cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6395091
title: What is a Good School, and Can Parents Tell? Evidence on the Multidimensionality of School Output

description: The package contains all the code necessary to reproduce the figures and tables in Beuermann, Jackson, Navarro-Sola and Pardo (forthcoming). "What is a Good School, and Can Parents Tell? Evidence on the Multidimensionality of School Output." Review of Economic Studies. Detailed instructions are also given about requesting access to the raw data.
DOI: 10.6084/m9.figshare.19467485
title: Supp. Table_W. Cogulans_Distance matrix.csv

description: Distance matrix showing the pairwise identity of W. coagulans with homologous sequences that are retrieved by BLAST search
DOI: 10.6084/m9.figshare.19467485.v2
title: Supp. Table_W. Cogulans_Distance matrix.csv

description: Distance matrix showing the pairwise identity of W. coagulans with homologous sequences that are retrieved by BLAST search
DOI: 10.6084/m9.figshare.19467485.v1
title: Supp. Table_W. Cogulans_Distance matrix.csv

description: Distance matrix showing the pairwise identity of W. coagulans with homologous sequences that are retrieved by BLAST search
DOI: 10.5517/ccdc.csd.cc256wx6
title: CCDC 2002628: Experimental Crystal Structure Determination

description: Related Article: Tony Ho-Ching Fung, Cheok-Lam Wong, Wai-Kit Tang, Ming-Yi Leung, Kam-Hung Low, Vivian Wing-Wah Yam|2022|Chem.Commun.|58|4231|doi:10.1039/D2CC00107A
DOI: 10.5517/ccdc.csd.cc28phs8
title: CCDC 2106040: Experimental Crystal Structure Determination

description: Related Article: Dinesh Bista, Alexander P. Aydt, Kevin J. Anderton, Daniel W. Paley, Theodore A. Betley, Arthur C. Reber, Vikas Chauhan, Amymarie K. Bartholomew, Xavier Roy, Shiv N. Khanna|2022|J.Am.Chem.Soc.|144|5172|doi:10.1021/jacs.2c00731
DOI: 10.6084/m9.figshare.19467629
title: Supp Table_Lysozyme.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 in the presence of Lysozymes at concentration 100, 200 and 300 mg/L, and comparison with the control set without pancreatin. The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.6084/m9.figshare.19467629.v2
title: Supp Table_Lysozyme.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 in the presence of Lysozymes at concentration 100, 200 and 300 mg/L, and comparison with the control set without pancreatin. The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.6084/m9.figshare.19467629.v1
title: Supp Table_Lysozyme.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 in the presence of Lysozymes at concentration 100, 200 and 300 mg/L, and comparison with the control set without pancreatin. The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.5517/ccdc.csd.cc29lc2c
title: CCDC 2132802: Experimental Crystal Structure Determination

description: Related Article: Tony Ho-Ching Fung, Cheok-Lam Wong, Wai-Kit Tang, Ming-Yi Leung, Kam-Hung Low, Vivian Wing-Wah Yam|2022|Chem.Commun.|58|4231|doi:10.1039/D2CC00107A
DOI: 10.6084/m9.figshare.19467479
title: Supp. FASTA 16S_W. coagulans strain LMG S-31876.txt

description: 16S rDNA sequence of W. coagulans strain LMG S-31876
DOI: 10.6084/m9.figshare.19467479.v2
title: Supp. FASTA 16S_W. coagulans strain LMG S-31876.txt

description: 16S rDNA sequence of W. coagulans strain LMG S-31876
DOI: 10.6084/m9.figshare.19467479.v1
title: Supp. FASTA 16S_W. coagulans strain LMG S-31876.txt

description: 16S rDNA sequence of W. coagulans strain LMG S-31876
DOI: 10.6084/m9.figshare.19467626
title: Fig. 6_Pancreatin.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 in the presence of 0.5 % pancreatin, and comparison with the control set without pancreatin. The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.6084/m9.figshare.19467626.v2
title: Fig. 6_Pancreatin.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 in the presence of 0.5 % pancreatin, and comparison with the control set without pancreatin. The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.6084/m9.figshare.19467626.v1
title: Fig. 6_Pancreatin.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 in the presence of 0.5 % pancreatin, and comparison with the control set without pancreatin. The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.6084/m9.figshare.16437278
title: Adsorption performance of activated carbon synthesis by ZnCl<sub>2</sub>, KOH, H<sub>3</sub>PO<sub>4</sub> with different activation temperatures from mixed fruit seeds

description: In this study, new activated carbons (ACs) were synthesized from a mixture of lemon and orange seeds (LOS) for toxic metal removal from aqueous solutions. Adsorbents have been produced by chemical activation with different activation agents (with H<sub>3</sub>PO<sub>4</sub>, ZnCl<sub>2</sub> and KOH) and activation temperature (600°C, 700°C, 800°C). The elemental analysis, FT-IR, XRD and SEM analyses were performed to determine the characterization of the ACs. A series of batch adsorption experiments were done to research the influence of various parameters such as pH, adsorbent dosage, contact time, temperature, the complexing agents on the toxic metal ions (Cu(II), Cr(III) and Ni(II)) removal capacity of ACs. Adsorption equilibration time was 60 min, the adsorption capacity was 118.02 mg/g for Ni(II) ions, 146.03 mg/g for Cr(III) ions and 150.45 mg/g for Cu(II) ions. The adsorption of toxic metal ions was observed as a maximum at pH = 5 on AC-ZnCl<sub>2</sub> (600°C) produced under N<sub>2</sub> atmosphere. The adsorption process was fitted with a Langmuir isotherm model and a pseudo-second-order kinetic equation, showing the metal ions adsorption on AC was monolayer coverage. Thermodynamic studies show that the adsorption is endothermic and spontaneous in nature. AC produced from the LOS mixture has not been encountered in the literature. A simple, easy-to-apply method has been developed for a new adsorbent prepared from a mixture of LOS with environmentally friendly, easy to produce, reusable, cost-effective, non-toxic and with good adsorption-desorption capacity. Therefore, this study will contribute to the world economy in terms of environmental and wastewater cleaning.
DOI: 10.6084/m9.figshare.16437278.v2
title: Adsorption performance of activated carbon synthesis by ZnCl<sub>2</sub>, KOH, H<sub>3</sub>PO<sub>4</sub> with different activation temperatures from mixed fruit seeds

description: In this study, new activated carbons (ACs) were synthesized from a mixture of lemon and orange seeds (LOS) for toxic metal removal from aqueous solutions. Adsorbents have been produced by chemical activation with different activation agents (with H<sub>3</sub>PO<sub>4</sub>, ZnCl<sub>2</sub> and KOH) and activation temperature (600°C, 700°C, 800°C). The elemental analysis, FT-IR, XRD and SEM analyses were performed to determine the characterization of the ACs. A series of batch adsorption experiments were done to research the influence of various parameters such as pH, adsorbent dosage, contact time, temperature, the complexing agents on the toxic metal ions (Cu(II), Cr(III) and Ni(II)) removal capacity of ACs. Adsorption equilibration time was 60 min, the adsorption capacity was 118.02 mg/g for Ni(II) ions, 146.03 mg/g for Cr(III) ions and 150.45 mg/g for Cu(II) ions. The adsorption of toxic metal ions was observed as a maximum at pH = 5 on AC-ZnCl<sub>2</sub> (600°C) produced under N<sub>2</sub> atmosphere. The adsorption process was fitted with a Langmuir isotherm model and a pseudo-second-order kinetic equation, showing the metal ions adsorption on AC was monolayer coverage. Thermodynamic studies show that the adsorption is endothermic and spontaneous in nature. AC produced from the LOS mixture has not been encountered in the literature. A simple, easy-to-apply method has been developed for a new adsorbent prepared from a mixture of LOS with environmentally friendly, easy to produce, reusable, cost-effective, non-toxic and with good adsorption-desorption capacity. Therefore, this study will contribute to the world economy in terms of environmental and wastewater cleaning.
DOI: 10.6084/m9.figshare.19467611
title: Fig. 3_pH 3 and 7.2.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 at pH 3.0 and pH 7.2. The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.6084/m9.figshare.19467611.v1
title: Fig. 3_pH 3 and 7.2.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 at pH 3.0 and pH 7.2. The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.6084/m9.figshare.19467614
title: Fig. 4_gastric juice.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 in the presence of simulated gastric juice (pH 3.0) and control (pH 7.2). The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.6084/m9.figshare.19467614.v1
title: Fig. 4_gastric juice.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 in the presence of simulated gastric juice (pH 3.0) and control (pH 7.2). The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.6084/m9.figshare.19467623
title: Fig. 5_Bile.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 in the presence of 0.3% bile, and compared with the control set without bile. The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.6084/m9.figshare.19467623.v2
title: Fig. 5_Bile.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 in the presence of 0.3% bile, and compared with the control set without bile. The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.6084/m9.figshare.19467623.v1
title: Fig. 5_Bile.xlsx

description: Viable plate count of W. coagulans strain LMG S-31876 in the presence of 0.3% bile, and compared with the control set without bile. The results are expressed as mean ± standard deviation of log10 CFU/mL.
DOI: 10.5281/zenodo.6346701
title: NinePoint Medical labeled esophageal OCT scans

description: Raw patient esophageal OCT labelled scans available for segmentation and dysplasia classification. The link contains an executable which will download the scan data on your local system Click here to download the datasets.
DOI: 10.6084/m9.figshare.19469192.v1
title: ON/OFF domains shape receptive field structure in mouse visual cortex

description: Database containing the data in Tring, Duan & Ringach "ON/OFF domains shape receptive field structure in mouse visual cortex". See example_code.m (a Matlab script) for a description of the database structure. <br>
DOI: 10.6084/m9.figshare.19469192
title: ON/OFF domains shape receptive field structure in mouse visual cortex

description: Database containing the data in Tring, Duan & Ringach "ON/OFF domains shape receptive field structure in mouse visual cortex". See example_code.m (a Matlab script) for a description of the database structure. <br>
DOI: 10.6084/m9.figshare.19316576.v2
title: GC_SRF: A new generalized strategy for obtaining the lithospheric thickness from S-wave receiver functions and its application to southeastern Tibet

description: Shared SX_Deconv source code and the S wave receiver functions used in the paper "GC_SRF: A new generalized strategy for obtaining the lithospheric thickness from S-wave receiver functions and its application to southeastern Tibet" submitted to Journal of Geophysical Research: Solid Earth.<br>Data statement:./SX_Deconv-JGR : The SX_Deconv source code with an prepared example (XR.ST09).<br>./S_Receiver_Functions-JGR : S receiver functions obtained following the GC_SRF strategy.
DOI: 10.6084/m9.figshare.17085461.v1
title: Forecast values of wind power.xlsx

description: This excel shows the forecast values of wind power at the<i> t<sup>th</sup></i> time and <i>i</i><sup><i>t</i>h</sup> bus in the IEEE 30-bus system.
DOI: 10.5281/zenodo.5555990
title: CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data

description: To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by (i) most published genomes being &lt;1x coverage, (ii) ancient DNA fragments being typically &lt;80 bps. These characteristics preclude state-of-the-art CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, an algorithm tailored for genotyping deletion and duplication events in genomes with low depths of coverage. Simulations and down-sampling experiments show that CONGA can genotype deletions &gt;1 kbps with F-scores &gt;0.75 at &gt;=1x, and distinguish between heterozygous and homozygous states. Using CONGA, we analyse deletion events at 10,018 loci in 56 ancient human genomes spanning the last 50,000 years, with coverages 0.4x-26x. We show that inter-individual genetic diversity measured using deletions and SNPs are highly correlated, as in modern-day genomes, confirming that deletion frequencies broadly reflect demographic history. We also identify signatures of strong purifying selection on deletions in ancient-genomes, such as an excess of singletons compared to those in SNPs. CONGA paves the way for systematic studies of drift, mutation load, and adaptation in ancient and modern-day gene pools through the lens of CNVs.
description: Here we deposit the CNV predictions and genotype sets of CONGA used in simulation and real data analysis (as well as the predictions of FREEC , CNVnator, GenomeSTRiP and mrCaNaVaR)
DOI: 10.5281/zenodo.5555989
title: CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data

description: To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by (i) most published genomes being &lt;1x coverage, (ii) ancient DNA fragments being typically &lt;80 bps. These characteristics preclude state-of-the-art CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, an algorithm tailored for genotyping deletion and duplication events in genomes with low depths of coverage. Simulations and down-sampling experiments show that CONGA can genotype deletions &gt;1 kbps with F-scores &gt;0.75 at &gt;=1x, and distinguish between heterozygous and homozygous states. Using CONGA, we analyse deletion events at 10,018 loci in 56 ancient human genomes spanning the last 50,000 years, with coverages 0.4x-26x. We show that inter-individual genetic diversity measured using deletions and SNPs are highly correlated, as in modern-day genomes, confirming that deletion frequencies broadly reflect demographic history. We also identify signatures of strong purifying selection on deletions in ancient-genomes, such as an excess of singletons compared to those in SNPs. CONGA paves the way for systematic studies of drift, mutation load, and adaptation in ancient and modern-day gene pools through the lens of CNVs.
description: Here we deposit the CNV predictions and genotype sets of CONGA used in simulation and real data analysis (as well as the predictions of FREEC , CNVnator, GenomeSTRiP and mrCaNaVaR)
DOI: 10.6084/m9.figshare.19330541.v1
title: Contributions of trans locus transcripts to protein abundance prediction models

description: Supplementary Tables S1-S7.<br>Protein and mRNA levels correlate only moderately across samples. The availability of proteogenomics data sets with protein and transcript measurements from matching samples is providing new opportunities to assess the degree to which protein levels in a system can be predicted from mRNA information. We analyzed large proteogenomics datasets from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) containing 13 637 proteins with matching transcriptome data from up to 958 tumor or normal adjacent tissue samples each, and trained models to predict protein abundance from the transcriptome of a sample using different algorithms and feature sets.<br>
DOI: 10.6084/m9.figshare.17085461
title: Forecast values of wind power and the substitution benefit and its percentage of market participants.xlsx

description: This excel shows the forecast values of wind power at the<i> t<sup>th</sup></i> time and <i>i</i><sup><i>t</i>h</sup> bus and list the detail information of substitution benefit and its percentage of all participants at different times in the modified IEEE 30-bus system.
DOI: 10.6084/m9.figshare.19330541.v2
title: Interpreting the importance of transcript features in protein abundance prediction models

description: Supplementary Tables S1-S7.<br>Protein and mRNA levels correlate only moderately across samples. The availability of proteogenomics data sets with protein and transcript measurements from matching samples is providing new opportunities to assess the degree to which protein levels in a system can be predicted from mRNA information. We analyzed large proteogenomics datasets from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) containing 13 637 proteins with matching transcriptome data from up to 958 tumor or normal adjacent tissue samples each, and trained models to predict protein abundance from the transcriptome of a sample using different algorithms and feature sets.<br>
DOI: 10.5519/qd.tesrnxnu
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (751 records)
DOI: 10.5281/zenodo.6399251
title: Appendix of "Impact of Change Granularity in Refactoring Detection"

description: This is the dataset for ICPC 2022 Impact of Change Granularity in Refactoring Detection, which contains data about coarse-grained refactorings in 19 open source repositories. There are 19 csv files in this dataset. Each of the csv contains 8 rows: 1. repository: repository name <br> 2. commit(s): commit SHA-1 hash<br> 3. detected_refactoring_type: refactoring type detected in that commit<br> 4. description: description for that refactoring<br> 5. leftSideLocations: refactoring start place<br> 6. rightSideLocations: refactoring end place<br> 7. is_effective: whether this refactoring is a coarse-grained refactoring (null for refactoring whose coarse-granularity is equal to 1)<br> 8. granularity: coarse-granularity of this refactoring Note that refactorings detected using RefactoringMiner(2.2) with invalid locations has been excluded.
DOI: 10.18739/a2416t08t
title: International Tundra Experiment (ITEX) Arctic System Science (ARCSS) 1x5 square subplots at Barrow and Atqasuk, Alaska, 2011-2014

description: These files contain data representing the plant cover and counts of individuals in 5, 10" by 10" square subplots at Barrow and Atqasuk in a text tab delimited format. The 5 subplots were established in existing plots. These include 96 International Tundra Experiment (ITEX) plots and a subset of 30 Arctic System Science (ARCSS) grid plots in Barrow and 96 ITEX plots and a subset of 30 ARCSS grid plots in Atqasuk. The data presented were collected from 2011-20XX.
DOI: 10.18739/a2sp1k
title: Plant density measurements in the International Tundra Experiment (ITEX) and Arctic System Science Program (ARCSS) plots at Barrow and Atqasuk, Alaska, 2011-2017

description: These files contain data representing the plant cover and counts of individuals in 5, 10cm by 10cm square subplots at Barrow and Atqasuk in a text tab delimited format. The 5 subplots were established in existing plots. These include 96 International Tundra Experiment (ITEX) plots and a subset of 30 Arctic System Science Program (ARCSS) grid plots in Barrow and 96 ITEX plots and a subset of 30 ARCSS grid plots in Atqasuk. The data presented were collected from 2011-2017.
DOI: 10.18739/a2hq3rz77
title: Plant density measurements in International Tundra Experiment (ITEX) and Arctic System Science Program (ARCSS) plots at Barrow and Atqasuk, Alaska 2018

description: Arctic ecosystems are changing in response to arctic warming, which is proceeding more than twice as fast as the global average. The International Tundra Experiment (ITEX) was established in the early 1990s to understand the effects of warming and environmental variability on tundra vegetation properties and ecosystem function. The ITEX program has been extremely valuable for detection of changes in tundra plant and ecosystem responses to experimental warming and to background climate change across sites that span the major ecosystems of the Arctic These files contain data representing the plant cover and counts of individuals in 5, 10” by 10” square subplots at Barrow and Atqasuk in a text tab delimited format. The 5 subplots were established in existing plots. These include 96 ITEX plots and a subset of 30 ARCSS grid plots in Barrow and 96 ITEX plots and a subset of 30 ARCSS grid plots in Atqasuk. The data presented were collected during the 2018 field season.
DOI: 10.18739/a22r3nx5w
title: Plant density measurements in International Tundra Experiment (ITEX) and Arctic System Science Program (ARCSS) plots at Barrow and Atqasuk, Alaska 2019

description: Arctic ecosystems are changing in response to arctic warming, which is proceeding more than twice as fast as the global average. The International Tundra Experiment (ITEX) was established in the early 1990s to understand the effects of warming and environmental variability on tundra vegetation properties and ecosystem function. The ITEX program has been extremely valuable for detection of changes in tundra plant and ecosystem responses to experimental warming and to background climate change across sites that span the major ecosystems of the Arctic. These files contain data representing the plant cover and counts of individuals in 5, 10” by 10” square subplots at Barrow(Utqiaġvik) and Atqasuk in a text tab delimited format. The 5 subplots were established in existing plots. These include 96 ITEX plots and a subset of 30 ARCSS grid plots in Barrow and 96 ITEX plots and a subset of 30 ARCSS grid plots in Atqasuk. The data presented were collected during the 2019 field season.
DOI: 10.5066/p9lqqj2j
title: SARS-CoV-2 Data from National Wastewater Surveillance System Surge Capacity Sampling, September 2021

description: Wastewater-based epidemiology (WBE) is used to determine the consumption of, or exposure to, chemicals or pathogens in human populations, and is conducted by collecting representative samples of untreated wastewater (influent) to quantify pathogens shed in the population served by the sampled wastewater system. The Centers for Disease Control and Prevention (CDC) and the US Department of Health and Human Services (HHS), in collaboration with the United States Geological Survey (USGS) and other agencies throughout the federal government, initiated the National Wastewater Surveillance System (NWSS) in response to the COVID-19 pandemic to conduct WBE using analytical methods for the collection and analysis of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in wastewater influent. The data generated by NWSS helps public health officials to better understand the extent of SARS-CoV-2 infections in communities. Surge capacity sampling to support NWSS and carried out by the USGS was conducted in September 2021 in six states (Colorado, Missouri, Utah, North Carolina, Ohio, and Wisconsin). 354 samples from 25 wastewater treatment plants (WWTP) representing 26 distinct service areas (one facility has two treatment areas) were analyzed using ddPCR (digital droplet polymerase chain reaction) for SARS-CoV-2 using standard CDC assays targeting N2- and E-genes plus the wastewater marker pepper mild mottle virus (PMMoV). Results for both genes are included in this data release (708 records).