cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14320480
title: De novo sequencing of Bletilla striata (Orchidaceae) transcriptome and identification of genes involved in polysaccharide biosynthesis

description: Abstract Bletilla striata polysaccharide (BSP) is the main component of Bletilla striata, which has important pharmacological and pharmacological effects; however, due to the lack of genetic data, the metabolic pathways of BSP remain unclear. For this study, 11 representative resources of B. striata were analyzed, and the BSP contents of the different samples were significantly different; however, the monosaccharide composition of BSP was glucose and mannose. The representative samples were selected to observe their life history in situ, which were then divided and cultured in a greenhouse. Finally, samples from various organs of different plants were combined for transcriptome sequencing using the Illumina system. Our results summarized the BSP metabolic pathway, and we found that there were eight enzyme genes involved in biosynthesis, but these genes showed tissue specificity. Following qRT-PCR validation and comparative analysis, manA showed the highest expression; however, there were significant differences between the two germplasm resources in which the BSP content was significantly different, while UGP2, GPI, PMM, and GMPP had significant differences between the two samples. In summary, this study lays the foundation for further research into BSP metabolism and other physiological processes at the molecular level.
DOI: 10.6084/m9.figshare.14320503
title: Characterization of three new mitochondrial genomes of Coraciiformes (Megaceryle lugubris, Alcedo atthis, Halcyon smyrnensis) and insights into their phylogenetics

description: Abstract Coraciiformes contains more than 200 species with great differences on external morphology and life-style. The evolutionary relationships within Coraciiformes and the phylogenetic placement of Coraciiformes in Aves are still questioned. Mitochondrial genome (mitogenome) sequences are popular markers in molecular phylogenetic studies of birds. This study presented the genome characteristics of three new mitogenomes in Coraciiformes and explored the phylogenetic relationships among Coraciiformes and other five related orders with mitogenome data of 30 species. The sizes of three mitogenomes were 17,383 bp (Alcedo atthis), 17,892 bp (Halcyon smyrnensis) and 17,223 bp (Megaceryle lugubris). Each mitogenome contained one control region and 37 genes that were common in vertebrate mitogenomes. The organization of three mitogenomes was identical to the putative ancestral gene order in Aves. Among 13 available Coraciiform mitogenomes, 12 protein coding genes showed indications of negative selection, while the MT-ND6 presented sign of positive selection or relaxed purifying selection. The phylogenetic results supported that Upupidae and Bucerotidae should be separated from Coraciiformes, and that Coraciiformes is more closely related to Piciformes than to Strigiformes, Trogoniformes and Cuculiformes. Our study provide valuable data for further phylogenetic investigation of Coraciiformes.
DOI: 10.6084/m9.figshare.6456218.v1
title: Diversity of nitrate, oxalate, vitamin C and carotenoid contents in different spinach accessions and their correlation with various morphological traits

description: Spinach (<i>Spinacia oleracea</i> L.) accumulates high amounts of carotenoids, vitamin C, nitrate and oxalate. Breeding to reduce nitrate and oxalate levels and increase vitamin C and carotenoid levels is a major target in spinach nutritional quality improvement. Here we investigate natural variations in the levels of nitrate, oxalate, vitamin C, and total carotenoid in 98 spinach accessions, and correlations among these four nutritional components and 12 important morphological traits. Our results showed that the concentrations of nitrate, oxalate, vitamin C, and total carotenoid ranged from 0.21–3.83, 2.38–34.72, 0.51–1.30, and 0.18–0.58 mg g<sup>−1</sup> fresh weight (FW), respectively. Moderate positive correlations were observed between the levels of oxalate and vitamin C, and between vitamin C and total carotenoid, whereas the levels of nitrate were correlated weakly and negatively with those of vitamin C and total carotenoid. The nitrate contents of crinkle-leaf accessions were significant higher than those of smooth-leaf accessions, and the smooth-leaf accessions had significantly higher concentrations of oxalate and vitamin C than crinkle-leaf accessions. Furthermore, hierarchical clustering analysis identified eight spinach accessions that could be served as starting materials for breeding new spinach cultivars with increased levels of vitamin C and carotenoids and simultaneously decreased accumulation of nitrate and oxalate.
DOI: 10.25402/fon.20087819.v1
title: Supplementary Tables – Clinical effectiveness outcomes and healthcare resource utilization of patients diagnosed with small-cell lung cancer

description:   
<strong>Supplemental Table 1. Summary of Treatment Distribution for Patients with eSCLC by Regimen-based Line for 1L, 2L, and 3L</strong>
  
<strong>Supplemental Table 2. Treatment Regimen Distribution for Patients with eSCLC by Regimen-Based Line of Treatment for 1L, 2L, and 3L</strong>
  
<strong>Supplemental Table 3. Healthcare Resource Utilization by Performance Status for 1L Therapy</strong>
  
<strong>Supplemental Table 4. Mixed Model for General Physical Symptoms</strong>
  
<strong>Supplemental Table 5. Mixed Model for Treatment Side Effects</strong>
  
<strong>Supplemental Table 6. Mixed Model for Acute Distress</strong>
  
<strong>Supplemental Table 7. Mixed Model for Despair</strong>
  
<strong>Supplemental Table 8. Mixed Model for Impaired Ambulation</strong>
  
<strong>Supplemental Table 9. Mixed Model for Impaired Performance</strong>
  
<strong>Supplemental Table 10. Demographic Characteristics, Clinical Characteristics, and Comorbidities of Patients with eSCLC by Systemic Treatment</strong>
DOI: 10.6084/m9.figshare.14320482
title: The complete chloroplast genome of Papaver setigerum and comparative analyses in Papaveraceae

description: Abstract Papaver setigerum is an annual herb that is closely related to the opium poppy, P. somniferum. Genetic resources for P. setigerum are scarce. In the present study, we assembled the complete chloroplast (cp) genome of P. setigerum based on genome skimming data, and we conducted comparative cp genome analyses to study the evolutionary pattern in Papaveraceae. The cp genome of P. setigerum is 152,862 bp in length with a typical quadripartite structure. Comparative analyses revealed no gene rearrangement in the Papaveraceae family, although differences were evident in genome size, gene losses, as well as inverted repeats (IR) region expansion and contraction. The rps15 gene has been lost from the genomes of Meconopsis racemosa, Coreanomecon hylomeconoides, P. orientale, P. somniferum, and P. setigerum, and the ycf15 gene is found only in C. hylomeconoides. Moreover, 13 cpDNA markers, including psbA-trnH, rps16-trnQ, trnS-trnG, trnC-petN, trnE-trnT, trnL-trnF, trnF-ndhJ, petA-psbJ, ndhF-rpl32, rpl32-trnL, ccsA-ndhD, ndhE-ndhG, and rps15-ycf1, were identified with relatively high levels of variation within Papaver, which will be useful for species identification in this genus. Among those markers, psbA-trnH is the best one to distinguish P. somniferum and P. setigerum.
DOI: 10.6084/m9.figshare.14320482.v1
title: The complete chloroplast genome of Papaver setigerum and comparative analyses in Papaveraceae

description: Abstract Papaver setigerum is an annual herb that is closely related to the opium poppy, P. somniferum. Genetic resources for P. setigerum are scarce. In the present study, we assembled the complete chloroplast (cp) genome of P. setigerum based on genome skimming data, and we conducted comparative cp genome analyses to study the evolutionary pattern in Papaveraceae. The cp genome of P. setigerum is 152,862 bp in length with a typical quadripartite structure. Comparative analyses revealed no gene rearrangement in the Papaveraceae family, although differences were evident in genome size, gene losses, as well as inverted repeats (IR) region expansion and contraction. The rps15 gene has been lost from the genomes of Meconopsis racemosa, Coreanomecon hylomeconoides, P. orientale, P. somniferum, and P. setigerum, and the ycf15 gene is found only in C. hylomeconoides. Moreover, 13 cpDNA markers, including psbA-trnH, rps16-trnQ, trnS-trnG, trnC-petN, trnE-trnT, trnL-trnF, trnF-ndhJ, petA-psbJ, ndhF-rpl32, rpl32-trnL, ccsA-ndhD, ndhE-ndhG, and rps15-ycf1, were identified with relatively high levels of variation within Papaver, which will be useful for species identification in this genus. Among those markers, psbA-trnH is the best one to distinguish P. somniferum and P. setigerum.
DOI: 10.6084/m9.figshare.14320531
title: The complete chloroplast genome sequence of Gynostemma yixingense and comparative analysis with congeneric species

description: Abstract Gynostemma yixingense, an important medicinal member of the Cucurbitaceae family, is an endemic herbaceous species distributed in East China. It is morphologically similar to the plants in the same genus, which resulted in some confusion in identification and application. Meanwhile, there are still some controversies in taxonomy. Herein, the complete chloroplast genome sequence of G. yixingense was obtained by Illumina paired-end sequencing technology and compared to other chloroplast genome sequences of congeneric species. The complete chloroplast genome of G. yixingense is 157,910 bp in length with 36.94% GC content and contains a large single-copy (LSC) region of 86,791 bp, a small single-copy (SSC) region of 18,635 bp and a pair of inverted repeat (IR) regions of 26,242 bp. The whole genome contains 133 unique genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. In addition, 74 simple sequence repeats (SSRs) were identified, most of which were A/T rich. The phylogenetic analysis indicated that G. yixingense had the closest relationship to G. laxiflorum. The result of this study provided an important theoretical basis for chloroplast genome and phylogenetic analysis of G. yixingense.
DOI: 10.6084/m9.figshare.14320531.v1
title: The complete chloroplast genome sequence of Gynostemma yixingense and comparative analysis with congeneric species

description: Abstract Gynostemma yixingense, an important medicinal member of the Cucurbitaceae family, is an endemic herbaceous species distributed in East China. It is morphologically similar to the plants in the same genus, which resulted in some confusion in identification and application. Meanwhile, there are still some controversies in taxonomy. Herein, the complete chloroplast genome sequence of G. yixingense was obtained by Illumina paired-end sequencing technology and compared to other chloroplast genome sequences of congeneric species. The complete chloroplast genome of G. yixingense is 157,910 bp in length with 36.94% GC content and contains a large single-copy (LSC) region of 86,791 bp, a small single-copy (SSC) region of 18,635 bp and a pair of inverted repeat (IR) regions of 26,242 bp. The whole genome contains 133 unique genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. In addition, 74 simple sequence repeats (SSRs) were identified, most of which were A/T rich. The phylogenetic analysis indicated that G. yixingense had the closest relationship to G. laxiflorum. The result of this study provided an important theoretical basis for chloroplast genome and phylogenetic analysis of G. yixingense.
DOI: 10.6084/m9.figshare.23751811.v1
title: Additional file 9 of The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones

description: Additional file 9: Table S7. Quantitative analysis of phytohormones.
DOI: 10.6084/m9.figshare.23751814
title: Additional file 10 of The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones

description: Additional file 10: Table S8. DEGs consistent with the change of phytohormones.
DOI: 10.6084/m9.figshare.23751793
title: Additional file 3 of The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones

description: Additional file 3: Table S1. Gene-specific primers for qRT-PCR.
DOI: 10.6084/m9.figshare.20088011.v1
title: Additional file 1 of KAZN as a diagnostic marker in ovarian cancer: a comprehensive analysis based on microarray, mRNA-sequencing, and methylation data

description: Additional file 1: Supplementary Table 1. Clinical feature information of samples in each dataset.
DOI: 10.6084/m9.figshare.20088011
title: Additional file 1 of KAZN as a diagnostic marker in ovarian cancer: a comprehensive analysis based on microarray, mRNA-sequencing, and methylation data

description: Additional file 1: Supplementary Table 1. Clinical feature information of samples in each dataset.
DOI: 10.5281/zenodo.10651231
title: Economic inequality shapes the agency-communion content of gender stereotypes

description: These files contain data and syntaxes from Moreno-Bella et al. (2023)
DOI: 10.5281/zenodo.10651232
title: Economic inequality shapes the agency-communion content of gender stereotypes

description: These files contain data and syntaxes from Moreno-Bella et al. (2023)
DOI: 10.5281/zenodo.10642065
title: Data Processing Pipeline and Products from the NANOGrav 12.5-Year Data Set: Dispersion Measure Mis-Estimation with Varying Bandwidths

description: This Zenodo dataset contains the data processing pipeline, as well as the data products, corresponding to the scientific journal paper "NANOGrav 12.5-Year Data Set: Dispersion Measure Mis-Estimation with Varying Bandwidths". The processing pipeline is structured as follows:



1_fit_dispersion_3terms.py  reads the .tim files (containing the times-of-arrival), creates the broadband and narrowband datasets, and fits a dispersion model to both datasets using three parameters.

2_plot_fits_differences.py creates the residual plots showing the differences in the fitted values of the parameters.

3_autocovariance.py calculates the autocovariance function of the differences in the fitted values, and creates the corresponding plots.

All the files starting with "plot" are convenience scripts for creating the plots presented in the paper.

All the files starting with "sophia" are utility functions created by the authors that are used in the main pipeline.

The folder "NANOGrav_12yv4" contains the dataset analyzed in this work.

The folder "timing_analysis" contains utility functions created by the NANOGrav collaboration that are used in the main pipeline.


Please do not hesitate to send all your questions, concerns, or commentaries to sophia.sosa@nanograv.org
DOI: 10.5281/zenodo.10642066
title: Data Processing Pipeline and Products from the NANOGrav 12.5-Year Data Set: Dispersion Measure Mis-Estimation with Varying Bandwidths

description: This Zenodo dataset contains the data processing pipeline, as well as the data products, corresponding to the scientific journal paper "NANOGrav 12.5-Year Data Set: Dispersion Measure Mis-Estimation with Varying Bandwidths". The processing pipeline is structured as follows:



1_fit_dispersion_3terms.py  reads the .tim files (containing the times-of-arrival), creates the broadband and narrowband datasets, and fits a dispersion model to both datasets using three parameters.

2_plot_fits_differences.py creates the residual plots showing the differences in the fitted values of the parameters.

3_autocovariance.py calculates the autocovariance function of the differences in the fitted values, and creates the corresponding plots.

All the files starting with "plot" are convenience scripts for creating the plots presented in the paper.

All the files starting with "sophia" are utility functions created by the authors that are used in the main pipeline.

The folder "NANOGrav_12yv4" contains the dataset analyzed in this work.

The folder "timing_analysis" contains utility functions created by the NANOGrav collaboration that are used in the main pipeline.


Please do not hesitate to send all your questions, concerns, or commentaries to sophia.sosa@nanograv.org
DOI: 10.6084/m9.figshare.20088014
title: Additional file 2 of KAZN as a diagnostic marker in ovarian cancer: a comprehensive analysis based on microarray, mRNA-sequencing, and methylation data

description: Additional file 2: Supplementary Table 2. Differentially methylated CpG sites in the KAZN gene body region.
DOI: 10.6084/m9.figshare.20088014.v1
title: Additional file 2 of KAZN as a diagnostic marker in ovarian cancer: a comprehensive analysis based on microarray, mRNA-sequencing, and methylation data

description: Additional file 2: Supplementary Table 2. Differentially methylated CpG sites in the KAZN gene body region.
DOI: 10.5281/zenodo.10651331
title: Genome Scale Metabolic Modeling and Metabolic Flux Analysis Scripts for Weber et al (2024)

description: This folder contains the .mat and script files for the paper "Glutamine Metabolism is Systemically Different Between Primary and Induced Pluripotent StemCell-Derived Brain Microvascular Endothelial Cells". For any questions. please contact acylne@umd.edu and bmoiz@umd.edu
DOI: 10.5281/zenodo.10651332
title: Genome Scale Metabolic Modeling and Metabolic Flux Analysis Scripts for Weber et al (2024)

description: This folder contains the .mat and script files for the paper "Glutamine Metabolism is Systemically Different Between Primary and Induced Pluripotent StemCell-Derived Brain Microvascular Endothelial Cells". For any questions. please contact acylne@umd.edu and bmoiz@umd.edu
DOI: 10.6084/m9.figshare.5932333
title: Late Paleocene–early Eocene granitoids in the Jiamusi Massif, NE China: Zircon U–Pb ages, geochemistry, and tectonic implications

description: Northeast (NE) China is characterized by large areas of Mesozoic and Paleozoic granitoids, whereas Cenozoic granitoids are scarce. This paper reports LA-ICP-MS zircon U–Pb ages and whole-rock geochemical data for late Paleocene–early Eocene granitoids from the Jiamusi Massif, NE China, in order to determine their petrogenesis and tectonic implications. Geochronological data indicate that the granodiorite and dioritic porphyry from the Wudingshan pluton formed at 51.5 ± 0.3 Ma and 56.3 ± 0.8 Ma, respectively. The biotite–quartz diorite, biotite granodiorite, and dioritic porphyry have high SiO<sub>2</sub> (68.38–70.06 wt.%), Al<sub>2</sub>O<sub>3</sub> (15.34–15.79 wt.%), and Na<sub>2</sub>O (3.96–4.49 wt.%) contents, low MgO contents (1.10–1.26 wt.%), A/CNK ratios of 0.99–1.11, and are classified as medium- to high-K calc-alkaline and weakly peraluminous I-type granitoids. They are enriched in LREEs and LILEs, and depleted in HFSEs, with Nb/Ta ratios of 10.4–15.0. Moreover, they have negative Nb–Ta–Ti anomalies, indicating that they were derived from continental crust. Combining with the previously published isotopic data and regional geological results, we suggest that the late Paleocene–early Eocene granitoids (56–52 Ma) were probably derived from partial melting of juvenile lower crust, and formed in an active continental margin setting, possibly related to subduction slab rollback of the Paleo-Pacific Plate.
DOI: 10.6084/m9.figshare.21393894
title: Additional file 2 of Role of a lipid metabolism-related lncRNA signature in risk stratification and immune microenvironment for colon cancer

description: Additional file 2: Table S1. Genes related to lipid metabolism.
DOI: 10.6084/m9.figshare.20087916
title: Additional file 11 of HBV genome-enriched single cell sequencing revealed heterogeneity in HBV-driven hepatocellular carcinoma (HCC)

description: Additional file 11: Table S10. All detected Integration Events. All the detected HBV integration events for single cells from tumor and bulk tissue from adjacent normal. There are totally 471 HBV integrations observed from single cells in tumor and 17 HBV integrations observed from adjacent normal.
DOI: 10.6084/m9.figshare.5932333.v1
title: Late Paleocene–early Eocene granitoids in the Jiamusi Massif, NE China: Zircon U–Pb ages, geochemistry, and tectonic implications

description: Northeast (NE) China is characterized by large areas of Mesozoic and Paleozoic granitoids, whereas Cenozoic granitoids are scarce. This paper reports LA-ICP-MS zircon U–Pb ages and whole-rock geochemical data for late Paleocene–early Eocene granitoids from the Jiamusi Massif, NE China, in order to determine their petrogenesis and tectonic implications. Geochronological data indicate that the granodiorite and dioritic porphyry from the Wudingshan pluton formed at 51.5 ± 0.3 Ma and 56.3 ± 0.8 Ma, respectively. The biotite–quartz diorite, biotite granodiorite, and dioritic porphyry have high SiO<sub>2</sub> (68.38–70.06 wt.%), Al<sub>2</sub>O<sub>3</sub> (15.34–15.79 wt.%), and Na<sub>2</sub>O (3.96–4.49 wt.%) contents, low MgO contents (1.10–1.26 wt.%), A/CNK ratios of 0.99–1.11, and are classified as medium- to high-K calc-alkaline and weakly peraluminous I-type granitoids. They are enriched in LREEs and LILEs, and depleted in HFSEs, with Nb/Ta ratios of 10.4–15.0. Moreover, they have negative Nb–Ta–Ti anomalies, indicating that they were derived from continental crust. Combining with the previously published isotopic data and regional geological results, we suggest that the late Paleocene–early Eocene granitoids (56–52 Ma) were probably derived from partial melting of juvenile lower crust, and formed in an active continental margin setting, possibly related to subduction slab rollback of the Paleo-Pacific Plate.
DOI: 10.6084/m9.figshare.23751811
title: Additional file 9 of The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones

description: Additional file 9: Table S7. Quantitative analysis of phytohormones.
DOI: 10.6084/m9.figshare.20087925.v1
title: Additional file 14 of HBV genome-enriched single cell sequencing revealed heterogeneity in HBV-driven hepatocellular carcinoma (HCC)

description: Additional file 14: Table S13. Genome regions where CNV amplification is significantly associated with decreasing rate of rare HBV integration carrying cells, when focusing on chr11, whose CNV differentiated clone 1 vs. clones 2, 3, 4.