cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10278410
title: MOESM2 of OmicsARules: a R package for integration of multi-omics datasets via association rules mining

description: Additional file 2: Table S1. General information of three real datasets downloaded from TCGA. Table S2. Top 20 rules identified from BRCA mRNA dataset. Table S3. Top 20 rules identified from BRCA DNA methylation. Table S4. Top 20 rules identified from ESCA mRNA dataset. Table S5. Top 20 rules identified from ESCA DNA methylation dataset. Table S6. Top 20 rules identified from LUAD mRNA dataset. Table S7. Top 20 rules identified from LUAD DNA methylation dataset. Table S8. Top 20 rules identified from the combined BRCA mRNA and DNA methylation datasets. Table S9. Top 20 rules identified from the combined ESCA mRNA and DNA methylation datasets. Table S10. Top 20 rules identified from the combined LUAD mRNA and DNA methylation datasets.
DOI: 10.6084/m9.figshare.10278410.v1
title: MOESM2 of OmicsARules: a R package for integration of multi-omics datasets via association rules mining

description: Additional file 2: Table S1. General information of three real datasets downloaded from TCGA. Table S2. Top 20 rules identified from BRCA mRNA dataset. Table S3. Top 20 rules identified from BRCA DNA methylation. Table S4. Top 20 rules identified from ESCA mRNA dataset. Table S5. Top 20 rules identified from ESCA DNA methylation dataset. Table S6. Top 20 rules identified from LUAD mRNA dataset. Table S7. Top 20 rules identified from LUAD DNA methylation dataset. Table S8. Top 20 rules identified from the combined BRCA mRNA and DNA methylation datasets. Table S9. Top 20 rules identified from the combined ESCA mRNA and DNA methylation datasets. Table S10. Top 20 rules identified from the combined LUAD mRNA and DNA methylation datasets.
DOI: 10.6084/m9.figshare.6608519
title: The synchronization and adaptation of Neurospora crassa circadian and conidiation rhythms to short light-dark cycles

description: These are supplementary materials for the paper submitted to a journal.
DOI: 10.6084/m9.figshare.8179871.v1
title: MOESM6 of Using hyperspectral analysis as a potential high throughput phenotyping tool in GWAS for protein content of rice quality

description: Additional file 6: Table S3. Summary of gene annotation.
DOI: 10.6084/m9.figshare.8179886
title: MOESM8 of Using hyperspectral analysis as a potential high throughput phenotyping tool in GWAS for protein content of rice quality

description: Additional file 8: TableÂ S5. MAF of all identified SNPs.
DOI: 10.6084/m9.figshare.8181443
title: Low-temperature tolerance and transcriptome analyses during seed germination of <i>Anabasis aphylla</i>

description: This study aimed to explore differences in the low-temperature tolerance of a desert plant, <i>Anabasis aphylla</i>, at different seed germination stages during the fall using transcriptome sequencing to identify related genes. The survival rate of the seeds decreased with lower temperatures at different germination stages, and the tolerance of the stages in decreasing order was as follows: imbibition (I) ≈ testa rupture (II) &gt; testa removal (III) &gt; elongation (IV). Superoxide dismutase, peroxidase, and catalase activities and the malondialdehyde content showed a downward trend after stage II. Transcriptome sequencing of seeds, including ripe and dry dominant seeds (W1) and seeds during different germination stages [imbibition (W2), testa removal (W3), and elongation (W4)] was performed. Some genes were downregulated during seed germination, which mainly included cytochrome P450, oleosin, ethylene-responsive transcription factor, and low temperature-induced protein. This study suggests that downregulated of some genes may result in a decrease in low-temperature tolerance.
DOI: 10.6084/m9.figshare.8181443.v1
title: Low-temperature tolerance and transcriptome analyses during seed germination of <i>Anabasis aphylla</i>

description: This study aimed to explore differences in the low-temperature tolerance of a desert plant, <i>Anabasis aphylla</i>, at different seed germination stages during the fall using transcriptome sequencing to identify related genes. The survival rate of the seeds decreased with lower temperatures at different germination stages, and the tolerance of the stages in decreasing order was as follows: imbibition (I) ≈ testa rupture (II) &gt; testa removal (III) &gt; elongation (IV). Superoxide dismutase, peroxidase, and catalase activities and the malondialdehyde content showed a downward trend after stage II. Transcriptome sequencing of seeds, including ripe and dry dominant seeds (W1) and seeds during different germination stages [imbibition (W2), testa removal (W3), and elongation (W4)] was performed. Some genes were downregulated during seed germination, which mainly included cytochrome P450, oleosin, ethylene-responsive transcription factor, and low temperature-induced protein. This study suggests that downregulated of some genes may result in a decrease in low-temperature tolerance.
DOI: 10.6084/m9.figshare.8179871
title: MOESM6 of Using hyperspectral analysis as a potential high throughput phenotyping tool in GWAS for protein content of rice quality

description: Additional file 6: Table S3. Summary of gene annotation.
DOI: 10.5281/zenodo.10670569
title: Dataset related to article: Interval between contrast administration and T1-weighted MRI for cerebral adrenoleukodystrophy: a single-case observation

description: The database contains the T1 RM images of the patient at different time points and level of contrast injection
DOI: 10.5281/zenodo.10670570
title: Dataset related to article: Interval between contrast administration and T1-weighted MRI for cerebral adrenoleukodystrophy: a single-case observation

description: The database contains the T1 RM images of the patient at different time points and level of contrast injection
DOI: 10.6084/m9.figshare.8179721.v1
title: Additional file 1: of MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip

description: Table S1. PCR primer sets used in this study. Table S2. Summary of databases searched. Table S3. Genes with significant contribution to human CL/P (identified through single gene studies). Table S4. Genes with significant contribution to human CL/P (identified through multiple genes studies). Table S5. Genes with significant contribution to human CL/P (unknown coding genes). Table S6. Genes without significant contribution to human CL/P. Table S7. CL/P candidate genes with significant signals in GWAS. Table S8. CL/P candidate genes without significant signals in GWAS. Table S9. GO terms enriched with genes associated with cleft lip with/without cleft palate (CL/P) in humans. Table S10. GO Biological Process terms enriched with human CL/P genes (FDR &lt; 0.005). Table S11. GO Molecular Function terms enriched with human CL/P genes (FDR &lt; 0.005). Table S12. GO Cellular Component terms enriched with human CL/P genes (FDR &lt; 0.05). Table S13. Top 30 Human Phenotype Ontology Categories. Table S14. KEGG pathways enriched with genes associated with cleft lip with/without cleft palate (CL/P) in humans. (ZIP 292 kb)
DOI: 10.5281/zenodo.10670323
title: TOMCAT Tropospheric Ozone

description: Global 3-D simulations of tropospheric ozone (TO3) from the TOMCAT chemical transport model (2008-2017) output at two satellite local solar overpass times (09.30 & 13.30 LST). The ozone data (2-daily overpass times) is provided as 3-D fields on the 2.8°×2.8° horizontal model grid. Atmospheric pressure (Pa) and temperature (K) have also included to provide vertical information on the ozone distribution up to 10 hPa. The ozone data has units of mass mixing ratio (1.0E-9). This work was undertaken primarily as long-term science activities of the NERC - National Centre for Earth Observation.

These model runs were used in the accepted (2024) manuscript in Atmospheric Chemistry and Physics (ACP) titled "Quantifying the tropospheric ozone radiative effect and its temporal evolution in the satellite-era". The DOI for the preprint is doi: 10.5194/egusphere-2023-1513.
DOI: 10.5281/zenodo.10670324
title: TOMCAT Tropospheric Ozone

description: Global 3-D simulations of tropospheric ozone (TO3) from the TOMCAT chemical transport model (2008-2017) output at two satellite local solar overpass times (09.30 & 13.30 LST). The ozone data (2-daily overpass times) is provided as 3-D fields on the 2.8°×2.8° horizontal model grid. Atmospheric pressure (Pa) and temperature (K) have also included to provide vertical information on the ozone distribution up to 10 hPa. The ozone data has units of mass mixing ratio (1.0E-9). This work was undertaken primarily as long-term science activities of the NERC - National Centre for Earth Observation.

These model runs were used in the accepted (2024) manuscript in Atmospheric Chemistry and Physics (ACP) titled "Quantifying the tropospheric ozone radiative effect and its temporal evolution in the satellite-era". The DOI for the preprint is doi: 10.5194/egusphere-2023-1513.
DOI: 10.6084/m9.figshare.8179811.v1
title: Additional file 1: of Rifampin resistance and its fitness cost in Riemerella anatipestifer

description: Table S1. Primers and descriptions used in this study (XLSX 10 kb)
DOI: 10.6084/m9.figshare.21285753.v1
title: Additional file 1 of The value of multiparameter combinations for predicting difficult airways by ultrasound

description: Additional file 1.
DOI: 10.6084/m9.figshare.21285828
title: Additional file 1 of Circular RNA circPVT1 promotes nasopharyngeal carcinoma metastasis via the β-TrCP/c-Myc/SRSF1 positive feedback loop

description: Additional file 1: Supplemental Table 1. Clinicopathological data of 60 NPC and 26 NPE tissues measured by qRT-PCR.
DOI: 10.6073/pasta/4dfce38fb126d46a928e29c3764314ba
title: Climate data for D1 data loggers (CR23X and CR1000), 2000 - ongoing, daily.

description: Climatological data were collected from a Niwot Ridge climate station (D1) throughout the year. From July 5 2000 through October 23 2013, data were recorded using a Campbell Instruments CR23X data logger. Subsequently, data were recorded using a Campbell Instruments CR1000 data logger. Maximum and minimum values are recorded instantaneously, with a sampling interval of 5 seconds. Daily averages and totals were calculated from 17,280 individual measurements. This instrument was programmed to generate both hourly and daily output. Beginning in June 25 2009, 10 minute output was also generated. Daily output generated by the logger ended in 2014. Beginning in 2014, daily values were calculated from the native resolution data (ten minute).
DOI: 10.6073/pasta/26b14b7160bbc9718726123c781dcb2f
title: Handheld Microclimate Data from Californian Drylands 2023.

description: Handheld microclimate data (temperature and relative humidity) collected using the Mengshen Temperature and Humidity Meter at two aridity gradients across California. Microsites included the open, shrub, and two artificial shelter types: square and triangle. Wind speed was recorded using Kestrel handheld device. Surface Ground Temperature was recorded using a laser meter.
DOI: 10.13020/ksqw-at86
title: Scripts for flow and transport in discrete fracture networks and dead-end fracture identification
DOI: 10.6084/m9.figshare.23304101
title: Eretmocerus Data for: <strong>Effects of fluorescent dust and protein markers on the foraging behavior of a whitefly parasitoid, </strong><em><strong>Eretmocerus emiratus</strong></em><strong> (Hymenoptera: Aphelinidae)</strong>

description: Mark-release-recapture studies require the application of a taggant to the arthropod under investigation before release at the study site so that recaptured specimens are identifiable. This mark must not affect the dispersal or foraging behavior of the targeted organism. In this study, groups of <em>Eretmocerus eremicus</em> Rose and Zolnerowich (Hymenoptera: Aleyrodidae), a whitefly parasitoid, were marked externally with fluorescent dust or a liquid protein, or internally with a protein incorporated in their diet. Subsequently, the mark treatments' effects on foraging behavior were compared to unmarked parasitoids. For the most part, marked specimens behaved similarly to their unmarked counterparts. However, there was an increase in host feeding, probing, and grooming activities exhibited by parasitoids exposed to certain mark treatments.
DOI: 10.6084/m9.figshare.23304101.v1
title: Eretmocerus Data for: <strong>Effects of fluorescent dust and protein markers on the foraging behavior of a whitefly parasitoid, </strong><em><strong>Eretmocerus emiratus</strong></em><strong> (Hymenoptera: Aphelinidae)</strong>

description: Mark-release-recapture studies require the application of a taggant to the arthropod under investigation before release at the study site so that recaptured specimens are identifiable. This mark must not affect the dispersal or foraging behavior of the targeted organism. In this study, groups of <em>Eretmocerus eremicus</em> Rose and Zolnerowich (Hymenoptera: Aleyrodidae), a whitefly parasitoid, were marked externally with fluorescent dust or a liquid protein, or internally with a protein incorporated in their diet. Subsequently, the mark treatments' effects on foraging behavior were compared to unmarked parasitoids. For the most part, marked specimens behaved similarly to their unmarked counterparts. However, there was an increase in host feeding, probing, and grooming activities exhibited by parasitoids exposed to certain mark treatments.
DOI: 10.5517/ccdc.csd.cc2fxw08
title: CCDC 2262070: Experimental Crystal Structure Determination

description: Related Article: R. Radhakrishnan, N.E.H. Mustaphi, N.K. Sebbar, J.T. Mague, A.A. Thiruvalluvar|2023|Acta Crystallogr.,Sect.E:Cryst.Commun.|79|545|doi:10.1107/S2056989023004139
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.cc2dcsvf
title: CCDC 2215875: Experimental Crystal Structure Determination

description: Related Article: Jessica P. Metherall, Michael R. Probert, Michael J. Hall|2022|CSD Communication|||
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.cc2g07b2
title: CCDC 2264343: Experimental Crystal Structure Determination

description: Related Article: Anthony Linden, Manuel Scherer, Karl Gademann|2023|CSD Communication|||
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.cc2g07mc
title: CCDC 2264352: Experimental Crystal Structure Determination

description: Related Article: Anthony Linden, Bin Huang, Karl Gademann|2023|CSD Communication|||
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.cc2g07nd
title: CCDC 2264353: Experimental Crystal Structure Determination

description: Related Article: Anthony Linden, Bin Huang, Karl Gademann|2023|CSD Communication|||
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.cc2g07pf
title: CCDC 2264354: Experimental Crystal Structure Determination

description: Related Article: Anthony Linden, Bin Huang, Karl Gademann|2023|CSD Communication|||
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.cc2g07vl
title: CCDC 2264359: Experimental Crystal Structure Determination

description: Related Article: Anthony Linden, Hiromu Hattori, Karl Gademann|2023|CSD Communication|||
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.cc2g07yp
title: CCDC 2264362: Experimental Crystal Structure Determination

description: Related Article: Anthony Linden, Advaita Panchagnula, Karl Gademann|2023|CSD Communication|||
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.8011762
title: TN412 Gradients 5 Underway Thermosalinograph Data

description: Near-surface temperature and salinity data for the Gradients 5 cruise (January 22 – Februrary 18, 2023) were acquired through the use of a thermosalinograph (THSL) system aboard the research vessel R/V Thompson. This cruise started off the coast of San Diego, California, dipped down below the equator, and ended in Honolulu, Hawaii. Data were acquired every minute. The time zone of the data is in UTC.
DOI: 10.5281/zenodo.8011761
title: TN412 Gradients 5 Underway Thermosalinograph Data

description: Near-surface temperature and salinity data for the Gradients 5 cruise (January 22 – Februrary 18, 2023) were acquired through the use of a thermosalinograph (THSL) system aboard the research vessel R/V Thompson. This cruise started off the coast of San Diego, California, dipped down below the equator, and ended in Honolulu, Hawaii. Data were acquired every minute. The time zone of the data is in UTC.
DOI: 10.25345/c5d21rv2k
title: MassIVE MSV000092113 - Increasing the Throughput and Reproducibility of Activity-Based Proteome Profiling Studies with Hyperplexing and Intelligent Data Acquisition
title: Intelligent data acquisition (IDA) strategies, such as real-time database search (RTS), have improved the depth of proteome coverage for experiments that utilize isobaric labels and gas phase purification techniques (i.e., SPS-MS3). While most applications of IDA have been focused on the analysis of protein abundance, these approaches have recently been applied to activity-based proteome profiling (ABPP) studies aimed at characterization of protein site engagement by small molecules. In this work, we extend IDA capabilities offered by vendor software through a new program called InSeqAPI. First, we demonstrate robust performance of InSeqAPI in the analysis of biotinylated cysteine peptides from ABPP experiments. Then, we describe PairQuant, a method within InSeqAPI designed for the hyperplexing approach that utilizes protein-level isotopic labeling and peptide-level TMT labeling.
DOI: 10.5281/zenodo.8011696
title: Enhancer design manuscript data and models

description: This repository holds the trained DNA accessibility and enhancer activity models, and the data used to train and evaluate the model. <strong>Files for DNA accessibility models:</strong> <strong>Accessibility_models_training_data.tar.gz</strong> &lt;fold&gt;_sequences_&lt;set&gt;.fa FASTA files with DNA sequences of genomic regions from train/val/test sets. &lt;fold&gt;_sequences_activity_&lt;set&gt;.txt Files with accessibility scores for sequences from train/val/test sets. <strong>Accessibility_model_files.tar.gz</strong> model.h5 and model.json files for each Results_&lt;fold&gt;_&lt;tissue&gt;_DeepSTARR2_&lt;rep&gt; <strong>Accessibility_models_test_set_predictions.rds</strong> RDS object with predictions for accessibility <strong>Files for enhancer activity models:</strong> <strong>EnhancerActivity_model_files.tar.gz</strong> &lt;fold&gt;_sequences_&lt;set&gt;.fa FASTA files with DNA sequences of genomic regions from train/val/test sets. &lt;fold&gt;_sequences_activity_&lt;set&gt;.txt Files with enhancer activity labels for sequences from train/val/test sets. <strong>EnhancerActivity_model_files.tar.gz</strong> model.h5, model.json and Model_evaluation.pdf files for each Results_&lt;fold&gt;_&lt;tissue&gt;_&lt;rep&gt; <strong>EnhancerActivity_models_clean_evaluation_data.rds</strong> RDS object with sequences used for final evaluation of the models <strong>EnhancerActivity_models_results_per_tissue_test_set.rds</strong> RDS object with predictions and results of the enhancer activity models
DOI: 10.5281/zenodo.8011697
title: Enhancer design manuscript data and models

description: This repository holds the trained DNA accessibility and enhancer activity models, and the data used to train and evaluate the model. <strong>Files for DNA accessibility models:</strong> <strong>Accessibility_models_training_data.tar.gz</strong> &lt;fold&gt;_sequences_&lt;set&gt;.fa FASTA files with DNA sequences of genomic regions from train/val/test sets. &lt;fold&gt;_sequences_activity_&lt;set&gt;.txt Files with accessibility scores for sequences from train/val/test sets. <strong>Accessibility_model_files.tar.gz</strong> model.h5 and model.json files for each Results_&lt;fold&gt;_&lt;tissue&gt;_DeepSTARR2_&lt;rep&gt; <strong>Accessibility_models_test_set_predictions.rds</strong> RDS object with predictions for accessibility <strong>Files for enhancer activity models:</strong> <strong>EnhancerActivity_model_files.tar.gz</strong> &lt;fold&gt;_sequences_&lt;set&gt;.fa FASTA files with DNA sequences of genomic regions from train/val/test sets. &lt;fold&gt;_sequences_activity_&lt;set&gt;.txt Files with enhancer activity labels for sequences from train/val/test sets. <strong>EnhancerActivity_model_files.tar.gz</strong> model.h5, model.json and Model_evaluation.pdf files for each Results_&lt;fold&gt;_&lt;tissue&gt;_&lt;rep&gt; <strong>EnhancerActivity_models_clean_evaluation_data.rds</strong> RDS object with sequences used for final evaluation of the models <strong>EnhancerActivity_models_results_per_tissue_test_set.rds</strong> RDS object with predictions and results of the enhancer activity models
DOI: 10.5281/zenodo.7992491
title: Lack of funds for consent document translation impedes inclusive enrollment

description: Data on all consent events for patients who participated in clinical trials at UCLA from January 2013 to December 2018.
description: This work was funded by: The Cancer Center Support Grant P30 CA016042
DOI: 10.5281/zenodo.7992490
title: Lack of funds for consent document translation impedes inclusive enrollment

description: Data on all consent events for patients who participated in clinical trials at UCLA from January 2013 to December 2018.
description: This work was funded by: The Cancer Center Support Grant P30 CA016042