cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17056307
title: Nonparametric estimation and inference for spatiotemporal epidemic models

description: Epidemic modelling is an essential tool to understand the spread of the novel coronavirus and ultimately assist in disease prevention, policymaking, and resource allocation. In this article, we establish a state-of-the-art interface between classic mathematical and statistical models and propose a novel space-time epidemic modelling framework to study the spatial-temporal pattern in the spread of infectious diseases. We propose a quasi-likelihood approach via the penalised spline approximation and alternatively reweighted least-squares technique to estimate the model. The proposed estimators are consistent, and the asymptotic normality is established for the constant coefficients. Utilizing spatiotemporal analysis, our proposed model enhances the dynamics of the epidemiological mechanism and dissects the spatiotemporal structure of the spreading disease. We evaluate the numerical performance of the proposed method through a simulation example. Finally, we apply the proposed method in the study of the devastating COVID-19 pandemic.
DOI: 10.6084/m9.figshare.6570545.v1
title: Additional file 5: of miR-25 modulates triacylglycerol and lipid accumulation in goat mammary epithelial cells by repressing PGC-1beta

description: Table S4. 30 lipid metabolism-associated genes. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.17056307.v1
title: Nonparametric estimation and inference for spatiotemporal epidemic models

description: Epidemic modelling is an essential tool to understand the spread of the novel coronavirus and ultimately assist in disease prevention, policymaking, and resource allocation. In this article, we establish a state-of-the-art interface between classic mathematical and statistical models and propose a novel space-time epidemic modelling framework to study the spatial-temporal pattern in the spread of infectious diseases. We propose a quasi-likelihood approach via the penalised spline approximation and alternatively reweighted least-squares technique to estimate the model. The proposed estimators are consistent, and the asymptotic normality is established for the constant coefficients. Utilizing spatiotemporal analysis, our proposed model enhances the dynamics of the epidemiological mechanism and dissects the spatiotemporal structure of the spreading disease. We evaluate the numerical performance of the proposed method through a simulation example. Finally, we apply the proposed method in the study of the devastating COVID-19 pandemic.
DOI: 10.6084/m9.figshare.17056471
title: Additional file 2 of A NAC transcription factor OsNAC3 positively regulates ABA response and salt tolerance in rice

description: Additional file 2.
DOI: 10.6084/m9.figshare.17056471.v1
title: Additional file 2 of A NAC transcription factor OsNAC3 positively regulates ABA response and salt tolerance in rice

description: Additional file 2.
DOI: 10.6084/m9.figshare.11813601
title: Production of ancient dissolved organic carbon in Arctic Ocean sediment: A pathway of carbon cycling in the extreme environment

description: Concentration and carbon isotope values of sediment TOC, hydrocarbon and porewater DOC
DOI: 10.6084/m9.figshare.8667884
title: Arbuscular mycorrhizal fungal diversity is affected by soil salinity and soil nutrients in typical saline-sodic grasslands dominated by <i>Leymus chinensis</i>

description: Restoring and reconstructing the salt-affected degraded ecosystem is receiving more and more attention in many parts of the world, especially semi-arid areas. Unfortunately, knowledge about the potential role of natural arbuscular mycorrhizal (AM) fungi was limited. This work examined the regional factors that drove the variations in AM fungal diversity in Songnen Plain, a typical saline-sodic degraded grassland. Soils were sampled in 45 random sites, 150 operational taxonomic units (OTUs) belonging to Glomeromycota were identified. Among these OTUs, 129 and 103 OTUs were classified to Glomerales and <i>Glomus</i>, respectively. The coefficients of variation of total diversity index were 35.61% and the total effects of soil salinity and nutrients collectively accounted for 31.2, 11.8, 47.3, and 64.2% of the variations in Sobs, Chao, Shannon, and Simpson indices, respectively. The climatic variables and geographical location had no significant effects on the variations of AM fungal diversity. Multiple linear regression models showed that soil pH, electrical conductivity (EC), available N and organic C were the most main influencing factors. This research highlighted the wide distribution of AM fungi and thus might promote the development of new techniques that apply natural AM fungi to restore saline-sodic degraded grasslands.
DOI: 10.6084/m9.figshare.8667884.v1
title: Arbuscular mycorrhizal fungal diversity is affected by soil salinity and soil nutrients in typical saline-sodic grasslands dominated by <i>Leymus chinensis</i>

description: Restoring and reconstructing the salt-affected degraded ecosystem is receiving more and more attention in many parts of the world, especially semi-arid areas. Unfortunately, knowledge about the potential role of natural arbuscular mycorrhizal (AM) fungi was limited. This work examined the regional factors that drove the variations in AM fungal diversity in Songnen Plain, a typical saline-sodic degraded grassland. Soils were sampled in 45 random sites, 150 operational taxonomic units (OTUs) belonging to Glomeromycota were identified. Among these OTUs, 129 and 103 OTUs were classified to Glomerales and <i>Glomus</i>, respectively. The coefficients of variation of total diversity index were 35.61% and the total effects of soil salinity and nutrients collectively accounted for 31.2, 11.8, 47.3, and 64.2% of the variations in Sobs, Chao, Shannon, and Simpson indices, respectively. The climatic variables and geographical location had no significant effects on the variations of AM fungal diversity. Multiple linear regression models showed that soil pH, electrical conductivity (EC), available N and organic C were the most main influencing factors. This research highlighted the wide distribution of AM fungi and thus might promote the development of new techniques that apply natural AM fungi to restore saline-sodic degraded grasslands.
DOI: 10.6084/m9.figshare.25182362.v3
title: the new Tai Chi elastic band exercise and elastic band resistance training.zip

description: This is the paper data.
DOI: 10.6084/m9.figshare.17056474
title: Additional file 1 of Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers

description: Additional file 1: Table S1. The repeats number of different SSR motifs. Table S2. The proportion of each population in the genetic structure analysis. Figure S1. The best K-value of the genetic structure based on STRUCTURE analysis.
DOI: 10.6084/m9.figshare.17056474.v1
title: Additional file 1 of Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers

description: Additional file 1: Table S1. The repeats number of different SSR motifs. Table S2. The proportion of each population in the genetic structure analysis. Figure S1. The best K-value of the genetic structure based on STRUCTURE analysis.
DOI: 10.5281/zenodo.10666117
title: Review: A Systematic Review of Dairy Cow Health, Welfare, and Behaviour in Year Round Loose Range Housing - Data File

description: Systematic Review Data File
DOI: 10.5281/zenodo.10664897
title: Data from: To Be or Not to Be Tetraploid - The Impact of Marker Ploidy on Genomic Prediction and GWAS of Potato

description: Data analyzed in the study "To Be or Not to Be Tetraploid - The Impact of Marker Ploidy on Genomic Prediction and GWAS of Potato" (Aalborg and Nielsen, 2024), including GBS data, across-year-corrected phenotype data of 762 MASPOT panel clones and 18 parents of five phenotypes chipping quality, length/width ratio, senescence, dry matter content, and yield, the parentage of the 762 MASPOT clones (incomplete 18-parent full-diallel cross). 

The GBS data includes the MQ30 filtered tetraploid and allele frequency genotypes of the full panel with SNPEff annotation (relative to the DMv4.03 S. tuberosum reference genome), the SNP depth at each position, a file of positions analyzed in the study (31,007 markers), and genotype matrices of the filtered (complete filtration strategy in study) tetraploid and allele frequency markers.
DOI: 10.5281/zenodo.10664896
title: Data from: To Be or Not to Be Tetraploid - The Impact of Marker Ploidy on Genomic Prediction and GWAS of Potato

description: Data analyzed in the study "To Be or Not to Be Tetraploid - The Impact of Marker Ploidy on Genomic Prediction and GWAS of Potato" (Aalborg and Nielsen, 2024), including GBS data, across-year-corrected phenotype data of 762 MASPOT panel clones and 18 parents of five phenotypes chipping quality, length/width ratio, senescence, dry matter content, and yield, the parentage of the 762 MASPOT clones (incomplete 18-parent full-diallel cross). 

The GBS data includes the MQ30 filtered tetraploid and allele frequency genotypes of the full panel with SNPEff annotation (relative to the DMv4.03 S. tuberosum reference genome), the SNP depth at each position, a file of positions analyzed in the study (31,007 markers), and genotype matrices of the filtered (complete filtration strategy in study) tetraploid and allele frequency markers.
DOI: 10.6084/m9.figshare.17056609
title: Additional file 1 of Impact of intraoperative medial collateral ligament injury on outcomes after total knee arthroplasty: a meta-analysis and systematic review

description: Additional file 1. Detailed search strategy of Pubmed.
DOI: 10.6084/m9.figshare.17056609.v1
title: Additional file 1 of Impact of intraoperative medial collateral ligament injury on outcomes after total knee arthroplasty: a meta-analysis and systematic review

description: Additional file 1. Detailed search strategy of Pubmed.
DOI: 10.6084/m9.figshare.17056619
title: Additional file 9 of Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses

description: Additional file 9: Table S1. List of HM gene families in Arabidopsis, O. sativa (rice), T. aestivum, H. vulgare, S. bicolor, S. viridis, S. italica, and Z. mays genomes. Table S2. Ka, Ks, and Ka/Ks values of each Gramineae duplication gene pair. Table S3. Ka, Ks, and Ka/Ks values of duplication gene pairs between Arabidopsis and each Gramineae species. Table S4. Ka, Ks, and Ka/Ks values of duplication gene pairs between rice and each Gramineae species. Table S5. Common DEGs among different classes.
DOI: 10.6084/m9.figshare.17056619.v1
title: Additional file 9 of Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses

description: Additional file 9: Table S1. List of HM gene families in Arabidopsis, O. sativa (rice), T. aestivum, H. vulgare, S. bicolor, S. viridis, S. italica, and Z. mays genomes. Table S2. Ka, Ks, and Ka/Ks values of each Gramineae duplication gene pair. Table S3. Ka, Ks, and Ka/Ks values of duplication gene pairs between Arabidopsis and each Gramineae species. Table S4. Ka, Ks, and Ka/Ks values of duplication gene pairs between rice and each Gramineae species. Table S5. Common DEGs among different classes.
DOI: 10.6084/m9.figshare.19153772
title: Spatio-temporal distribution and mechanism of Cenozoic magmatism in the South China Sea and adjacent areas: Insight from seismic, geochemical and geochronological data

description: Cenozoic magmatism was highly active in the South China Sea (SCS), and mostly dominated by basalts. The magmatic rocks are mainly distributed in the lower slope and subbasins of the SCS, in addition to sporadic and small-scale Cenozoic volcanism on the SCS shelf. This paper presents a complete map of the Cenozoic magmatic rocks of the SCS with magmatic rock boundaries. This paper also presents an analysis of geological survey and published data in terms of seismic profiles, ages, geochemistry and isotopic systematics of the Cenozoic magmatic complexes of the SCS and adjacent areas. Many of wells or dredges are located in magmatic rocks identified by seismic profiles. Three periods of magmatic activity are distinguished: (1) a pre-spreading period (&gt;33 Ma); (2) a syn-spreading period (33–15 Ma) and (3) a post-spreading period (&lt;15 Ma). The thickest volcanic rocks encountered more than 1000 m (possibly Oligocene to Miocene) in the Boayan 1/1A well in the Palawan Trough of the southern SCS during Cenozoic. The oldest magmatic rocks are andesites (62.5 ± 2.2 Ma) in the northern SCS (offshore) and andesites (65 ± 3 Ma) in Penghu (on land). The latest modern magmatic activity was detected in 1923 offshore of a submarine volcanic eruption (10°09´29″N, 109°00′50″E, 20 m below sea level) and along the shore of a volcanic eruption in the Philippines. Cenozoic magmatic rocks of the SCS include at least 1008 rock bodies: the smallest is 0.00012 km<sup>2</sup>, the largest is 1528 km<sup>2</sup> and the total area covers 46,309 km<sup>2</sup>. The Yangjiang-Yitong fault and Zhongnan-Reedbank fault divide the magmatic rocks into two different sections in the eastern and western SCS. The ages of the magmatic rocks in the eastern SCS are mostly older than those in the western SCS. The magmatic rocks in the northern, southern, eastern, western SCS and adjacent areas, and SCS basin are related to extension, subduction+collision, subduction, extrusion, extension+cooling+subsidence, respectively.
DOI: 10.6084/m9.figshare.19153772.v1
title: Spatio-temperal distribution and mechenism of Cenozoic magmatism in the South China Sea and adjacent areas: Insight from seismic, geochemical and geochronological data

description: Cenozoic magmatism was highly active in the South China Sea (SCS), and mostly dominated by basalts. The magmatic rocks are mainly distributed in the lower slope and subbasins of the SCS, in addition to sporadic and small-scale Cenozoic volcanism on the SCS shelf. This paper presents a complete map of the Cenozoic magmatic rocks of the SCS with magmatic rock boundaries. This paper also presents an analysis of geological survey and published data in terms of seismic profiles, ages, geochemistry and isotopic systematics of the Cenozoic magmatic complexes of the SCS and adjacent areas. Many of wells or dredges are located in magmatic rocks identified by seismic profiles. Three periods of magmatic activity are distinguished: (1) a pre-spreading period (&gt;33 Ma); (2) a syn-spreading period (33–15 Ma) and (3) a post-spreading period (&lt;15 Ma). The thickest volcanic rocks encountered more than 1000 m (possibly Oligocene to Miocene) in the Boayan 1/1A well in the Palawan Trough of the southern SCS during Cenozoic. The oldest magmatic rocks are andesites (62.5 ± 2.2 Ma) in the northern SCS (offshore) and andesites (65 ± 3 Ma) in Penghu (on land). The latest modern magmatic activity was detected in 1923 offshore of a submarine volcanic eruption (10°09´29″N, 109°00′50″E, 20 m below sea level) and along the shore of a volcanic eruption in the Philippines. Cenozoic magmatic rocks of the SCS include at least 1008 rock bodies: the smallest is 0.00012 km<sup>2</sup>, the largest is 1528 km<sup>2</sup> and the total area covers 46,309 km<sup>2</sup>. The Yangjiang-Yitong fault and Zhongnan-Reedbank fault divide the magmatic rocks into two different sections in the eastern and western SCS. The ages of the magmatic rocks in the eastern SCS are mostly older than those in the western SCS. The magmatic rocks in the northern, southern, eastern, western SCS and adjacent areas, and SCS basin are related to extension, subduction+collision, subduction, extrusion, extension+cooling+subsidence, respectively.
DOI: 10.6084/m9.figshare.19153772.v3
title: Spatio-temporal distribution and mechanism of Cenozoic magmatism in the South China Sea and adjacent areas: Insight from seismic, geochemical and geochronological data

description: Cenozoic magmatism was highly active in the South China Sea (SCS), and mostly dominated by basalts. The magmatic rocks are mainly distributed in the lower slope and subbasins of the SCS, in addition to sporadic and small-scale Cenozoic volcanism on the SCS shelf. This paper presents a complete map of the Cenozoic magmatic rocks of the SCS with magmatic rock boundaries. This paper also presents an analysis of geological survey and published data in terms of seismic profiles, ages, geochemistry and isotopic systematics of the Cenozoic magmatic complexes of the SCS and adjacent areas. Many of wells or dredges are located in magmatic rocks identified by seismic profiles. Three periods of magmatic activity are distinguished: (1) a pre-spreading period (&gt;33 Ma); (2) a syn-spreading period (33–15 Ma) and (3) a post-spreading period (&lt;15 Ma). The thickest volcanic rocks encountered more than 1000 m (possibly Oligocene to Miocene) in the Boayan 1/1A well in the Palawan Trough of the southern SCS during Cenozoic. The oldest magmatic rocks are andesites (62.5 ± 2.2 Ma) in the northern SCS (offshore) and andesites (65 ± 3 Ma) in Penghu (on land). The latest modern magmatic activity was detected in 1923 offshore of a submarine volcanic eruption (10°09´29″N, 109°00′50″E, 20 m below sea level) and along the shore of a volcanic eruption in the Philippines. Cenozoic magmatic rocks of the SCS include at least 1008 rock bodies: the smallest is 0.00012 km<sup>2</sup>, the largest is 1528 km<sup>2</sup> and the total area covers 46,309 km<sup>2</sup>. The Yangjiang-Yitong fault and Zhongnan-Reedbank fault divide the magmatic rocks into two different sections in the eastern and western SCS. The ages of the magmatic rocks in the eastern SCS are mostly older than those in the western SCS. The magmatic rocks in the northern, southern, eastern, western SCS and adjacent areas, and SCS basin are related to extension, subduction+collision, subduction, extrusion, extension+cooling+subsidence, respectively.
DOI: 10.6084/m9.figshare.19153772.v2
title: Spatio-temperal distribution and mechenism of Cenozoic magmatism in the South China Sea and adjacent areas: Insight from seismic, geochemical and geochronological data

description: Cenozoic magmatism was highly active in the South China Sea (SCS), and mostly dominated by basalts. The magmatic rocks are mainly distributed in the lower slope and subbasins of the SCS, in addition to sporadic and small-scale Cenozoic volcanism on the SCS shelf. This paper presents a complete map of the Cenozoic magmatic rocks of the SCS with magmatic rock boundaries. This paper also presents an analysis of geological survey and published data in terms of seismic profiles, ages, geochemistry and isotopic systematics of the Cenozoic magmatic complexes of the SCS and adjacent areas. Many of wells or dredges are located in magmatic rocks identified by seismic profiles. Three periods of magmatic activity are distinguished: (1) a pre-spreading period (&gt;33 Ma); (2) a syn-spreading period (33–15 Ma) and (3) a post-spreading period (&lt;15 Ma). The thickest volcanic rocks encountered more than 1000 m (possibly Oligocene to Miocene) in the Boayan 1/1A well in the Palawan Trough of the southern SCS during Cenozoic. The oldest magmatic rocks are andesites (62.5 ± 2.2 Ma) in the northern SCS (offshore) and andesites (65 ± 3 Ma) in Penghu (on land). The latest modern magmatic activity was detected in 1923 offshore of a submarine volcanic eruption (10°09´29″N, 109°00′50″E, 20 m below sea level) and along the shore of a volcanic eruption in the Philippines. Cenozoic magmatic rocks of the SCS include at least 1008 rock bodies: the smallest is 0.00012 km<sup>2</sup>, the largest is 1528 km<sup>2</sup> and the total area covers 46,309 km<sup>2</sup>. The Yangjiang-Yitong fault and Zhongnan-Reedbank fault divide the magmatic rocks into two different sections in the eastern and western SCS. The ages of the magmatic rocks in the eastern SCS are mostly older than those in the western SCS. The magmatic rocks in the northern, southern, eastern, western SCS and adjacent areas, and SCS basin are related to extension, subduction+collision, subduction, extrusion, extension+cooling+subsidence, respectively.
DOI: 10.6084/m9.figshare.6570929
title: Intact NIST monoclonal antibody characterization—Proteoforms, glycoforms—Using CE-MS and CE-LIF

description: Determining and linking the structural heterogeneity of recombinant antibodies to function is critical in the biopharmaceutical industry. We introduce a new microfluidic capillary electrophoresis—mass spectrometry (μCE-MS) approach to characterize intact monoclonal antibody (mAb) and simultaneously quantifying distinct variants. Our MS analysis of intact NIST mAb (RM8671) shows 18 variants identified amongst proteolytic and glycolytic modifications with a range of relative abundances between 0.1% and 100%. In order to verify our quantitative MS results, we used an established system based on capillary electrophoresis—with laser induced fluorescence (CE-LIF) for profiling the N-glycans. All major glycans were identified and further substantiated by exoglycosidase digestion. Interestingly, the µCE-MS analysis of intact NIST mAb consistently yielded higher amounts of G2FG2F-Hex glycoform (~3.4%), whereas the CE-LIF analysis indicates that only 1.4% of G2F-Gal is present. Therefore, the additional hexose adduct observed in µCE-MS may have been the glycation product of the mAb. Further analysis of deglycosylated mAb with µCE-MS made it possible to reveal the glycation with 10.5% of one hexose product and 4.9% of two hexose product in the intact deglycosylated antibody. An integrated solution using two orthogonal and complementary techniques for characterizing antibody glycosylation is provided here.
DOI: 10.6084/m9.figshare.6570929.v2
title: Intact NIST monoclonal antibody characterization—Proteoforms, glycoforms—Using CE-MS and CE-LIF

description: Determining and linking the structural heterogeneity of recombinant antibodies to function is critical in the biopharmaceutical industry. We introduce a new microfluidic capillary electrophoresis—mass spectrometry (μCE-MS) approach to characterize intact monoclonal antibody (mAb) and simultaneously quantifying distinct variants. Our MS analysis of intact NIST mAb (RM8671) shows 18 variants identified amongst proteolytic and glycolytic modifications with a range of relative abundances between 0.1% and 100%. In order to verify our quantitative MS results, we used an established system based on capillary electrophoresis—with laser induced fluorescence (CE-LIF) for profiling the N-glycans. All major glycans were identified and further substantiated by exoglycosidase digestion. Interestingly, the µCE-MS analysis of intact NIST mAb consistently yielded higher amounts of G2FG2F-Hex glycoform (~3.4%), whereas the CE-LIF analysis indicates that only 1.4% of G2F-Gal is present. Therefore, the additional hexose adduct observed in µCE-MS may have been the glycation product of the mAb. Further analysis of deglycosylated mAb with µCE-MS made it possible to reveal the glycation with 10.5% of one hexose product and 4.9% of two hexose product in the intact deglycosylated antibody. An integrated solution using two orthogonal and complementary techniques for characterizing antibody glycosylation is provided here.