cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14306508
title: Effect of different feeding methods on rumen microbes in growing Chinese Tan sheep

description: ABSTRACT We evaluated the difference between rumen bacteria in Tan sheep fed either by grazing or in a feedlot. The aim was to provide a theoretical basis for ruminant nutrition and meat quality based on rumen fermentation. Twenty-four three-month-old Tan sheep were randomly and equally divided into two groups, the grazing group and ration group. Five sheep of each group were selected for slaughter at six months of age. Ruminal contents were collected and assessed to identify rumen bacteria, based on 16S rDNA sequencing analysis. A total of 17 phyla were identified, among which Bacteroidetes, Firmicutes, and Proteobacteria were dominant in both groups. The abundance of Firmicutes was higher in grazing group than in the ration group, while that of Proteobacteria was opposite. Besides the dominant phyla differences, the abundance of Fibrobacteres, Tenericutes, Elusimicrobia, and Cyanobacteria was significantly higher in the grazing group compared with the ration group. At genus level, a total of 174 genera were identified. The abundance of Rikenellaceae_RC9_gut_group, Dialister, Lachnospiraceae_NA, Catonella, Ruminococcaceae_UCG-014, Lachnospiraceae_NK3A20_group, and Fibrobacter in the grazing group was higher than in the ration group. However, the abundance of Succinivibrionaceae_NA was lower in the grazing group, and Succinivibrionaceae_UCG-001 showed a decreasing trend in the grazing group. The two feeding methods may influence the rumen bacterial composition, including the abundance of dominant bacteria, as well as the cellulolytic- and carbohydrate-degrading bacteria in the rumen of Tan sheep.
DOI: 10.6084/m9.figshare.14306508.v1
title: Effect of different feeding methods on rumen microbes in growing Chinese Tan sheep

description: ABSTRACT We evaluated the difference between rumen bacteria in Tan sheep fed either by grazing or in a feedlot. The aim was to provide a theoretical basis for ruminant nutrition and meat quality based on rumen fermentation. Twenty-four three-month-old Tan sheep were randomly and equally divided into two groups, the grazing group and ration group. Five sheep of each group were selected for slaughter at six months of age. Ruminal contents were collected and assessed to identify rumen bacteria, based on 16S rDNA sequencing analysis. A total of 17 phyla were identified, among which Bacteroidetes, Firmicutes, and Proteobacteria were dominant in both groups. The abundance of Firmicutes was higher in grazing group than in the ration group, while that of Proteobacteria was opposite. Besides the dominant phyla differences, the abundance of Fibrobacteres, Tenericutes, Elusimicrobia, and Cyanobacteria was significantly higher in the grazing group compared with the ration group. At genus level, a total of 174 genera were identified. The abundance of Rikenellaceae_RC9_gut_group, Dialister, Lachnospiraceae_NA, Catonella, Ruminococcaceae_UCG-014, Lachnospiraceae_NK3A20_group, and Fibrobacter in the grazing group was higher than in the ration group. However, the abundance of Succinivibrionaceae_NA was lower in the grazing group, and Succinivibrionaceae_UCG-001 showed a decreasing trend in the grazing group. The two feeding methods may influence the rumen bacterial composition, including the abundance of dominant bacteria, as well as the cellulolytic- and carbohydrate-degrading bacteria in the rumen of Tan sheep.
DOI: 10.6084/m9.figshare.23740538
title: Additional file 4 of Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.20070783.v1
title: Additional file 1 of Combined transcriptome and metabolome analysis of Nerium indicum L. elaborates the key pathways that are activated in response to witches’ broom disease

description: Additional file 1: Supplementary Table 1. Summary of transcriptome sequencing of infected and non-infected Nerium indicum L. tissues. Supplementary Table 2. Differential expression of genes between infected (NOWP) and non-infected (NOHP) N. indicum phloem. Supplementary Table 3. Differential expression of genes between infected (NOWS) and non-infected (NOHS) N. indicum stem. Supplementary Table 4. List of differentially expressed genes that were enriched in specific pathways in WBD infected N. indicum phloem (NOWP) and stem tip (NOWS) as compared to controls i.e., NOHP and NOHS, respectively. Supplementary Table 5. Details of the differentially accumulated metabolites between infected (NOWP) and non-infected (NOHP) N. indicum phloem. Supplementary Table 6. Details of the differentially accumulated metabolites between infected (NOWS) and non-infected (NOHS) N. indicum stem tip. Supplementary Table 7. Pathway specific differential accumulation of metabolites in infected N. indicum phloem and stem as compared to non-infected tissues.
DOI: 10.6084/m9.figshare.19549736.v1
title: Additional file 2 of Exploring genetic association of insomnia with allergic disease and asthma: a bidirectional Mendelian randomization study

description: Additional file 2: Table S2. Detailed information on genetic instruments. Table S3. SNPs used in current Mendelian randomization analysis.
DOI: 10.6084/m9.figshare.14302746.v1
title: Additional file 3 of Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms

description: Additional file 2: Table S1. Metabolites identified in bloom.
DOI: 10.6084/m9.figshare.11684145.v2
title: Polymorphisms in dipeptidyl peptidase 4 reduce host cell entry of Middle East respiratory syndrome coronavirus

description: Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) causes a severe respiratory disease in humans. The MERS-CoV spike (S) glycoprotein mediates viral entry into target cells. For this, MERS-CoV S engages the host cell protein dipeptidyl peptidase 4 (DPP4, CD26) and the interface between MERS-CoV S and DPP4 has been resolved on the atomic level. Here, we asked whether naturally-occurring polymorphisms in DPP4, that alter amino acid residues required for MERS-CoV S binding, influence cellular entry of MERS-CoV. By screening of public databases, we identified fourteen such polymorphisms. Introduction of the respective mutations into DPP4 revealed that all except one (Δ346-348) were compatible with robust DPP4 expression. Four polymorphisms (K267E, K267N, A291P and Δ346-348) strongly reduced binding of MERS-CoV S to DPP4 and S protein-driven host cell entry, as determined using soluble S protein and S protein bearing rhabdoviral vectors, respectively. Two polymorphisms (K267E and A291P) were analyzed in the context of authentic MERS-CoV and were found to attenuate viral replication. Collectively, we identified naturally-occurring polymorphisms in DPP4 that negatively impact cellular entry of MERS-CoV and might thus modulate MERS development in infected patients.
DOI: 10.6084/m9.figshare.14302749.v1
title: Additional file 4 of Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms

description: Additional file 3: Table S2. Dynamics of bacterial community composition.
DOI: 10.25403/upresearchdata.25149149
title: Hereford genotypes for South Africa, Ireland, New Zealand, and Uruguay

description: This study aimed to develop a better understanding of the local adaptation and selection of South African, Irish, Uruguayan, and New Zealand Hereford populations in their respective environments. Before analyses, a total of 1 693 individual genotypes were received where 1 538 individuals for the four populations remained after quality control for further downstream data analyses. All individuals were genotyped using seven different arrays, as listed in Table1.
Descriptive genomic diversity parameters were estimated as HE, HO, FIS, MAF, and LD using PLINK v 1.9. All populations showed a moderate level of heterozygosity with HE values ranging from 0.359 to 0.391, and HO values ranging from 0.352 to 0.388. FIS values were -0.00475 to 0.0189 with MAF values ranging from 0.24 to 0.29 and LD ranging from 0.41 to 0.70. Population structure was visualised through principal component analysis. Each population showed to have a distinct cluster with some overlap between clusters. Intra-population genomic relatedness was determined through ROH. The detectRUNS package was used in R and a consecutive runs method was applied. The Irish and New Zealand populations showed to have the lowest degree of intra-population relatedness. A high level of genetic differentiation was observed in all populations. Selection signatures and candidate genes were identified using ROH for an intra-population approach and Pairwise Wright’s FST for an inter-population approach. Most notably, intra-population candidate genes related to traits of adaptation where the KDR and KIT genes were identified. Inter-population comparisons revealed 60 candidate genes related to traits of adaptation, production, and quality. The most common trait identified was that of bovine respiratory disease susceptibility. Five candidate genes, namely ARL6, ENOPH1, PPARGC1A, SCD5, and SNCA, were found to overlap between four of the six inter-population comparisons. Production and quality-related traits aligned with the breeding objectives of each population. The candidate genes related to adaptability traits showed that each population is adapted to its environment. Overall, each population showed to be genomically diverse and adapted to its geographically separated production region.
DOI: 10.6084/m9.figshare.23740686
title: Additional file 5 of Small extracellular vesicles-transported lncRNA TDRKH-AS1 derived from AOPPs-treated trophoblasts initiates endothelial cells pyroptosis through PDIA4/DDIT4 axis in preeclampsia

description: Additional file 5: Table S4. Differentially expressed genes (DEGs) induced by overexpression TDRKH-AS1 in HUVECs. p value of both DESeq2 and edgeR less than 0.05 is considered to be differentially expressed genes.
DOI: 10.6084/m9.figshare.14306496.v1
title: Trehalose addition to a Tris-fructose egg yolk extender on quality of ram sperm preserved at 0 °C

description: ABSTRACT The present study investigated the effects of various concentrations of trehalose in Tris-fructose egg yolk diluent on ram semen preservation at 0 ℃. Semen was collected by artificial vagina ejaculation from six rams of proven fertility. High-quality ejaculates were diluted with 0 (control), 5, 10, 15, and 20 mM trehalose of Tris-fructose egg yolk extender and control (tris-fructose egg yolk extender without trehalose), respectively. Then, the ejaculates were diluted to a concentration of 5×108 sperm/mL, cooled to 0 ℃ for 90 min, and maintained at that temperature for twelve days. The diluted semen samples were examined, and their sperm progressive motility, membrane functionality, and acrosome integrity recorded at 0, 24, 72, 144, 216, and 288 h. Two hundred ninety-six ewes were transcervically inseminated with the 216-h control (without trehalose) or the optimal trehalose concentration group semen, and the pregnancy and lambing rates were measured. No significant differences were established in the sperm progressive motility and membrane functionality among the control and 5, 10, 15, and 20 mM groups. The sperm samples of trehalose addition groups had no significant difference in the acrosome integrity of sperm, but they were, nonetheless, significantly higher than those in the control. No significant difference was detected in the lambing and pregnancy rates between the 5 mM and control groups. These results suggest that ram sperm is capable of fertilization after cooling and preservation at 0 ℃ by the use of 5 mM trehalose for Tris-fructose egg yolk diluent. Under these conditions, ram sperm can be more effectively preserved than under other four concentrations of diluents.
DOI: 10.6084/m9.figshare.20070840
title: Additional file 2 of Nutrition-wide association study of microbiome diversity and composition in colorectal cancer patients

description: Additional file 2: Table S1. Daily diet consumption and Spearman correlation between dietary factors and microbial alpha-diversity. Table S2. Pairwise correlations for relative abundances of different phylogenetical levels in low fruit-vegetable and high fruit/low meat-poultry dietary groups. Table S3. Spearman correlation coefficients between dietary factors and relative abundance of microbial taxonomy. Table S4. Crude p-values for Spearman correlation between dietary factors and relative abundance of microbial taxonomy. Table S5. False discovery rate adjusted p-values for Spearman correlation between dietary factors and relative abundance of microbial taxonomy.
DOI: 10.6084/m9.figshare.20070840.v1
title: Additional file 2 of Nutrition-wide association study of microbiome diversity and composition in colorectal cancer patients

description: Additional file 2: Table S1. Daily diet consumption and Spearman correlation between dietary factors and microbial alpha-diversity. Table S2. Pairwise correlations for relative abundances of different phylogenetical levels in low fruit-vegetable and high fruit/low meat-poultry dietary groups. Table S3. Spearman correlation coefficients between dietary factors and relative abundance of microbial taxonomy. Table S4. Crude p-values for Spearman correlation between dietary factors and relative abundance of microbial taxonomy. Table S5. False discovery rate adjusted p-values for Spearman correlation between dietary factors and relative abundance of microbial taxonomy.
DOI: 10.6084/m9.figshare.7489943.v1
title: Additional file 17: of Genome-wide analysis of the pentatricopeptide repeat gene family in different maize genomes and its important role in kernel development

description: Table S11. List of PPR genes associated with kernel-related traits. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.14305700
title: Effect of Zr Content on the Distribution Characteristic of the 14H and 18R LPSO Phases

description: Abstract Zirconium (Zr) is an essential element in Mg-Zn and Mg-Zn-Y system magnesium alloys. In this study, an interesting phenomenon that the content of Zr element could influence the size and the morphology of the long period stacking ordered (LPSO) phases, which has never been reported by previous works before. The Mg98.5-xZn0.5Y1Zrx (x =0, 0.1, 0.2 and 0.3 at. %) magnesium alloys were fabricated by directional solidification, and the effects of the Zr content on the distribution characteristics of the bulk LPSO phases (18R) and the lamellar LPSO phases (14H) were investigated. The directional solidification technology showed good controllability in LPSO phase’s distribution, and the morphology of LPSO phases in Mg98.5-xZn0.5Y1Zrx (x =0, 0.1, 0.2 and 0.3 at. %) alloys were observed clearly. The results showed that the amount and the morphology of the 14H and 18R LPSO phases within grains continuously decreased with the Zr content increasing. The continuous 14H lamellar structure changed to discontinuous. In addition, Zr element exhibited purification ability on the grain boundaries and refined effect on the 14H and 18R LPSO phases. This can be attributed to the influence of Zr atoms on stacking fault energy (SFE) and the attraction of Zr atoms to Mg atoms.
DOI: 10.6084/m9.figshare.19549532.v1
title: Additional file 1 of Association of latent class analysis-derived subphenotypes of acute kidney injury with mortality in critically ill patients with cardiovascular disease: a retrospective cohort study

description: Additional file 1: Table S1. The association between each variable and 28-day mortality by univariate logistic regression.
DOI: 10.6084/m9.figshare.19549532
title: Additional file 1 of Association of latent class analysis-derived subphenotypes of acute kidney injury with mortality in critically ill patients with cardiovascular disease: a retrospective cohort study

description: Additional file 1: Table S1. The association between each variable and 28-day mortality by univariate logistic regression.
DOI: 10.25625/cdby3d
title: Replication Data for: Unraveling Femtosecond Spin and Charge Dynamics with EUV T-MOKE Spectroscopy

description: Data and code for the publication Probst et al, Unraveling Femtosecond Spin and Charge Dynamics with EUV T-MOKE Spectroscopy, arXiv:2306.02783 [cond-mat.mtrl-sci] (2023)
DOI: 10.6084/m9.figshare.14306465.v1
title: Effect of fermented soybean meal supplementation on some growth performance, blood chemical parameters, and fecal microflora of finishing pigs

description: ABSTRACT This study evaluated the effect of fermented soybean meal (FSBM) supplementation on growth performance, meat quality, blood biochemical parameters, and fecal microflora of finishing pigs. Thirty-two crossbred pigs (Duroc × Landrance × Yorkshire) (66-day-old, 67.95±0.25 kg) were randomly allocated to two treatments and fed diets containing soybean meal and FSBM. The average daily gain (ADG), average daily feed intake (ADFI), feed conversion ratio (FCR), blood biochemical parameters, and meat quality index were measured. At the end of experiment, the fecal microflora of finishing pigs was analyzed with 16S rDNA techniques. Results revealed that pigs fed FSBM had a greater ADG and lower cooking loss relative to control group (basal diets). Compared with the control group, the triglyceride content in the serum of the group fed FSBM increased significantly, and the creatinine content in the serum decreased notably. Fermented soybean meal enhanced the abundance of Bacteroidetes, Prevotellaceae, Bcteroidales, Bacteroidia, but inhibited the growth of Firmicutes, Clostridia, Clostridiales, and Ruminococcaceae in the intestine of pigs. Therefore, we can speculate that FSBM may play an important role in animal production. Dietary FSBM supplementation may be beneficial to some aspects of growth performance and the diversity of fecal microflora in finishing pigs.
DOI: 10.6084/m9.figshare.19549713.v1
title: Additional file 4 of DNA methylation molecular subtypes for prognosis prediction in lung adenocarcinoma

description: Additional file 4. Table S1: The univariate Cox regression shown 1103 CpG sites were identified as potential DNA methylation biomarkers for OS in LUAD patients. Table S2: The multivariate Cox regression analysis of the 864 methylation sites with T, N, M, stage, gender, and age as covariates recognized 205 independent prognosis-related CpG sites. Table S3: The genomic annotation of the above 205 CpG sites was used to identify overall 237 corresponding promoter genes. Table S4: The functional enrichment analysis of these 237 genes. Table S5: The differences expression among the 7 clusters.
DOI: 10.6084/m9.figshare.14306496
title: Trehalose addition to a Tris-fructose egg yolk extender on quality of ram sperm preserved at 0 °C

description: ABSTRACT The present study investigated the effects of various concentrations of trehalose in Tris-fructose egg yolk diluent on ram semen preservation at 0 ℃. Semen was collected by artificial vagina ejaculation from six rams of proven fertility. High-quality ejaculates were diluted with 0 (control), 5, 10, 15, and 20 mM trehalose of Tris-fructose egg yolk extender and control (tris-fructose egg yolk extender without trehalose), respectively. Then, the ejaculates were diluted to a concentration of 5×108 sperm/mL, cooled to 0 ℃ for 90 min, and maintained at that temperature for twelve days. The diluted semen samples were examined, and their sperm progressive motility, membrane functionality, and acrosome integrity recorded at 0, 24, 72, 144, 216, and 288 h. Two hundred ninety-six ewes were transcervically inseminated with the 216-h control (without trehalose) or the optimal trehalose concentration group semen, and the pregnancy and lambing rates were measured. No significant differences were established in the sperm progressive motility and membrane functionality among the control and 5, 10, 15, and 20 mM groups. The sperm samples of trehalose addition groups had no significant difference in the acrosome integrity of sperm, but they were, nonetheless, significantly higher than those in the control. No significant difference was detected in the lambing and pregnancy rates between the 5 mM and control groups. These results suggest that ram sperm is capable of fertilization after cooling and preservation at 0 ℃ by the use of 5 mM trehalose for Tris-fructose egg yolk diluent. Under these conditions, ram sperm can be more effectively preserved than under other four concentrations of diluents.
DOI: 10.6084/m9.figshare.16928450.v1
title: Additional file 3 of Pregnancy- and lactation-associated osteoporosis with vertebral fractures: a systematic review

description: Additional file 3.
DOI: 10.6084/m9.figshare.19549640
title: Additional file 2 of Comprehensive analysis of lncRNA-mRNAs co-expression network identifies potential lncRNA biomarkers in cutaneous squamous cell carcinoma

description: Additional file 2.
DOI: 10.6084/m9.figshare.23684896
title: SupMat_Acid1_10water_SofQs.dat from Molecular interactions in short-chain perfluoroalkyl carboxylic acids and aqueous solutions

description: S(Q) experimental data from figure 3 of Benmore et al. for the acid 1:10 water solutions.
DOI: 10.6084/m9.figshare.23684896.v1
title: SupMat_Acid1_10water_SofQs.dat from Molecular interactions in short-chain perfluoroalkyl carboxylic acids and aqueous solutions

description: S(Q) experimental data from figure 3 of Benmore et al. for the acid 1:10 water solutions.
DOI: 10.6084/m9.figshare.20070783
title: Additional file 1 of Combined transcriptome and metabolome analysis of Nerium indicum L. elaborates the key pathways that are activated in response to witches’ broom disease

description: Additional file 1: Supplementary Table 1. Summary of transcriptome sequencing of infected and non-infected Nerium indicum L. tissues. Supplementary Table 2. Differential expression of genes between infected (NOWP) and non-infected (NOHP) N. indicum phloem. Supplementary Table 3. Differential expression of genes between infected (NOWS) and non-infected (NOHS) N. indicum stem. Supplementary Table 4. List of differentially expressed genes that were enriched in specific pathways in WBD infected N. indicum phloem (NOWP) and stem tip (NOWS) as compared to controls i.e., NOHP and NOHS, respectively. Supplementary Table 5. Details of the differentially accumulated metabolites between infected (NOWP) and non-infected (NOHP) N. indicum phloem. Supplementary Table 6. Details of the differentially accumulated metabolites between infected (NOWS) and non-infected (NOHS) N. indicum stem tip. Supplementary Table 7. Pathway specific differential accumulation of metabolites in infected N. indicum phloem and stem as compared to non-infected tissues.
DOI: 10.6084/m9.figshare.16928450
title: Additional file 3 of Pregnancy- and lactation-associated osteoporosis with vertebral fractures: a systematic review

description: Additional file 3.
DOI: 10.6084/m9.figshare.23684905
title: SupMat_Neat_Acids_SofQs.dat from Molecular interactions in short-chain perfluoroalkyl carboxylic acids and aqueous solutions

description: S(Q) experimental data from figure 3 of Benmore et al. for the pure acids.
DOI: 10.6084/m9.figshare.19289594
title: Tracing of fly larval segments

description: This is a tracing data of segment boundaries in freely crawling third instar Drosophila larvae, which was used on Sun et al.