cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12991367.v1
title: GeneticData

description: Directory contains genetic datasets postprocessing not raw data.<br>AF_98pops.txt: Contains Allele frequency per population starting at the second column with location information on the first columns. <br>eigenVect_out251500_run1Bay: This is the 1st eigenvector for the test phase of Bayenv obtained from step 251500 from run1 out of three runs. We ran multiple different runs and checked convergence across and mixing within. <br><br>Qscore_clean.txt: Qscore estimates from running NGSAdmix using K=2. Columns contain individual tree ID, popID, lat-long-ele.<br><br>
DOI: 10.6084/m9.figshare.13012574
title: ROP DATA.xlsx

description: Data of infants eligible for screening in 4 study SNCUs
DOI: 10.6096/10.6096/msec.laos.6
title: Weather station data, Houay Pano, Laos

description: <p>Meteorological data (hourly temperature in °C, relative humidity in %, wind run in km, global radiation in J cm-2) from the Houay Pano catchment (Laos)</p>
DOI: 10.26300/bahh-3188
title: ID_12
DOI: 10.5281/zenodo.4053558
title: Novel Coronavirus (COVID-19) Cases in The Netherlands

description: On 27 February 2020, the first case of COVID-19 disease was confirmed in The Netherlands by RIVM (National Institute for Public Health and the Environment). In the weeks after, thousands of people were diagnosed with the infectious disease. Data on COVID-19 case counts are important for research and applications on various topics like epidemiology and statistics. This dataset contains reported case counts derived from official sources like RIVM (National Institute for Public Health and the Environment), LCPS (National Coordination Center for Patient Distribution), and NICE (National Intensive Care Evaluation). Data from these sources are collected, standardized, and published in various formats on a daily basis. The README document in this repository provides an overview of the available datasets, their file location(s), and codebooks. Copies of the original data are stored in the folder named 'raw_data'. Scripts to process the raw data into standardized files can be found in the folder workflows.
DOI: 10.6084/m9.figshare.13012556
title: Supplementary Table 1: Morphological Data and Comparisons

description: Morphological data for Achalinus zugorum and comparisons
DOI: 10.6084/m9.figshare.13012556.v1
title: Supplementary Table 1: Morphological Data and Comparisons

description: Morphological data for Achalinus zugorum and comparisons
DOI: 10.26300/ht0t-r685
title: ID_13
DOI: 10.26300/jhc6-7x78
title: ID_14
DOI: 10.26300/jcxv-5m37
title: ID_15
DOI: 10.21227/a8mb-1186
title: PRIME-FP20: Ultra-Widefield Fundus Photography Vessel Segmentation Dataset

description: The PRIME-FP20 dataset is established for development and evaluation of retinal vessel segmentation algorithms in ultra-widefield (UWF) fundus photography (FP). PRIME-FP20 provides 15 high-resolution UWF FP images acquired using the Optos 200Tx camera (Optos plc, Dunfermline, United Kingdom), the corresponding labeled binary vessel maps, and the corresponding binary masks for the valid data region for the images. For each UWF FP image, a concurrently captured UWF fluorescein angiography (FA) is also included.
DOI: 10.26300/jb18-6z37
title: ID_16
DOI: 10.21227/mej4-nn54
title: PRIME-FP20: Ultra-Widefield Fundus Photography Vessel Segmentation Dataset

description: The PRIME-FP20 dataset is established for development and evaluation of retinal vessel segmentation algorithms in ultra-widefield (UWF) fundus photography (FP). PRIME-FP20 provides 15 high-resolution UWF FP images acquired using the Optos 200Tx camera (Optos plc, Dunfermline, United Kingdom), the corresponding labeled binary vessel maps, and the corresponding binary masks for the valid data region for the images. For each UWF FP image, a concurrently captured UWF fluorescein angiography (FA) is also included.
DOI: 10.21227/7wca-sy54
title: PRIME-FP20: Ultra-Widefield Fundus Photography Vessel Segmentation Dataset

description: The PRIME-FP20 dataset is established for development and evaluation of retinal vessel segmentation algorithms in ultra-widefield (UWF) fundus photography (FP). PRIME-FP20 provides 15 high-resolution UWF FP images acquired using the Optos 200Tx camera (Optos plc, Dunfermline, United Kingdom), the corresponding labeled binary vessel maps, and the corresponding binary masks for the valid data region for the images. For each UWF FP image, a concurrently captured UWF fluorescein angiography (FA) is also included.
DOI: 10.26300/tz1j-4621
title: ID_18
DOI: 10.21227/ya5t-9w58
title: Supplemental Data to Submission Mattes et al. IEEE TMI 2020

description: The data uploaded here shall support the paperDecision Tree Analysis of ...which has been submitted to IEEE Transactions on Medical Imaging (2020, September 25) by the authorsJulian Mattes, Wolfgang Fenz, Stefan Thumfart, Gerhard Haitchi, Pierre Schmit, Franz A. FellnerDuring review the data shall only be visible for the reviewers of this paper. Afterwards this abstract will be modified and complemented and a dataset image will be uploaded.
DOI: 10.26300/6pqr-0j45
title: ID_19
DOI: 10.26300/4rsp-an42
title: ID_20
DOI: 10.26300/fa2a-af13
title: ID_21
DOI: 10.26300/0rjf-1s74
title: ID_22
DOI: 10.26300/6dj0-5392
title: ID_23
DOI: 10.6084/m9.figshare.12673190
title: Raw data of the article entitled "Performance if ion chromatography to measure picomoles of magnesium in nanoliter samples"

description: Raw data of the article entitled "Performance if ion chromatography to measure picomoles of magnesium in nanoliter samples"
DOI: 10.6084/m9.figshare.12673190.v1
title: Raw data of the article entitled "Performance if ion chromatography to measure picomoles of magnesium in nanoliter samples"

description: Raw data of the article entitled "Performance if ion chromatography to measure picomoles of magnesium in nanoliter samples"
DOI: 10.15468/lleufg
title: GRIIS Checklist of Introduced and Invasive Species - Suriname

description: The Global Register of Introduced and Invasive Species (GRIIS) presents validated and verified national checklists of introduced (alien) and invasive alien species at the country, territory, and associated island level. Checklists are living entities, especially for biological invasions given the growing nature of the problem. GRIIS checklists are based on a published methodology and supported by the Integrated Publishing Tool that jointly enable ongoing improvements and updates to expand their taxonomic coverage and completeness. Phase 1 of the project focused on developing validated and verified checklists of countries that are Party to the Convention on Biological Diversity (CBD). Phase 2 aimed to achieve global coverage including non-party countries and all overseas territories of countries, e.g. those of the Netherlands, France, and the United Kingdom. All kingdoms of organisms occurring in all environments and systems are covered. Checklists are reviewed and verified by networks of country or species experts. Verified checklists/ species records, as well as those under review, are presented on the online GRIIS website (www.griis.org) in addition to being published through the GBIF Integrated Publishing Tool.
DOI: 10.26300/ykc5-kz88
title: ID_24
DOI: 10.15468/vnkabc
title: Global Register of Introduced and Invasive Species - Switzerland

description: The Global Register of Introduced and Invasive Species (GRIIS) presents validated and verified national checklists of introduced (alien) and invasive alien species at the country, territory, and associated island level. Checklists are living entities, especially for biological invasions given the growing nature of the problem. GRIIS checklists are based on a published methodology and supported by the Integrated Publishing Tool that jointly enable ongoing improvements and updates to expand their taxonomic coverage and completeness. Phase 1 of the project focused on developing validated and verified checklists of countries that are Party to the Convention on Biological Diversity (CBD). Phase 2 aimed to achieve global coverage including non-party countries and all overseas territories of countries, e.g. those of the Netherlands, France, and the United Kingdom. All kingdoms of organisms occurring in all environments and systems are covered. Checklists are reviewed and verified by networks of country or species experts. Verified checklists/ species records, as well as those under review, are presented on the online GRIIS website (www.griis.org) in addition to being published through the GBIF Integrated Publishing Tool.
DOI: 10.26300/w8gf-ws61
title: ID_25
DOI: 10.15468/r88y8n
title: Global Register of Introduced and Invasive Species - Turkey

description: The Global Register of Introduced and Invasive Species (GRIIS) presents validated and verified national checklists of introduced (alien) and invasive alien species at the country, territory, and associated island level. Checklists are living entities, especially for biological invasions given the growing nature of the problem. GRIIS checklists are based on a published methodology and supported by the Integrated Publishing Tool that jointly enable ongoing improvements and updates to expand their taxonomic coverage and completeness. Phase 1 of the project focused on developing validated and verified checklists of countries that are Party to the Convention on Biological Diversity (CBD). Phase 2 aimed to achieve global coverage including non-party countries and all overseas territories of countries, e.g. those of the Netherlands, France, and the United Kingdom. All kingdoms of organisms occurring in all environments and systems are covered. Checklists are reviewed and verified by networks of country or species experts. Verified checklists/ species records, as well as those under review, are presented on the online GRIIS website (www.griis.org) in addition to being published through the GBIF Integrated Publishing Tool.
DOI: 10.5281/zenodo.3529860
title: MACREL software benchmark data set: Simulated metagenomes with sequencing quality, errors profile and abundance distributions derived from real samples

description: These metagenomes were used in the benchmarking of FACS pipeline, and were designed after NGLess benchmark dataset (doi.org/10.5281/zenodo.2560288). Metagenomes were simulated with ART-bin-MountRainier-2016.06.05 using real abundance profiles (.abund files) available elsewhere, and proGenomes' representative contigs as reference genomes. There are available metagenomes with 40, 60 and 80 M (million of reads) based in the reference genomes and abundances of the following samples: <pre><code>SAMEA2466916 SAMEA2466953 SAMEA2466965 SAMEA2621107 SAMEA2621229 SAMEA2621247</code></pre> To convert them from the CRAM format back to fastq files: <pre><code> ## 1. converting from cram to bam format: samtools view -b -T refgenome.fa -o file.bam file.cram ## 2. sorting the bam file: samtools sort -n file.bam -o input_sorted.bam # sort reads by identifier-name (-n) ## 3. converting from bam to fastq format: bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq </code></pre>
description: {"references": ["Alves, Renato, Coelho, Luis Pedro, Huerta-Cepas, Jaime, & Bork, Peer. (2019). Simulated metagenomes with quality and abundance distributions derived from real samples (Version 1.0.1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.2560288"]}
DOI: 10.5281/zenodo.3529859
title: MACREL software benchmark data set: Simulated metagenomes with sequencing quality, errors profile and abundance distributions derived from real samples

description: These metagenomes were used in the benchmarking of FACS pipeline, and were designed after NGLess benchmark dataset (doi.org/10.5281/zenodo.2560288). Metagenomes were simulated with ART-bin-MountRainier-2016.06.05 using real abundance profiles (.abund files) available elsewhere, and proGenomes' representative contigs as reference genomes. There are available metagenomes with 40, 60 and 80 M (million of reads) based in the reference genomes and abundances of the following samples: <pre><code>SAMEA2466916 SAMEA2466953 SAMEA2466965 SAMEA2621107 SAMEA2621229 SAMEA2621247</code></pre> To convert them from the CRAM format back to fastq files: <pre><code> ## 1. converting from cram to bam format: samtools view -b -T refgenome.fa -o file.bam file.cram ## 2. sorting the bam file: samtools sort -n file.bam -o input_sorted.bam # sort reads by identifier-name (-n) ## 3. converting from bam to fastq format: bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq </code></pre>
description: {"references": ["Alves, Renato, Coelho, Luis Pedro, Huerta-Cepas, Jaime, & Bork, Peer. (2019). Simulated metagenomes with quality and abundance distributions derived from real samples (Version 1.0.1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.2560288"]}
DOI: 10.6084/m9.figshare.12991367
title: GeneticData

description: Directory contains genetic datasets postprocessing not raw data.<br>AF_98pops.txt: Contains Allele frequency per population starting at the second column with location information on the first columns. <br>eigenVect_out251500_run1Bay: This is the 1st eigenvector for the test phase of Bayenv obtained from step 251500 from run1 out of three runs. We ran multiple different runs and checked convergence across and mixing within. <br><br>Qscore_clean.txt: Qscore estimates from running NGSAdmix using K=2. Columns contain individual tree ID, popID, lat-long-ele.<br><br><pre>SNPdataset.txt: Contains the full SNP dataset used in this paper in 012 format, post SNP calling using dDocent and a series of custom filtering steps.</pre>MAF_parentals.txt: Allele frequency estimates per SNP for the parental groups.<br>98PopIDs: List of hybrid zone pops used in all analyses. <br>PopInd.txt: List of pops, individuals and groups they belong to.<br>LocF_98hybrids.txt: File containing per loci variance components from hierfstat. These can be used to calculate all the Fstats at various levels. Loci are indicated as rownames. col1: Group varcomp, col2: Pops varcomp, col3: Ind varcomp, col4: error term.
DOI: 10.6084/m9.figshare.12991367.v3
title: GeneticData

description: Directory contains genetic datasets postprocessing not raw data.<br>AF_98pops.txt: Contains Allele frequency per population starting at the second column with location information on the first columns. <br>eigenVect_out251500_run1Bay: This is the 1st eigenvector for the test phase of Bayenv obtained from step 251500 from run1 out of three runs. We ran multiple different runs and checked convergence across and mixing within. <br><br>Qscore_clean.txt: Qscore estimates from running NGSAdmix using K=2. Columns contain individual tree ID, popID, lat-long-ele.<br><br><pre>SNPdataset.txt: Contains the full SNP dataset used in this paper in 012 format, post SNP calling using dDocent and a series of custom filtering steps.</pre>MAF_parentals.txt: Allele frequency estimates per SNP for the parental groups.<br>98PopIDs: List of hybrid zone pops used in all analyses. <br>PopInd.txt: List of pops, individuals and groups they belong to.<br>LocF_98hybrids.txt: File containing per loci variance components from hierfstat. These can be used to calculate all the Fstats at various levels. Loci are indicated as rownames. col1: Group varcomp, col2: Pops varcomp, col3: Ind varcomp, col4: error term.
DOI: 10.6084/m9.figshare.12991367.v2
title: GeneticData

description: Directory contains genetic datasets postprocessing not raw data.<br>AF_98pops.txt: Contains Allele frequency per population starting at the second column with location information on the first columns. <br>eigenVect_out251500_run1Bay: This is the 1st eigenvector for the test phase of Bayenv obtained from step 251500 from run1 out of three runs. We ran multiple different runs and checked convergence across and mixing within. <br><br>Qscore_clean.txt: Qscore estimates from running NGSAdmix using K=2. Columns contain individual tree ID, popID, lat-long-ele.<br><br><pre>SNPdataset.txt: Contains the full SNP dataset used in this paper in 012 format, post SNP calling using dDocent and a series of custom filtering steps.</pre>MAF_parentals.txt: Allele frequency estimates per SNP for the parental groups.<br>98PopIDs: List of hybrid zone pops used in all analyses. <br>PopInd.txt: List of pops, individuals and groups they belong to.<br><br>
DOI: 10.6084/m9.figshare.13012655
title: GEA_bayenv

description: convergence_soil: trios estimated from Bayenv for each of the soil variables. Determined as the median across three bayenv runs. <br>convergence_clim: trios estimated from Bayenv for each of the climateNA variables. Determined as the median across three bayenv runs. <br>
DOI: 10.6084/m9.figshare.13012655.v1
title: GEA_bayenv

description: convergence_soil: trios estimated from Bayenv for each of the soil variables. Determined as the median across three bayenv runs. <br>convergence_clim: trios estimated from Bayenv for each of the climateNA variables. Determined as the median across three bayenv runs. <br>
DOI: 10.6084/m9.figshare.13012661
title: Data mining analyses for precision medicine in acromegaly

description: <b>Context:</b> Predicting which acromegaly patients could benefit from somatostatin receptor ligand (SRL) is crucial to avoid months of ineffective treatment for non-responding cases. Although many biomarkers linked to SRL response have been identified, there is no consensus criterion on how to assign pharmacologic treatment according to biomarker levels. <b>Objective:</b> Our aim is to provide better predictive tools for a more accurate acromegaly patient stratification regarding the ability to respond to SRL. <b>Design and patients:</b> Retrospective multicenter study of 71 acromegaly patients. <b>Methods:</b> We used advanced mathematical modelling and artificial intelligence to predict SRL response combining molecular and clinical information. <b>Results:</b> Different models of patient stratification were obtained regarding SRL response, with a much higher accuracy when the studied cohort is fragmented according to relevant clinical characteristics. Considering all the models, a patient stratification based on the extrasellar growth of the tumor, sex, age and the expression of E-cadherin, <i>GHRL</i>, <i>IN1-GHRL</i>, <i>DRD2</i>, <i>SSTR5</i> and <i>PEBP1</i> is proposed, with accuracies that stand between 71 to 95%. Furthermore, we show an association between extrasellar growth and high BMI for SRL non-responding patients. <b>Conclusion.</b> The use of data mining is necessary for implementation of personalized medicine in acromegaly and requires an interdisciplinary effort between computer science, mathematics, biology and medicine. This new methodology opens a door to more precise personalized medicine for acromegaly patients.
DOI: 10.6084/m9.figshare.13012292
title: R0160_20170428a_videos

description: Rat 0160, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13012292.v1
title: R0160_20170428a_videos

description: Rat 0160, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12618725
title: SupplementaryData.xlsx

description: Raw data generated during our study, entitled as "The effect of long-term ultra-endurance exercise and SOD2 genotype on telomere shortening with age"
DOI: 10.6084/m9.figshare.12618725.v2
title: SupplementaryData.xlsx

description: Raw data generated during our study, entitled as "The effect of long-term ultra-endurance exercise and SOD2 genotype on telomere shortening with age"
DOI: 10.6084/m9.figshare.12618725.v1
title: SupplementaryData.xlsx

description: Raw data generated during our study, entitled as "The effect of long-term ultra-endurance exercise and SOD2 genotype on telomere shortening with age"
DOI: 10.6084/m9.figshare.13012586.v1
title: INTROGRESS_files

description: IntroLoci.txt: Contains IDs of all loci that can be used for introgress analyses.<br>The zipped folder outFiles contains output from running INTROGRESS:::::<br>HomoP1*: Per SNP and per individual estimate of parent one's ancestry and CIs around the estimate as obtained from running INTROGRESS in parametric mode.<br>HomoP2*: Per SNP and per individual estimate of parent two's ancestry and CIs around the estimate as obtained from running INTROGRESS in parametric mode.<br>
DOI: 10.6084/m9.figshare.13012586
title: INTROGRESS_files

description: IntroLoci.txt: Contains IDs of all loci that can be used for introgress analyses.<br>The zipped folder outFiles contains output from running INTROGRESS:::::<br>HomoP1*: Per SNP and per individual estimate of parent one's ancestry and CIs around the estimate as obtained from running INTROGRESS in parametric mode.<br>HomoP2*: Per SNP and per individual estimate of parent two's ancestry and CIs around the estimate as obtained from running INTROGRESS in parametric mode.<br>
DOI: 10.6084/m9.figshare.3761562.v1621
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.5517/ccdc.csd.cc21y719
title: CCDC 1904920: Experimental Crystal Structure Determination

description: Related Article: Surajit Mondal, Niladri Patra, Hari Pada Nayek, Sumit K. Hira, Soumit Chatterjee, Swapan Dey|2020|Photochem.Photobiol.Sci.|19|1211|doi:10.1039/D0PP00140F
DOI: 10.5517/ccdc.csd.cc21y72b
title: CCDC 1904921: Experimental Crystal Structure Determination

description: Related Article: Surajit Mondal, Niladri Patra, Hari Pada Nayek, Sumit K. Hira, Soumit Chatterjee, Swapan Dey|2020|Photochem.Photobiol.Sci.|19|1211|doi:10.1039/D0PP00140F
DOI: 10.5517/ccdc.csd.cc232stt
title: CCDC 1939106: Experimental Crystal Structure Determination

description: Related Article: Lifang Bian|2019|CSD Communication|||
description: Related Article: Lifang Bian, Huili Ma, Wenpeng Ye, Anqi Lv, He Wang, Wenyong Jia, Long Gu, Huifang Shi, Zhongfu An, Wei Huang|2020|Sci.China.Chem.|63|1443|doi:10.1007/s11426-020-9761-x
DOI: 10.5517/ccdc.csd.cc232svv
title: CCDC 1939107: Experimental Crystal Structure Determination

description: Related Article: Lifang Bian|2019|CSD Communication|||
description: Related Article: Lifang Bian, Huili Ma, Wenpeng Ye, Anqi Lv, He Wang, Wenyong Jia, Long Gu, Huifang Shi, Zhongfu An, Wei Huang|2020|Sci.China.Chem.|63|1443|doi:10.1007/s11426-020-9761-x
DOI: 10.5517/ccdc.csd.cc232sww
title: CCDC 1939108: Experimental Crystal Structure Determination

description: Related Article: Lifang Bian|2019|CSD Communication|||
description: Related Article: Lifang Bian, Huili Ma, Wenpeng Ye, Anqi Lv, He Wang, Wenyong Jia, Long Gu, Huifang Shi, Zhongfu An, Wei Huang|2020|Sci.China.Chem.|63|1443|doi:10.1007/s11426-020-9761-x
DOI: 10.5517/ccdc.csd.cc2380zd
title: CCDC 1944133: Experimental Crystal Structure Determination

description: Related Article: Surajit Mondal, Niladri Patra, Hari Pada Nayek, Sumit K. Hira, Soumit Chatterjee, Swapan Dey|2020|Photochem.Photobiol.Sci.|19|1211|doi:10.1039/D0PP00140F
DOI: 10.6084/m9.figshare.12992909
title: EnvironData

description: This directory contains environmental values (soil & climate) for all the populations in the hybrid zone and the pure parentals: P. strobiformis (SWWP) & P. flexilis (LP).
DOI: 10.5517/ccdc.csd.cc23jg15
title: CCDC 1952226: Experimental Crystal Structure Determination

description: Related Article: Yue Yu, Yi-Chen Tao, Sheng-Nan Zou, Zhi-Zhou Li, Chang-Cun Yan, Ming-Peng Zhuo, Xue-Dong Wang, Liang-Sheng Liao|2020|Sci.China.Chem.|63|1477|doi:10.1007/s11426-019-9706-x
DOI: 10.6084/m9.figshare.12992909.v2
title: EnvironData

description: This directory contains environmental values (soil & climate) for all the populations in the hybrid zone and the pure parentals: P. strobiformis (SWWP) & P. flexilis (LP).
DOI: 10.5517/ccdc.csd.cc23jg26
title: CCDC 1952227: Experimental Crystal Structure Determination

description: Related Article: Yue Yu, Yi-Chen Tao, Sheng-Nan Zou, Zhi-Zhou Li, Chang-Cun Yan, Ming-Peng Zhuo, Xue-Dong Wang, Liang-Sheng Liao|2020|Sci.China.Chem.|63|1477|doi:10.1007/s11426-019-9706-x