cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9768113
title: Metadata record for: Bayesian ages for pollen records since the last glaciation in North America

description: This dataset contains key characteristics about the data described in the Data Descriptor Bayesian ages for pollen records since the last glaciation in North America. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format 
 3. machine readable metadata file in ISA-Tab format (zipped folder)<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9768113.v2
title: Metadata record for: Bayesian ages for pollen records since the last glaciation in North America

description: This dataset contains key characteristics about the data described in the Data Descriptor Bayesian ages for pollen records since the last glaciation in North America. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format 
 3. machine readable metadata file in ISA-Tab format (zipped folder)<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9768113.v1
title: Metadata record for: Bayesian ages for pollen records since the last glaciation in North America

description: This dataset contains key characteristics about the data described in the Data Descriptor Bayesian ages for pollen records since the last glaciation in North America. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format 
 3. machine readable metadata file in ISA-Tab format (zipped folder)
DOI: 10.6084/m9.figshare.8195303
title: A Deep Eutectic Solvent as an Extraction Solvent to Separate and Preconcentrate Parabens in Water Samples Using in situ Liquid-Liquid Microextraction

description: In this study, an in situ deep eutectic solvent-liquid-liquid microextraction method together with high performance liquid chromatography was developed for the determination of parabens in aqueous sample. The hydrophobic deep eutectic solvent, formed in situ by the DL-menthol and decanoic acid was used as the extraction solvent. Various parameters affecting the extraction efficiency including the composition of deep eutectic solvent, temperature of sample solution, extraction time, solution pH and salt concentration were investigated and optimized. Under the optimum conditions, the linear range of calibration curves was in the range of 3-1000 ng mL-1. The limits of detection and limits of quantification were in the range of 0.6-0.8 and 2.0-2.5 ng mL-1, respectively. The relative standard deviations were less than 7.2% for both intra-day and inter-days analysis. Finally, the proposed method was successfully applied to determine four parabens in environmental water samples with acceptable recoveries.
DOI: 10.6084/m9.figshare.8195303.v1
title: A Deep Eutectic Solvent as an Extraction Solvent to Separate and Preconcentrate Parabens in Water Samples Using in situ Liquid-Liquid Microextraction

description: In this study, an in situ deep eutectic solvent-liquid-liquid microextraction method together with high performance liquid chromatography was developed for the determination of parabens in aqueous sample. The hydrophobic deep eutectic solvent, formed in situ by the DL-menthol and decanoic acid was used as the extraction solvent. Various parameters affecting the extraction efficiency including the composition of deep eutectic solvent, temperature of sample solution, extraction time, solution pH and salt concentration were investigated and optimized. Under the optimum conditions, the linear range of calibration curves was in the range of 3-1000 ng mL-1. The limits of detection and limits of quantification were in the range of 0.6-0.8 and 2.0-2.5 ng mL-1, respectively. The relative standard deviations were less than 7.2% for both intra-day and inter-days analysis. Finally, the proposed method was successfully applied to determine four parabens in environmental water samples with acceptable recoveries.
DOI: 10.6084/m9.figshare.8195318
title: TARGETED AND NON-TARGETED ANALYSIS BASED ON ULTRA HIGH PERFORMANCE LIQUID CHROMATOGRAPHY AND FOURIER TRANSFORM INFRARED SPECTROSCOPY FOR PARIS SPECIES OF DIFFERENT GEOGRAPHICAL ORIGINS

description: Various species of Paris have been used in treatments for their antitumor, antimicrobial, hemostatic, anthelmintic and immune-stimulating properties, among others. The bioactive markers of these plants including paris saponins I (PSI), paris saponins II (PSII), paris saponins VI (PSVI) and paris saponins VII (PSVII) are responsible for inhibiting nasopharyngeal carcinoma epithelial cell and ethanol-induced gastric lesions. This paper intends to comprehensively characterize the distribution of bioactive markers and illustrate the relationship between chemical profile and Paris spp.. A targeted quantitative analysis by ultra high performance liquid chromatography (UHPLC) was established for the simultaneous separation and determination of PSI, PSII, PSVI and PSVII. Non-targeted analysis based on Fourier transform infrared (FT-IR) spectroscopy, with the aid of partial least squares discriminant analysis (PLS-DA), was also performed. In addition, similarity analysis combining UHPLC and FT-IR spectroscopy were employed to evaluate Paris of different species and geographical origins. Quantitative analysis indicated that the content of saponins varied markedly, and the average total saponins of Paris axialis (PA) of a specific region (Baoshan) was higher than the other species. In addition, total saponins of P. polyphylla var. yunnanensis (PPY) collected from Xishuangbanna was higher than the same species of other regions. Non-targeted analysis indicated that PA was different from other species and PPY in the Baoshan differed from other regions. The results indicate that comprehensive analyses for geographical origin discrimination of herbal medicines are expected to be employed in further investigations.
DOI: 10.6084/m9.figshare.8195318.v1
title: TARGETED AND NON-TARGETED ANALYSIS BASED ON ULTRA HIGH PERFORMANCE LIQUID CHROMATOGRAPHY AND FOURIER TRANSFORM INFRARED SPECTROSCOPY FOR PARIS SPECIES OF DIFFERENT GEOGRAPHICAL ORIGINS

description: Various species of Paris have been used in treatments for their antitumor, antimicrobial, hemostatic, anthelmintic and immune-stimulating properties, among others. The bioactive markers of these plants including paris saponins I (PSI), paris saponins II (PSII), paris saponins VI (PSVI) and paris saponins VII (PSVII) are responsible for inhibiting nasopharyngeal carcinoma epithelial cell and ethanol-induced gastric lesions. This paper intends to comprehensively characterize the distribution of bioactive markers and illustrate the relationship between chemical profile and Paris spp.. A targeted quantitative analysis by ultra high performance liquid chromatography (UHPLC) was established for the simultaneous separation and determination of PSI, PSII, PSVI and PSVII. Non-targeted analysis based on Fourier transform infrared (FT-IR) spectroscopy, with the aid of partial least squares discriminant analysis (PLS-DA), was also performed. In addition, similarity analysis combining UHPLC and FT-IR spectroscopy were employed to evaluate Paris of different species and geographical origins. Quantitative analysis indicated that the content of saponins varied markedly, and the average total saponins of Paris axialis (PA) of a specific region (Baoshan) was higher than the other species. In addition, total saponins of P. polyphylla var. yunnanensis (PPY) collected from Xishuangbanna was higher than the same species of other regions. Non-targeted analysis indicated that PA was different from other species and PPY in the Baoshan differed from other regions. The results indicate that comprehensive analyses for geographical origin discrimination of herbal medicines are expected to be employed in further investigations.
DOI: 10.6084/m9.figshare.25243249.v1
title: Do urban-living yellow mongoose, Cynictis penicillata, experience a paradox of choice?

description: Dataset for the entitled "Do urban-living yellow mongoose, Cynictis penicillata, experience a paradox of choice?"
DOI: 10.6084/m9.figshare.6098219
title: ELLPMDA: Ensemble learning and link prediction for miRNA-disease association prediction

description: Recently, accumulating evidences have indicated miRNAs play critical roles in the progression and development of various human complex diseases, which pointed out that identifying miRNA-disease association could enable us to understand diseases at miRNA level. Thus, revealing more and more potential miRNA-disease associations is a vital topic in biomedical domain. However, it will be extremely expensive and time-consuming if we examine all the possible miRNA-disease pairs. Therefore, more accurate and efficient methods are being highly requested to detect potential miRNA-disease associations. In this study, we developed a computational model of Ensemble Learning and Link Prediction for miRNA-Disease Association prediction (ELLPMDA) to achieve this goal. By integrating miRNA functional similarity, disease semantic similarity, miRNA-disease association and Gaussian profile kernel similarity for miRNAs and diseases, we constructed a similarity network and utilized ensemble learning to combine rank results given by three classic similarity-based algorithms. To evaluate the performance of ELLPMDA, we exploited global and local Leave-One-Out Cross Validation (LOOCV), 5-fold Cross Validation (CV) and three kinds of case studies. As a result, the AUCs of ELLPMDA is 0.9181, 0.8181 and 0.9193+/−0.0002 in global LOOCV, local LOOCV and 5-fold CV, respectively, which significantly exceed almost all the previous methods. Moreover, in three distinct kinds of case studies for Kidney Neoplasms, Lymphoma, Prostate Neoplasms, Colon Neoplasms and Esophageal Neoplasms, 88%, 92%, 86%, 98% and 98% out of the top 50 predicted miRNAs has been confirmed, respectively. Besides, ELLPMDA is based on global similarity measure and applicable to new diseases without any known related miRNAs.
DOI: 10.6084/m9.figshare.19729734
title: Mapping seagrass meadows in coastal China using GEE

description: Seagrass meadows are virtual blue carbon ecosystems facing a dramatic decline on a global scale. Tracking the status and trends of seagrass meadows, which is still pending on large scales, is an emerging priority for their conservation and restoration. Here, we develop a semi-automatic procedure to identify and map seagrass meadows. Using Sentinel-2 data in Google Earth Engine (GEE) platform, a map is generated, showing a total of 11113.4 ha of seagrass meadows in coastal China in 2020. There exists the largest extent (6450.3 ha) in the coast of the South China Sea, while the second area (3909.5 ha) is in the Yellow Sea-Bohai Sea, and the seagrass meadows in the East China Sea cover about 753.6 ha. Our results provide the baseline data of seagrass meadows distribution in coastal China, and this study can be of reference for mapping seagrass meadows on a broader or even global scale.
DOI: 10.6084/m9.figshare.19729734.v1
title: Mapping seagrass meadows in coastal China using GEE

description: Seagrass meadows are virtual blue carbon ecosystems facing a dramatic decline on a global scale. Tracking the status and trends of seagrass meadows, which is still pending on large scales, is an emerging priority for their conservation and restoration. Here, we develop a semi-automatic procedure to identify and map seagrass meadows. Using Sentinel-2 data in Google Earth Engine (GEE) platform, a map is generated, showing a total of 11113.4 ha of seagrass meadows in coastal China in 2020. There exists the largest extent (6450.3 ha) in the coast of the South China Sea, while the second area (3909.5 ha) is in the Yellow Sea-Bohai Sea, and the seagrass meadows in the East China Sea cover about 753.6 ha. Our results provide the baseline data of seagrass meadows distribution in coastal China, and this study can be of reference for mapping seagrass meadows on a broader or even global scale.
DOI: 10.6084/m9.figshare.11865483
title: Table S2 from Genetic diversity, demographic history and neo-sex chromosomes in the critically endangered Raso lark

description: Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present day diversity can be shaped by ancient demographic events.
DOI: 10.6084/m9.figshare.11865483.v2
title: Table S2 from Genetic diversity, demographic history and neo-sex chromosomes in the critically endangered Raso lark

description: Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present day diversity can be shaped by ancient demographic events.
DOI: 10.6084/m9.figshare.15071554
title: Additional file 1 of Background and descriptive features of rabies-suspected animals in Central Luzon, Philippines

description: Additional File 1. Details of vaccination history in confirmed animals.
DOI: 10.6084/m9.figshare.15071554.v1
title: Additional file 1 of Background and descriptive features of rabies-suspected animals in Central Luzon, Philippines

description: Additional File 1. Details of vaccination history in confirmed animals.
DOI: 10.6084/m9.figshare.16584255
title: Additional file 1 of Diffuse leptomeningeal glioneuronal tumour (DLGNT) in children: the emerging role of genomic analysis

description: Additional file 1. Supplementary Tables 1 & 2: Single Nucleotide Variants (SNVs) and Copy Number Variants (CNVs) identified in case 1 from WGS, Supplementary Tables 3 & 4: SNVs and CNVs identified in case 2 from WGS
DOI: 10.6084/m9.figshare.16584255.v1
title: Additional file 1 of Diffuse leptomeningeal glioneuronal tumour (DLGNT) in children: the emerging role of genomic analysis

description: Additional file 1. Supplementary Tables 1 & 2: Single Nucleotide Variants (SNVs) and Copy Number Variants (CNVs) identified in case 1 from WGS, Supplementary Tables 3 & 4: SNVs and CNVs identified in case 2 from WGS
DOI: 10.6084/m9.figshare.25243249.v2
title: Do urban-living yellow mongoose, Cynictis penicillata, experience a paradox of choice?

description: Dataset for the titled "Do urban-living yellow mongoose, Cynictis penicillata, experience a paradox of choice?"
DOI: 10.6084/m9.figshare.16584303
title: Additional file 3 of Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata)

description: Additional file 3.
DOI: 10.6084/m9.figshare.16584303.v1
title: Additional file 3 of Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata)

description: Additional file 3.
DOI: 10.6084/m9.figshare.16584306
title: Additional file 4 of Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata)

description: Additional file 4.
DOI: 10.6084/m9.figshare.16584306.v1
title: Additional file 4 of Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata)

description: Additional file 4.
DOI: 10.6084/m9.figshare.16584309
title: Additional file 5 of Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata)

description: Additional file 5.
DOI: 10.6084/m9.figshare.16584309.v1
title: Additional file 5 of Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata)

description: Additional file 5.
DOI: 10.6084/m9.figshare.16584312
title: Additional file 6 of Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata)

description: Additional file 6.
DOI: 10.5522/04/24190683
title: Quantum dynamics of excited state proton transfer in green fluorescent protein

description: Data supporting the calculations in the paper. These include the input and output files for the Quantics program to run DD-vMCG and iMCG simulations of a GFP cluster model, as well as the database files with the quantum chemistry results. These files can be used together with Quantics to generate the data in the paper Bourne-Worster and Worth (JCP, 160, 065102, 2024). The input files are standard ascii files, grouped into directories for the different systems studied. The databases with the points calculated during the direct dynamics simulations are SQLite format with tables for geometries, energies, gradients etc. More details are in the paper. The Quantics program is a mostly Fortran code for running quantum dynamics simulations. It is open source and runs on linux workstations. It is freely available on request to the authors of the paper. For further details of the program see Comp. Phys. Comm., 248:107040–15, 2020.
DOI: 10.5522/04/24190683.v1
title: Quantum dynamics of excited state proton transfer in green fluorescent protein

description: Data supporting the calculations in the paper. These include the input and output files for the Quantics program to run DD-vMCG and iMCG simulations of a GFP cluster model, as well as the database files with the quantum chemistry results. These files can be used together with Quantics to generate the data in the paper Bourne-Worster and Worth (JCP, 160, 065102, 2024). The input files are standard ascii files, grouped into directories for the different systems studied. The databases with the points calculated during the direct dynamics simulations are SQLite format with tables for geometries, energies, gradients etc. More details are in the paper. The Quantics program is a mostly Fortran code for running quantum dynamics simulations. It is open source and runs on linux workstations. It is freely available on request to the authors of the paper. For further details of the program see Comp. Phys. Comm., 248:107040–15, 2020.
DOI: 10.6084/m9.figshare.16584312.v1
title: Additional file 6 of Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata)

description: Additional file 6.
DOI: 10.6084/m9.figshare.16584338
title: Additional file 1 of A tetraploidization event shaped the Aquilaria sinensis genome and contributed to the ability of sesquiterpenes synthesis

description: Additional file 1: Table S1. Number of Homologous Blocks and Gene Pairs Within a Genome or Between Genomes. Table S2. Number of Homologous Genes Within a Genome or Between Genomes. Table S3. Information about the Blocks Related to ECH Events in A. sinensis genome. Table S4. Information about the Blocks Related to AST Events in A. sinensis genome. Table S5. Information about the Blocks Related to ECH Events in Grape Genome. Table S6. Information about the Blocks Related to ECH Events in Cacao Genome. Table S7. Number of Collinearity Blocks, Gene Pairs, and Genes Related to Species Divergence Events Between Genomes. Table S8. Multiple Genome Alignment with Grape as Reference. Table S9. Genome Alignment Between Cacao and A.sinensis.Table S10. A. sinensis Gene Loss Rates and Gene Translocation with Grape as Reference Genome. Table S11. A. sinensis Gene Loss Rates and Gene Translocation with Cacao as Reference Genome. Table S12. Gene Loss in A. sinensis Using Grape and Cacao as References. Table S13. The Observed Distribution of Gene Loss and Translocation Numbers Fitted by Using Different Density Curves of Geometry Distribution. Table S14. Kernel Function Analysis of K S $${K}_{S}$$ Distribution Related to Duplication Events Within each Genome and Between Genomes (before Evolutionary Rate Correction). Table S15. Kernel Function Analysis of K S $${K}_{S}$$ Distribution Related to Duplication Events Within each Genome and Between Genomes (after Evolutionary Rate Correction). Table S16. The Information of Terpenoid Backbone Biosynthesis and Sesquiterpenoid Biosynthesis Genes in the Three Genomes by KEGG. Table S17. Sesquiterpenoid Biosynthesis Genes. Table S18. The Expression Values (TPM) of A. sinensis stems in Three States (intact, wounded 5 days and wounded 5 + 1 days) by RNA-sEq. Table S19. Genomic Data Information.