such as economic dispatch and LMP calculation. We provide a comprehensive economic data set for WECC and NPCC systems based on real-world grid operational data. Users can access the developed data set for generator aggregation, fuel cost, generator capacity, and line rating. This dataset can be found at Github as well. See https://github.com/enliten/ENLITEN-Grid-Econ-Data/.
DOI: 10.5281/zenodo.7813281
title: SLR Articles Corpus

description: The articles corpus for the SLR
DOI: 10.5281/zenodo.7813280
title: SLR Articles Corpus

description: The articles corpus for the SLR
DOI: 10.5281/zenodo.8106154
title: SLR Articles Corpus

description: The articles corpus for the SLR
DOI: 10.5281/zenodo.8106162
title: pleurophycus_gardneri_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8106161
title: pleurophycus_gardneri_spades_01.fasta.gz

description: .
DOI: 10.17909/6503-5145
title: Data from ERO for Stephan's Quintet Field
DOI: 10.5281/zenodo.8106191
title: tonicella_lineata_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8106190
title: tonicella_lineata_spades_01.fasta.gz

description: .