cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25340/r4/mofyar
title: Related Data for: Bilingual children’s perceived family language policy and its contribution to leisure reading

description: This study investigated and compared family language policies (FLPs) from the perspectives of two groups of Singaporean bilingual children: 2,971 English-Chinese and 780 English-Malay children (aged 9–11 years). It also examined how different FLP components – namely, language beliefs, practices, and management – influenced their leisure reading enjoyment and reading amount. We found that although both groups of children attached equal importance to their two languages, their language practices tilted towards their stronger language, English. Both groups of children also reported different patterns of language management efforts at home. Regression analyses revealed differential effects of language beliefs, practices, and management on reading enjoyment and amount in the children’s two languages. For both groups and all languages, language beliefs explained the least amount of variance in reading enjoyment and amount compared to language practices and management. For English, language management accounted for more variance than language practices, whereas for the children’s weaker language (i.e., their ethnic language), both language management and language practices were significant predictors. Results emphasize the critical role of FLP in maintaining children’s ethnic languages. Therefore, it is imperative for parents, educators, and policymakers to identify and implement strategies to bolster language management and practices within the home and school environments.
DOI: 10.6084/m9.figshare.12129165
title: Association of three beta-defensin gene (AvBD4, AvBD5, AvBD14) polymorphisms with carrier-state susceptibility to salmonella in chickens

description: 1. Chicken salmonellosis is a common zoonotic infectious disease transmitted both vertically and horizontally. Avian beta-defensins (gallinacins) play an important role in the innate defence of the host and provide broad-spectrum immunity against multiple pathogens. 2. To detect the relationship between immune genes and salmonella carrier status and susceptibility to salmonellosis in chickens, polymorphisms with carrier-state susceptibility to salmonella and, hence, developing salmonellosis, were investigated in three avian beta-defensin genes <i>(AvBD4, AvBD5,</i> and <i>AvBD14)</i> in a Chinese local chicken breed, based on a case-control study. 3. Fifteen, twenty and nineteen SNPs were found in <i>AvBD4, AvBD5</i> and <i>AvBD14</i>, respectively. Among the 54 total SNPs, four resulted in non-synonymous substitution of amino acid changes. Five SNPs in <i>AvBD5</i> and four SNPs in <i>AvBD14</i> were significantly associated with salmonellosis susceptibility (P &lt; 0.05). Using the PHASE program, thirteen, ten and twelve major haplotypes were constructed in <i>AvBD4, AvBD5</i> and <i>AvBD14</i>. Logistic regression analysis revealed that five haplotypes in <i>AvBD5</i> and six haplotypes in <i>AvBD14</i> were significantly associated with salmonellosis susceptibility, but no significant haplotype in <i>AvBD4</i> was detected. A total of six strongly susceptible haplotypes with odds ratio (OR) values greater than 2.0 and four strongly resistant haplotypes with OR value less than 0.5 were revealed in the three genes examined. 4. These results suggested that the <i>AvBD5</i> and <i>AvBD14</i> genes may play an important role in the susceptibility to salmonellosis in chickens.
DOI: 10.6084/m9.figshare.11920728
title: Functional microRNA screening for dietary vitamin E regulation of abdominal fat deposition in broilers

description: 1. Functional microRNA (miRNA) screening for abdominal fat tissue with different dietary vitamin E (VE) levels was performed to reveal miRNAs, genes and metabolic pathways involved in abdominal fat deposition in broilers. 2. A total of 240, one-day-old healthy female chicks were randomly allocated into five dietary treatments containing either 0, 20, 50, 75 or 100 IU DL-α-tocopherol acetate. The sequencing of miRNAs from abdominal fat tissues was performed. The target genes of miRNAs were predicted and enrichment analysis for these genes was performed. Diets supplemented with 50 IU VE significantly diminished abdominal fat deposition in broilers at day 35 of age. 3. A total of 29 miRNAs were differentially expressed between control and 50 IU VE treatment. Ten of the 23 target genes were enriched in four signalling pathways: tight junction, SNARE interactions in vesicular transport, regulation of autophagy and proteasome. 4. This study identified miRNA, target genes and pathways in dietary VE treatment for broilers, providing new insights into the miRNA regulation of abdominal fat deposition in broilers.
DOI: 10.6084/m9.figshare.11920728.v2
title: Functional microRNA screening for dietary vitamin E regulation of abdominal fat deposition in broilers

description: 1. Functional microRNA (miRNA) screening for abdominal fat tissue with different dietary vitamin E (VE) levels was performed to reveal miRNAs, genes and metabolic pathways involved in abdominal fat deposition in broilers. 2. A total of 240, one-day-old healthy female chicks were randomly allocated into five dietary treatments containing either 0, 20, 50, 75 or 100 IU DL-α-tocopherol acetate. The sequencing of miRNAs from abdominal fat tissues was performed. The target genes of miRNAs were predicted and enrichment analysis for these genes was performed. Diets supplemented with 50 IU VE significantly diminished abdominal fat deposition in broilers at day 35 of age. 3. A total of 29 miRNAs were differentially expressed between control and 50 IU VE treatment. Ten of the 23 target genes were enriched in four signalling pathways: tight junction, SNARE interactions in vesicular transport, regulation of autophagy and proteasome. 4. This study identified miRNA, target genes and pathways in dietary VE treatment for broilers, providing new insights into the miRNA regulation of abdominal fat deposition in broilers.
DOI: 10.6084/m9.figshare.12129165.v3
title: Association of three beta-defensin gene (AvBD4, AvBD5, AvBD14) polymorphisms with carrier-state susceptibility to salmonella in chickens

description: 1. Chicken salmonellosis is a common zoonotic infectious disease transmitted both vertically and horizontally. Avian beta-defensins (gallinacins) play an important role in the innate defence of the host and provide broad-spectrum immunity against multiple pathogens. 2. To detect the relationship between immune genes and salmonella carrier status and susceptibility to salmonellosis in chickens, polymorphisms with carrier-state susceptibility to salmonella and, hence, developing salmonellosis, were investigated in three avian beta-defensin genes <i>(AvBD4, AvBD5,</i> and <i>AvBD14)</i> in a Chinese local chicken breed, based on a case-control study. 3. Fifteen, twenty and nineteen SNPs were found in <i>AvBD4, AvBD5</i> and <i>AvBD14</i>, respectively. Among the 54 total SNPs, four resulted in non-synonymous substitution of amino acid changes. Five SNPs in <i>AvBD5</i> and four SNPs in <i>AvBD14</i> were significantly associated with salmonellosis susceptibility (P &lt; 0.05). Using the PHASE program, thirteen, ten and twelve major haplotypes were constructed in <i>AvBD4, AvBD5</i> and <i>AvBD14</i>. Logistic regression analysis revealed that five haplotypes in <i>AvBD5</i> and six haplotypes in <i>AvBD14</i> were significantly associated with salmonellosis susceptibility, but no significant haplotype in <i>AvBD4</i> was detected. A total of six strongly susceptible haplotypes with odds ratio (OR) values greater than 2.0 and four strongly resistant haplotypes with OR value less than 0.5 were revealed in the three genes examined. 4. These results suggested that the <i>AvBD5</i> and <i>AvBD14</i> genes may play an important role in the susceptibility to salmonellosis in chickens.
DOI: 10.6084/m9.figshare.12146157
title: Recombinant lactobacillin PlnK adjusts the gut microbiome distribution in broilers

description: 1. The heterologous expression and biological function of the Lactobacillus bacteriocin plantaricin K (PlnK) remain largely unknown. 2. In this study, PlnK was efficiently expressed in competent <i>E. coli</i> BL21 (used in transformation and protein expression) after 12 h, at 37°C and in 0.4 mmol/l isopropyl β- d-1-thiogalactopyranoside (IPTG). 3. The inhibitory bacterial spectrum of recombinant PlnK was investigated and indicated that levels of PlnK above 0.10 mg/ml produced an obvious inhibitory effect on gram-positive bacteria and gram-negative bacteria <i>in vitro</i>. 4. The effects of PlnK on intestinal immune function and the gut microbiome distribution in broilers were studied. The results revealed that, after consuming 2.50 × 10<sup>˗3</sup> mg/ml of PlnK in water for one week, at the phylum level, the abundance of <i>Firmicutes</i> was increased and the abundance of <i>Bacleroidetes</i> was decreased. At the family level, the abundance of <i>Lachnospiraceae, Ruminococcaceae</i> and <i>Streptococcaceae</i> were significantly improved, but the abundance of <i>Bacteroidaceae</i> was reduced. At the genus level, the abundances of <i>Lachnoclostridium, Streptococcus</i> and <i>Ruminococcaceae</i>-UCG-013, were significantly up-regulated, and the abundance of <i>Bacteroides</i> was down-regulated. 5. After oral liquid intake of PlnK for one week, levels of secretory immunoglobulin A (sIgA) in the duodenal mucus were not significantly increased, but the mRNA levels of <i>TLR</i>3, <i>MDA</i>5, <i>IFN-α, IFN-β, IFITM</i>3 and <i>IFITM</i>10 in the duodenum were significantly reduced. 6. This study demonstrated that the recombinant PlnK could adjust the intestinal microbiome distribution and downregulate the IFN pathway.
DOI: 10.6084/m9.figshare.12146157.v2
title: Recombinant lactobacillin PlnK adjusts the gut microbiome distribution in broilers

description: 1. The heterologous expression and biological function of the Lactobacillus bacteriocin plantaricin K (PlnK) remain largely unknown. 2. In this study, PlnK was efficiently expressed in competent <i>E. coli</i> BL21 (used in transformation and protein expression) after 12 h, at 37°C and in 0.4 mmol/l isopropyl β- d-1-thiogalactopyranoside (IPTG). 3. The inhibitory bacterial spectrum of recombinant PlnK was investigated and indicated that levels of PlnK above 0.10 mg/ml produced an obvious inhibitory effect on gram-positive bacteria and gram-negative bacteria <i>in vitro</i>. 4. The effects of PlnK on intestinal immune function and the gut microbiome distribution in broilers were studied. The results revealed that, after consuming 2.50 × 10<sup>˗3</sup> mg/ml of PlnK in water for one week, at the phylum level, the abundance of <i>Firmicutes</i> was increased and the abundance of <i>Bacleroidetes</i> was decreased. At the family level, the abundance of <i>Lachnospiraceae, Ruminococcaceae</i> and <i>Streptococcaceae</i> were significantly improved, but the abundance of <i>Bacteroidaceae</i> was reduced. At the genus level, the abundances of <i>Lachnoclostridium, Streptococcus</i> and <i>Ruminococcaceae</i>-UCG-013, were significantly up-regulated, and the abundance of <i>Bacteroides</i> was down-regulated. 5. After oral liquid intake of PlnK for one week, levels of secretory immunoglobulin A (sIgA) in the duodenal mucus were not significantly increased, but the mRNA levels of <i>TLR</i>3, <i>MDA</i>5, <i>IFN-α, IFN-β, IFITM</i>3 and <i>IFITM</i>10 in the duodenum were significantly reduced. 6. This study demonstrated that the recombinant PlnK could adjust the intestinal microbiome distribution and downregulate the IFN pathway.
DOI: 10.6084/m9.figshare.12129165.v2
title: Association of polymorphisms in three beta-defensin genes (<i>AvBD4, AvBD5, AvBD14</i>) with carrier-state susceptibility to salmonella in chickens

description: 1. Chicken salmonellosis is a common zoonotic infectious disease transmitted both vertically and horizontally. Avian beta-defensins (gallinacins) play an important role in the innate defence of the host and provide broad-spectrum immunity against multiple pathogens. 2. To detect the relationship between immune genes and salmonella carrier status and susceptibility to salmonellosis in chickens, polymorphisms with carrier-state susceptibility to salmonella and, hence, developing salmonellosis, were investigated in three avian beta-defensin genes <i>(AvBD4, AvBD5,</i> and <i>AvBD14)</i> in a Chinese local chicken breed, based on a case-control study. 3. Fifteen, twenty and nineteen SNPs were found in <i>AvBD4, AvBD5</i> and <i>AvBD14</i>, respectively. Among the 54 total SNPs, four resulted in non-synonymous substitution of amino acid changes. Five SNPs in <i>AvBD5</i> and four SNPs in <i>AvBD14</i> were significantly associated with salmonellosis susceptibility (P &lt; 0.05). Using the PHASE program, thirteen, ten and twelve major haplotypes were constructed in <i>AvBD4, AvBD5</i> and <i>AvBD14</i>. Logistic regression analysis revealed that five haplotypes in <i>AvBD5</i> and six haplotypes in <i>AvBD14</i> were significantly associated with salmonellosis susceptibility, but no significant haplotype in <i>AvBD4</i> was detected. A total of six strongly susceptible haplotypes with odds ratio (OR) values greater than 2.0 and four strongly resistant haplotypes with OR value less than 0.5 were revealed in the three genes examined. 4. These results suggested that the <i>AvBD5</i> and <i>AvBD14</i> genes may play an important role in the susceptibility to salmonellosis in chickens.
DOI: 10.6084/m9.figshare.12129267
title: Temperature-sensitive pathways may be involved in duck embryonic developmental recovery from blastoderm dormancy during hatching

description: 1. Birds’ newly oviposited blastoderms can survive several weeks in a dormant state during low-temperature storage. Previous studies demonstrated that there is a critical temperature range from 19 to 27°C for chicken embryos. Within this range, the embryo will diapause in a dormant state; once the temperature rises above this range, the blastoderm will break dormancy. 2. Clarifying the mechanism that initiates duck embryo developmental recovery from blastoderm dormancy will be helpful to change temperature control to improve hatching in poultry production. It was hypothesised that there might be some temperature-sensitive genes involved in initiating duck embryo developmental recovery from blastoderm dormancy. 3. To test this hypothesis, the transcriptome of the newly oviposited duck blastoderm and duck embryo (incubated for 48 hours) were sequenced to screen for differentially expressed genes with functions that had been predicted by bioinformatics. 4. The results showed that there were 2416 differentially expressed genes between the two groups, 53 of which were involved in temperature-sensitive pathways. The protein-protein interaction network combined these 53 temperature-sensitive genes and another group of 65 genes, which enriched the development pathway. These results suggested that temperature-sensitive genes may be involved in growth and development related pathways.
DOI: 10.6084/m9.figshare.12129267.v2
title: Temperature-sensitive pathways may be involved in duck embryonic developmental recovery from blastoderm dormancy during hatching

description: 1. Birds’ newly oviposited blastoderms can survive several weeks in a dormant state during low-temperature storage. Previous studies demonstrated that there is a critical temperature range from 19 to 27°C for chicken embryos. Within this range, the embryo will diapause in a dormant state; once the temperature rises above this range, the blastoderm will break dormancy. 2. Clarifying the mechanism that initiates duck embryo developmental recovery from blastoderm dormancy will be helpful to change temperature control to improve hatching in poultry production. It was hypothesised that there might be some temperature-sensitive genes involved in initiating duck embryo developmental recovery from blastoderm dormancy. 3. To test this hypothesis, the transcriptome of the newly oviposited duck blastoderm and duck embryo (incubated for 48 hours) were sequenced to screen for differentially expressed genes with functions that had been predicted by bioinformatics. 4. The results showed that there were 2416 differentially expressed genes between the two groups, 53 of which were involved in temperature-sensitive pathways. The protein-protein interaction network combined these 53 temperature-sensitive genes and another group of 65 genes, which enriched the development pathway. These results suggested that temperature-sensitive genes may be involved in growth and development related pathways.
DOI: 10.6084/m9.figshare.12146157.v1
title: Recombinant lactobacillin PlnK adjusts the gut microbiome distribution in broilers

description: 1. The heterologous expression and biological function of the Lactobacillus bacteriocin plantaricin K (PlnK) remain largely unknown. 2. In this study, PlnK was efficiently expressed in competent <i>E. coli</i> BL21 (used in transformation and protein expression) after 12 h, at 37℃ and in 0.4 mmol/l isopropyl β- d-1-thiogalactopyranoside (IPTG). 3. The inhibitory bacterial spectrum of recombinant PlnK was investigated and indicated that levels of PlnK above 0.10 mg/ml produced an obvious inhibitory effect on gram-positive bacteria and gram-negative bacteria <i>in vitro</i>. 4. The effects of PlnK on intestinal immune function and the gut microbiome distribution in broilers were studied. The results revealed that, after consuming 2.50×10<sup>˗3</sup> mg/ml of PlnK in water for one week, at the phylum level, the abundance of <i>Firmicutes</i> was increased and the abundance of <i>Bacleroidetes</i> was decreased. At the family level, the abundance of <i>Lachnospiraceae, Ruminococcaceae</i> and <i>Streptococcaceae</i> were significantly improved, but the abundance of <i>Ruminococcaceae</i> was reduced. At the genus level, the abundances of <i>Lachnoclostridium, Streptococcus</i> and <i>Ruminococcaceae</i>-UCG-013, were significantly up-regulated, and the abundance of <i>Bacteroides</i> was down-regulated. 5. After oral liquid intake of PlnK for one week, levels of secretory immunoglobulin A (sIgA) in the duodenal mucus were not significantly increased, but the mRNA levels of <i>TLR</i>3, <i>MDA</i>5, <i>IFN-α, IFN-β, IFITM</i>3 and <i>IFITM</i>10 in the duodenum were significantly reduced. 6. This study demonstrated that the recombinant PlnK could adjust the intestinal microbiome distribution and downregulate the IFN pathway.
DOI: 10.6084/m9.figshare.11941509
title: Identification of differentially expressed genes associated with egg production in black-boned chicken

description: 1. Muchuan black-bone chicken is well known in China for its meat quality and medicinal properties; however, its egg-laying performance is not ideal. To better understand the molecular mechanisms of black-boned chicken egg-laying, high-throughput RNA sequencing was performed to compare differences in the pituitary transcriptome between three high-rate (group H) and three low-rate (group L) egg production chickens. 2. In total, 171 differentially expressed genes (DEGs) were identified between the two groups, of which 113 were upregulated and 58 were downregulated in group L. Some of these genes are known to be related to hormone secretion or the regulation of reproductive processes; these include prolactin-releasing hormone (<i>PRLH</i>), distal-less homeobox 6 (<i>DLX6</i>), interferon regulatory factor 4 (<i>IRF4</i>), and cilia and flagella associated protein 69 (<i>CFAP69</i>). Notably, expression pattern analysis indicated that both <i>PRLH</i> and <i>DLX6</i> may influence egg-laying performance. 3. The dataset provided a foundation for discovering important genes and pathways involved in the chicken egg-laying process, and may help to improve understanding of the molecular mechanisms of chicken reproduction.
DOI: 10.6084/m9.figshare.11941509.v1
title: Identification of differentially expressed genes associated with egg production in black-boned chicken

description: 1. Muchuan black-bone chicken is well known in China for its meat quality and medicinal properties; however, its egg-laying performance is not ideal. To better understand the molecular mechanisms of black-boned chicken egg-laying, high-throughput RNA sequencing was performed to compare differences in the pituitary transcriptome between three high-rate (group H) and three low-rate (group L) egg production chickens. 2. In total, 171 differentially expressed genes (DEGs) were identified between the two groups, of which 113 were upregulated and 58 were downregulated in group L. Some of these genes are known to be related to hormone secretion or the regulation of reproductive processes; these include prolactin-releasing hormone (<i>PRLH</i>), distal-less homeobox 6 (<i>DLX6</i>), interferon regulatory factor 4 (<i>IRF4</i>), and cilia and flagella associated protein 69 (<i>CFAP69</i>). Notably, expression pattern analysis indicated that both <i>PRLH</i> and <i>DLX6</i> may influence egg-laying performance. 3. The dataset provided a foundation for discovering important genes and pathways involved in the chicken egg-laying process, and may help to improve understanding of the molecular mechanisms of chicken reproduction.
DOI: 10.6084/m9.figshare.11941509.v2
title: Identification of differentially expressed genes associated with egg production in black-boned chicken

description: 1. Muchuan black-bone chicken is well known in China for its meat quality and medicinal properties; however, its egg-laying performance is not ideal. To better understand the molecular mechanisms of black-boned chicken egg-laying, high-throughput RNA sequencing was performed to compare differences in the pituitary transcriptome between three high-rate (group H) and three low-rate (group L) egg production chickens. 2. In total, 171 differentially expressed genes (DEGs) were identified between the two groups, of which 113 were upregulated and 58 were downregulated in group L. Some of these genes are known to be related to hormone secretion or the regulation of reproductive processes; these include prolactin-releasing hormone (<i>PRLH</i>), distal-less homeobox 6 (<i>DLX6</i>), interferon regulatory factor 4 (<i>IRF4</i>), and cilia and flagella associated protein 69 (<i>CFAP69</i>). Notably, expression pattern analysis indicated that both <i>PRLH</i> and <i>DLX6</i> may influence egg-laying performance. 3. The dataset provided a foundation for discovering important genes and pathways involved in the chicken egg-laying process, and may help to improve understanding of the molecular mechanisms of chicken reproduction.
DOI: 10.5281/zenodo.8434007
title: Hydrogen Isotope Fingerprinting of Lipid Biomarkers in the Chinese Marginal Seas-Data

description: Hydrogen isotope data for lipid biomarkers extracted from surface sediments of the Chinese marginal seas.
DOI: 10.57841/casdc.0002876
title: 基于吸附效应和空间限域效应的高活性、高固溴能力的类层状电极在溴基液流电池中的应用
DOI: 10.5281/zenodo.8434006
title: Hydrogen Isotope Fingerprinting of Lipid Biomarkers in the Chinese Marginal Seas-Data

description: Hydrogen isotope data for lipid biomarkers extracted from surface sediments of the Chinese marginal seas.
DOI: 10.5281/zenodo.8303282
title: 2023 ASI OzSingleCell System Immunology Hackathon Dataset

description: Dataset for the 2023 ASI OzSingleCell System Immunology hackathon. The hackathon aims to bring together experimental (wet-lab) and computational (dry-lab) scientists working in the field of clonal biology, including those working with single-cell technologies like lentiviral barcoding, BCR/TCR clonotyping, and mitochondrial lineage tracing. Others from disparate fields such as UX/UI engineers, AI/ML, deep learning, graph neural networks, computer vision or image preprocessing, causal inference are also encouraged to attend. Data challenges may involve developing new methods for intra-/inter-clonal gene expression signatures, data architecture of clonotype information, or data visualisation. More information is available on our website: https://2023-asi-ozsinglecell-hackathon.github.io/system-immunology-hackathon/