cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3622289_d18
title: Additional file 4: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

description: Results from the Panther database gene set enrichment analysis (GSEA) comparing differences in GO categories between FDR significant contigs in large and small fish. FDR significant categories for Biological Process, Molecular Function, and Cellular Components are shown. (XLSX 24 kb)
DOI: 10.17863/cam.78009
title: MolE8 Models and Codes

description: The MolE8 code and the trained machine learning models are available for download from this Cambridge University repository
DOI: 10.6084/m9.figshare.c.3622355_d1
title: Additional file 5: Table S4. of A proteomic analysis of chondrogenic, osteogenic and tenogenic constructs from ageing mesenchymal stem cells

description: Presenting the classification of proteins in chondrogenic, osteogenic and tenogenic constructs using MatrisomeDB. (XLSX 23 kb)
DOI: 10.17863/cam.95549
title: Research Data Supporting "The Interdependence of the Thermal and Mechanical Cycling Behaviour In Ti2448 (Ti-24Nb-4Zr-8Sn, wt%)"

description: Data associated with the aforementioned publication, including SEM, mechanical testing and SXRD data from I12 beam line at Diamond Light Source. SEM images use BSE contrast. Mechanical testing data was performed in stress control. SXRD data was acquired in transmission Debye Scherrer geometry. Detailed acquisition parameters are detailed in the methods section of the manuscript.
DOI: 10.6084/m9.figshare.c.3622355_d6
title: Additional file 2: Table S2. of A proteomic analysis of chondrogenic, osteogenic and tenogenic constructs from ageing mesenchymal stem cells

description: Presenting details of the antibodies used for validation studies. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.25661804
title: Identification of hub genes in meat quality of grass carp (<i>Ctenopharyngodon idellus</i>) fed with faba bean by muscle tissue transcriptomic analysis

description: Crisp grass carp is a type of grass carp (<i>Ctenopharyngodon idella</i>) that has been fed faba beans. Flesh quality and expression of muscle quality-related genes in muscle of grass carp were evaluated. Compared with ordinary grass carp, 1901 differentially expressed genes (DEGs) were up-regulated and 1628 DEGs were down-regulated in crisp grass carp. The GO analysis results showed that the DEGs were enriched in ribosomes and proteins. Kyoto Encyclopaedia of genes and genomes (KEGG) pathway analysis results showed that amino acid metabolism was closely related to meat quality. COX3, ACADS, ACAT1, ECHS1, EHHADH, HADHAA, HADH, HMGCL, MCCC1 and MCCC2 were the top 10 hub genes most closely associated with other nodes and showed a strong positive correlation. Hardness was positively correlated with the COX3, ECHS1, ACADS, ACAT1, HADHA, HADH, HMGCL and MCCC1. These results have been demonstrated to play important roles in clarifying the molecular mechanism of muscle firmness increase in crisp grass carp. Feeding faba bean meal improved texture parameters of grass carp. A more comprehensive crisp grass carp transcriptome database was established. Several amino acid metabolism pathway that were closely related to meat quality were identified.
DOI: 10.6084/m9.figshare.25661804.v1
title: Identification of hub genes in meat quality of grass carp (<i>Ctenopharyngodon idellus</i>) fed with faba bean by muscle tissue transcriptomic analysis

description: Crisp grass carp is a type of grass carp (<i>Ctenopharyngodon idella</i>) that has been fed faba beans. Flesh quality and expression of muscle quality-related genes in muscle of grass carp were evaluated. Compared with ordinary grass carp, 1901 differentially expressed genes (DEGs) were up-regulated and 1628 DEGs were down-regulated in crisp grass carp. The GO analysis results showed that the DEGs were enriched in ribosomes and proteins. Kyoto Encyclopaedia of genes and genomes (KEGG) pathway analysis results showed that amino acid metabolism was closely related to meat quality. COX3, ACADS, ACAT1, ECHS1, EHHADH, HADHAA, HADH, HMGCL, MCCC1 and MCCC2 were the top 10 hub genes most closely associated with other nodes and showed a strong positive correlation. Hardness was positively correlated with the COX3, ECHS1, ACADS, ACAT1, HADHA, HADH, HMGCL and MCCC1. These results have been demonstrated to play important roles in clarifying the molecular mechanism of muscle firmness increase in crisp grass carp. Feeding faba bean meal improved texture parameters of grass carp. A more comprehensive crisp grass carp transcriptome database was established. Several amino acid metabolism pathway that were closely related to meat quality were identified.
DOI: 10.6084/m9.figshare.27600384.v1
title: Dietary supplementation with <i>Rehmannia glutinosa</i> catalpol improves broiler performance by regulating intestinal immune microenvironment

description: Plant extracts have been widely considered as a feed additive. <i>Rehmannia glutinosa</i> catalpol can promote the growth performance of the host, improve the immune response, and strengthen the intestinal barrier function of the host. The broilers were fed with <i>Rehmannia glutinosa</i> catalpol (0.01%), and the composition of caecum microbiota in broilers was explored by 16S rRNA gene sequencing. Finally, the changes of intestinal mucosa morphology and immune function were analysed by tissue staining and RT-qPCR. The proportion of thick-walled bacteria in the treatment group was higher than that in the control group. At the genus level, the relative abundance of <i>Faecalibacterium</i>, <i>Paraacteroides</i> and <i>Barnesiella</i> increased after the addition of <i>Rehmannia glutinosa</i> catalpol. The function prediction results of PICRUSt2 showed that the microbiota mainly participated in the biosynthesis and degradation/utilization/association pathway. The results of tissue staining and RT-qPCR showed that the caecum tissue morphology and immune barrier function of broilers were significantly improved after the addition of catalpol. The results of this study show that <i>Rehmannia glutinosa</i> catalpol in the diet may be beneficial to the intestinal health of broilers, which may be achieved by regulating the intestinal microbiota and enhancing the immune function of broilers. <i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could regulate the intestinal microbiota and its metabolic function of broiler<i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could improve intestinal immunity and barrier function of broiler<i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could improve the FCR of broiler by regulating intestinal morphology <i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could regulate the intestinal microbiota and its metabolic function of broiler <i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could improve intestinal immunity and barrier function of broiler <i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could improve the FCR of broiler by regulating intestinal morphology
DOI: 10.6084/m9.figshare.27958271.v1
title: What conservation insights can we drag from genome-wide SNPs data in Italian small goat breeds?

description: Italy is home to several indigenous goat breeds with great economic and cultural implications, but their genetic makeup remains largely unexplored. This study used the Illumina Goat SNP chip to genotype 142 samples from four Italian goat breeds: Capestrina, Fulva, Grigia Ciociara, and Bianca Monticellana. The genotypes were combined with genome-wide SNP data from 31 Italian breeds to evaluate the genetic profile of Lazio’s indigenous goats. After filtering, the dataset included 51,423 SNPs. Genetic structure and diversity were assessed using MDS, ADMIXTURE analysis and inbreeding coefficients. Focusing on the four Lazio breeds, we examined inbreeding levels (F<sub>ROH</sub>), effective population size (Ne), gene exchange, and runs of homozygosity islands (ROHi). The Bianca appeared highly inbred, whereas Fulva, Capestrina, and Grigia showed heterozygosity levels comparable to other breeds. The increased sample sizes highlighted changes in genetic composition, indeed, ADMIXTURE analysis revealed genetic substructures within Bianca and Fulva. The Ne was found to be declining, with Bianca having the lowest Ne, indicating high susceptibility to inbreeding and genetic drift. The NetView analysis identified two interconnected genetic groups corresponding to: Bianca and Fulva. Key contributors to genetic structure, representing ancestral genotypes, were identified, providing targets for conservation. Moreover, ROH analysis pinpointed individuals with excessive ROH and long homozygosity stretches, particularly in Capestrina and Bianca, which could be limited from breeding to preserve genetic diversity. Finally, ROHi revealed genes linked to coat colour, disease resistance, and heat stress tolerance. These conclusions emphasise the importance of local breeds in maintaining biodiversity and enhancing breeding strategies.
DOI: 10.6084/m9.figshare.c.3622355_d7
title: Additional file 3: Table S3. of A proteomic analysis of chondrogenic, osteogenic and tenogenic constructs from ageing mesenchymal stem cells

description: Presenting the proteins identified in PEAKS PTM using the human reviewed database. (XLSX 425 kb)
DOI: 10.6084/m9.figshare.c.3622355_d8
title: Additional file 8: Table S7. of A proteomic analysis of chondrogenic, osteogenic and tenogenic constructs from ageing mesenchymal stem cells

description: Presenting upstream log ratio molecule predicted activation p values of target molecules in the dataset. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.c.3622403_d1
title: MOESM1 of Analyzing the Chinese landscape in anti-diabetic drug research: leading knowledge production institutions and thematic communities

description: Additional file 1. Information of 430 institutes. The region information and all centrality measurements of 430 institutes are clearly presented.
DOI: 10.15468/dl.8xsbhn
title: Occurrence Download

description: A dataset containing 3377 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Medicago turbinata (L.) All."
 ]
}

 The dataset includes 3377 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033212-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3622403_d2
title: MOESM3 of Analyzing the Chinese landscape in anti-diabetic drug research: leading knowledge production institutions and thematic communities

description: Additional file 3. All keywords in each article. The keywords in different articles are listed, and their Chinese translation are also presented for reference.
DOI: 10.17863/cam.77496
title: Theoretical models of vaccinia virus strain Western Reserve protein E2

description: Theoretical models of vaccinia virus strain Western Reserve protein E2, as compared with the experimentally determined structure (PDB ID 7PHY) in the associated publication. Models were generated using AlphaFold2 and RoseTTAFols before deposition of the E2 crystal structure to the PDB. The template sequence was Vaccinia virus strain Western Reserve E2 protein (UniProt ID P21604; VACV_E2.fasta). The top 5 models produced by AlphaFold2 (ranked_0.pdb to ranked_4.pdb) and RoseTTAFold (RoseTTAFold_multimodel.pdb) are available, as are these models with the positional uncertainty of each residue converted into an estimated atomic displacement parameter using phenix.voyager and the ensembles of the E2 head and ring domains used for molecular replacement searches in the associated publication. For more information, see the README.txt file.
DOI: 10.6084/m9.figshare.25823072.v1
title: Genetic diversity and population structure of Canarian chicken using microsatellite DNA markers

description: The Canary Islands have historically been a crossway among at least three continents; therefore, the genetic influences on their local animal breeds have been extremely diverse. In the Canarian chicken population, genetic diversity is evident but it has never been studied. The aim of this study was to assess the population structure and genetic diversity within the Canarian chicken population, as well as between the Canarian chicken population, the Spanish local populations, and the commercial chicken populations with microsatellites, with a view to reinforce the official recognition of the breed, for the design and development of a conservation program. Blood samples were collected at random from 198 animals of the Canarian and compared with Spanish local and commercial strains, in order to determine differentiation and genetic relatedness. The five phenotypic varieties of Canarian chicken, the population structure and genetic diversity within the Canarian chicken population had a higher unbiased expected heterozygosity than the observed heterozygosity. Comparing the Canarian vs other local Spanish breeds and commercial strains, FST was relatively high (0.179) (0.164 – 0.195), the neighborhood network showed that the Canarian varieties did not cluster with the other Spanish breeds. The STRUCTURE, confirmed that the Rubilana variety differed from the other four Canary Islands. We conclude that the Canary Islands chicken population shows a differentiated genetic profile, versus other Spanish and cosmopolitan breeds. The theory that the existence of genetic varieties is based on the color of feathers was definitively discarded, except in the Rubilana population, which could be admitted as a genetically different variety. The Rubilana chicken variety appeared to be genetically differentiated from the other Canarian varieties.The Canarian varieties did not cluster with the other Spanish breeds.The theory of the existence of genetic varieties within the breed is discarded, except for the Rubilana population. The Rubilana chicken variety appeared to be genetically differentiated from the other Canarian varieties. The Canarian varieties did not cluster with the other Spanish breeds. The theory of the existence of genetic varieties within the breed is discarded, except for the Rubilana population.
DOI: 10.6084/m9.figshare.27958271
title: What conservation insights can we drag from genome-wide SNPs data in Italian small goat breeds?

description: Italy is home to several indigenous goat breeds with great economic and cultural implications, but their genetic makeup remains largely unexplored. This study used the Illumina Goat SNP chip to genotype 142 samples from four Italian goat breeds: Capestrina, Fulva, Grigia Ciociara, and Bianca Monticellana. The genotypes were combined with genome-wide SNP data from 31 Italian breeds to evaluate the genetic profile of Lazio’s indigenous goats. After filtering, the dataset included 51,423 SNPs. Genetic structure and diversity were assessed using MDS, ADMIXTURE analysis and inbreeding coefficients. Focusing on the four Lazio breeds, we examined inbreeding levels (F<sub>ROH</sub>), effective population size (Ne), gene exchange, and runs of homozygosity islands (ROHi). The Bianca appeared highly inbred, whereas Fulva, Capestrina, and Grigia showed heterozygosity levels comparable to other breeds. The increased sample sizes highlighted changes in genetic composition, indeed, ADMIXTURE analysis revealed genetic substructures within Bianca and Fulva. The Ne was found to be declining, with Bianca having the lowest Ne, indicating high susceptibility to inbreeding and genetic drift. The NetView analysis identified two interconnected genetic groups corresponding to: Bianca and Fulva. Key contributors to genetic structure, representing ancestral genotypes, were identified, providing targets for conservation. Moreover, ROH analysis pinpointed individuals with excessive ROH and long homozygosity stretches, particularly in Capestrina and Bianca, which could be limited from breeding to preserve genetic diversity. Finally, ROHi revealed genes linked to coat colour, disease resistance, and heat stress tolerance. These conclusions emphasise the importance of local breeds in maintaining biodiversity and enhancing breeding strategies.
DOI: 10.6084/m9.figshare.25823072
title: Genetic diversity and population structure of Canarian chicken using microsatellite DNA markers

description: The Canary Islands have historically been a crossway among at least three continents; therefore, the genetic influences on their local animal breeds have been extremely diverse. In the Canarian chicken population, genetic diversity is evident but it has never been studied. The aim of this study was to assess the population structure and genetic diversity within the Canarian chicken population, as well as between the Canarian chicken population, the Spanish local populations, and the commercial chicken populations with microsatellites, with a view to reinforce the official recognition of the breed, for the design and development of a conservation program. Blood samples were collected at random from 198 animals of the Canarian and compared with Spanish local and commercial strains, in order to determine differentiation and genetic relatedness. The five phenotypic varieties of Canarian chicken, the population structure and genetic diversity within the Canarian chicken population had a higher unbiased expected heterozygosity than the observed heterozygosity. Comparing the Canarian vs other local Spanish breeds and commercial strains, FST was relatively high (0.179) (0.164 – 0.195), the neighborhood network showed that the Canarian varieties did not cluster with the other Spanish breeds. The STRUCTURE, confirmed that the Rubilana variety differed from the other four Canary Islands. We conclude that the Canary Islands chicken population shows a differentiated genetic profile, versus other Spanish and cosmopolitan breeds. The theory that the existence of genetic varieties is based on the color of feathers was definitively discarded, except in the Rubilana population, which could be admitted as a genetically different variety. The Rubilana chicken variety appeared to be genetically differentiated from the other Canarian varieties.The Canarian varieties did not cluster with the other Spanish breeds.The theory of the existence of genetic varieties within the breed is discarded, except for the Rubilana population. The Rubilana chicken variety appeared to be genetically differentiated from the other Canarian varieties. The Canarian varieties did not cluster with the other Spanish breeds. The theory of the existence of genetic varieties within the breed is discarded, except for the Rubilana population.
DOI: 10.6084/m9.figshare.27600384
title: Dietary supplementation with <i>Rehmannia glutinosa</i> catalpol improves broiler performance by regulating intestinal immune microenvironment

description: Plant extracts have been widely considered as a feed additive. <i>Rehmannia glutinosa</i> catalpol can promote the growth performance of the host, improve the immune response, and strengthen the intestinal barrier function of the host. The broilers were fed with <i>Rehmannia glutinosa</i> catalpol (0.01%), and the composition of caecum microbiota in broilers was explored by 16S rRNA gene sequencing. Finally, the changes of intestinal mucosa morphology and immune function were analysed by tissue staining and RT-qPCR. The proportion of thick-walled bacteria in the treatment group was higher than that in the control group. At the genus level, the relative abundance of <i>Faecalibacterium</i>, <i>Paraacteroides</i> and <i>Barnesiella</i> increased after the addition of <i>Rehmannia glutinosa</i> catalpol. The function prediction results of PICRUSt2 showed that the microbiota mainly participated in the biosynthesis and degradation/utilization/association pathway. The results of tissue staining and RT-qPCR showed that the caecum tissue morphology and immune barrier function of broilers were significantly improved after the addition of catalpol. The results of this study show that <i>Rehmannia glutinosa</i> catalpol in the diet may be beneficial to the intestinal health of broilers, which may be achieved by regulating the intestinal microbiota and enhancing the immune function of broilers. <i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could regulate the intestinal microbiota and its metabolic function of broiler<i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could improve intestinal immunity and barrier function of broiler<i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could improve the FCR of broiler by regulating intestinal morphology <i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could regulate the intestinal microbiota and its metabolic function of broiler <i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could improve intestinal immunity and barrier function of broiler <i>λ</i> Dietary <i>Rehmannia glutinosa</i> catalpol could improve the FCR of broiler by regulating intestinal morphology
DOI: 10.6084/m9.figshare.c.3622403_d3
title: MOESM2 of Analyzing the Chinese landscape in anti-diabetic drug research: leading knowledge production institutions and thematic communities

description: Additional file 2. Tabular data of Fig.Â 3. All keywords in Fig.Â 3 are numbered by their frequency in each community, and the words in italics are research topic relevant to a given community than to other keywords and the bold words are more related to Chinese medicines.
DOI: 10.6084/m9.figshare.26367198
title: Effects of feeding enriched-olive cake on milk quality, metabolic response, and rumen fermentation and microbial composition in mid-lactating Holstein cows

description: The aim of this study was to evaluate the effects of supplementing OC enriched in polyphenols (EOC) to mid-lactating Holstein cows on milk quality, metabolic response, and rumen fermentation and microbiota. Twenty multiparous Holstein dairy cows (10 cows/group) were enrolled for 30 d in two homogeneous groups according to milk yield, days in milking, parity, and body condition score. The control group (CTR) received no supplemented concentrate, whereas the EOC group received concentrate with a 7% inclusion of EOC. Milk and blood samples were collected at 0 d and 30 d of treatment, while rumen fluid samples were collected after 30 d of treatment. Overall, the dietary supplementation of EOC did not affect milk yield and its quality, rumen pH, and rumen VFA. However, milk of EOC cows had lower C10:0, C12:0, C14:0, and C16:0 content, and greater C18:0, C18:1 cis-9, and C18:2 n6 content, compared with CTR cows. Regarding the rumen microbiota composition, EOC diet increased the relative abundance of <i>Bacteroidales_RF16_group</i>, <i>Absconditabacteriales_(SR1)</i>, and <i>Fibrobacteracea</i> in the rumen. On cow’s metabolism, EOC cows showed lower blood haptoglobin and greater ferric reducing antioxidant power (FRAP), cholesterol, and Zn levels compared with CTR cows. The supplementation of EOC led to a milder low-grade inflammatory response of cows and a positive modulation of cholesterol synthesis (probably at both intestinal and hepatic level). Supplementing EOC modulated rumen microbiota and improved the lipid profile of milk. Thereby, OC may be considered a valid feed to be included in the dairy cow’s diet leading to a positive effects on dairy cattle metabolism (less low-grade inflammatory response and oxidative stress) and at the same time giving an added value to the milk with a better profile of the fatty acids. Thanks to its nutritional properties, olive cake is a good alternative to conventional diet when integrated in the diet of dairy cattle, making animal production more sustainable. Diet supplemented with olive cake decreased milk medium-chain FAs C10:0, C12:0, C14:0 and C16:0, and increased long-chain FAs C18:0, C18:1 <i>cis-</i>9 and C18:2 n6 content. At animal level, it positively modulated rumen microbiota and it was able to increase blood cholesterol, Zn, and FRAP, and to decrease blood haptoglobin. Diet supplemented with olive cake clearly led to a milder inflammatory response of cows and improved the lipid profile of milk, being a good alternative to conventional feed.