cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13020075.v1
title: Variations of the <i>Escherichia coli</i> population in the digestive tract of broilers

description: We explored the between-group and temporal variations in the intestinal <i>Escherichia coli</i> populations of broilers under experimental conditions, taking both antimicrobial resistance and virulence into consideration. Four replicates of 45 commercial chicks were reared in four animal facilities. On their first day of life (Day 0), they were orally inoculated with two extended-spectrum-cephalosporin-resistant (ESCR) <i>E. coli</i> (2.72 log<sub>10</sub> CFU of a <i>bla</i><sub>CMY-2-</sub> and 2.55 log<sub>10</sub> CFU of a <i>bla</i><sub>CTX-M-</sub>carrying <i>E. coli</i>). Faecal samples were then collected weekly and caecal samples were obtained from birds sacrificed on Days 21 or 42. The total, ESC-, ciprofloxacin- and gentamicin-resistant <i>E. coli</i> populations were enumerated on MacConkey (MC) and MC-supplemented media, and eight virulence-associated genes (VAGs) (<i>iroN, iutA, iss, ompT, hlyF, vat</i>, <i>frz<sub>orf4</sub></i>, and <i>fyuA</i>) were sought by PCR on isolates obtained on MC agar. The results showed significant between-group differences in the size of the resistant sub-populations and the presence of VAGs. Contrary to <i>bla</i><sub>CTX-M</sub>-positive strains, <i>bla</i><sub>CMY</sub>-positive strains persisted up to Day 42, but represented only a minor fraction of the total <i>E. coli</i> population. The ESC-, gentamicin- and ciprofloxacin-resistant populations decreased over time. Isolates obtained during the first week contained a mean of 5.1 VAGs. The percentages of some VAG profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. The fluctuations or differences between <i>E. coli</i> isolates according to group, age, and faecal or caecal origin need to be considered when designing experimental protocols and seeking to improve colibacillosis control. <b>RESEARCH HIGHLIGHTS</b>Temporal variations in the intestinal <i>E. coli</i> populations of broilers was studied.The antibiotic-resistant populations decreased over time.Virulence profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42.Strains with the highest numbers of virulence genes were present during the first days. Temporal variations in the intestinal <i>E. coli</i> populations of broilers was studied. The antibiotic-resistant populations decreased over time. Virulence profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. Strains with the highest numbers of virulence genes were present during the first days.
DOI: 10.6084/m9.figshare.13186857.v1
title: Experimental infection of domestic geese (<i>Anser anser var. domesticus</i>) with H5N8 Gs/GD and H7N1 highly pathogenic avian influenza viruses

description: Prior to the emergence of the Asian-origin H5 Goose/Guangdong/1/96 (Gs/GD) lineage, highly pathogenic avian influenza viruses (HPAIV) had rarely caused high mortalities in domestic geese. In 2016/2017 European epidemics, H5N8 Gs/GD clade 2.3.4.4 Group B produced an unprecedented number of outbreaks in waterfowl holdings. In this study, the pathogenesis of H5N8 HPAIV in comparison with H7N1 HPAIV, and the role of domestic geese in the epidemiology of these viruses, were evaluated. Local and commercial geese (<i>Anser anser var. domesticus</i>) were intranasally inoculated with 10<sup>5</sup> ELD<sub>50</sub> of A/goose/Spain/IA17CR02699/2017 (H5N8) or A/Chicken/Italy/5093/1999 (H7N1) and monitored daily during 15 days. H5N8 was highly virulent to domestic geese, reaching 100% mortality by 10 days post-infection. Systemic microscopic necrotizing lesions associated with widespread AIV-antigen were detected by IHC techniques, the central nervous system being the most severely affected. High viral loads, measured by qRT-PCR, were present in all samples collected: oral and cloacal swabs, plasma tissues, and moderate levels in pool water. Domestic geese were also susceptible to H7N1 infection, as demonstrated by seroconversion and detection of viral RNA in tissues and plasma in some geese, but all lacked clinical signs. Viral shedding was confirmed in only some geese and was restricted to the oral route, but levels were high and still detected at the end of the study. Overall, H7N1 presents a lower lethality and shedding than H5N8 in geese; however, the viral shedding indicates that these species could play a role in the epidemiology of Gs/GD and other lineages of HPAIVs. <b>RESEARCH HIGHLIGHTS</b>H5N8 Gs/GD clade 2.3.4.4 Group B is highly virulent to domestic geese.The severity of H5N8 is associated with multisystemic replication.H7N1 can infect domestic geese but is avirulent to this species.Domestic geese could play a role in the epidemiology of Gs/GD HPAIVs. H5N8 Gs/GD clade 2.3.4.4 Group B is highly virulent to domestic geese. The severity of H5N8 is associated with multisystemic replication. H7N1 can infect domestic geese but is avirulent to this species. Domestic geese could play a role in the epidemiology of Gs/GD HPAIVs.
DOI: 10.6084/m9.figshare.13020075
title: Variations of the <i>Escherichia coli</i> population in the digestive tract of broilers

description: We explored the between-group and temporal variations in the intestinal <i>Escherichia coli</i> populations of broilers under experimental conditions, taking both antimicrobial resistance and virulence into consideration. Four replicates of 45 commercial chicks were reared in four animal facilities. On their first day of life (Day 0), they were orally inoculated with two extended-spectrum-cephalosporin-resistant (ESCR) <i>E. coli</i> (2.72 log<sub>10</sub> CFU of a <i>bla</i><sub>CMY-2-</sub> and 2.55 log<sub>10</sub> CFU of a <i>bla</i><sub>CTX-M-</sub>carrying <i>E. coli</i>). Faecal samples were then collected weekly and caecal samples were obtained from birds sacrificed on Days 21 or 42. The total, ESC-, ciprofloxacin- and gentamicin-resistant <i>E. coli</i> populations were enumerated on MacConkey (MC) and MC-supplemented media, and eight virulence-associated genes (VAGs) (<i>iroN, iutA, iss, ompT, hlyF, vat</i>, <i>frz<sub>orf4</sub></i>, and <i>fyuA</i>) were sought by PCR on isolates obtained on MC agar. The results showed significant between-group differences in the size of the resistant sub-populations and the presence of VAGs. Contrary to <i>bla</i><sub>CTX-M</sub>-positive strains, <i>bla</i><sub>CMY</sub>-positive strains persisted up to Day 42, but represented only a minor fraction of the total <i>E. coli</i> population. The ESC-, gentamicin- and ciprofloxacin-resistant populations decreased over time. Isolates obtained during the first week contained a mean of 5.1 VAGs. The percentages of some VAG profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. The fluctuations or differences between <i>E. coli</i> isolates according to group, age, and faecal or caecal origin need to be considered when designing experimental protocols and seeking to improve colibacillosis control. <b>RESEARCH HIGHLIGHTS</b>Temporal variations in the intestinal <i>E. coli</i> populations of broilers was studied.The antibiotic-resistant populations decreased over time.Virulence profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42.Strains with the highest numbers of virulence genes were present during the first days. Temporal variations in the intestinal <i>E. coli</i> populations of broilers was studied. The antibiotic-resistant populations decreased over time. Virulence profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. Strains with the highest numbers of virulence genes were present during the first days.
DOI: 10.5281/zenodo.4735169
title: Bertia moriformis SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735168
title: Bertia moriformis SPAdes preassembly

description: .
DOI: 10.6084/m9.figshare.14531556.v1
title: Kitchen_outlet_winGRU_saved_model

description: Window GRU trained model for Kitchen outlet
DOI: 10.6084/m9.figshare.14531556
title: Kitchen_outlet_winGRU_saved_model

description: Window GRU trained model for Kitchen outlet
DOI: 10.5281/zenodo.4735237
title: Bolitophila cinerea SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735236
title: Bolitophila cinerea SPAdes preassembly

description: .
DOI: 10.6084/m9.figshare.14531589
title: Dishwasher_winGRU_saved_model

description: WindowGRU trained model for dishwasher
DOI: 10.5281/zenodo.4735277
title: Boulengeromyrus knoepffleri SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735276
title: Boulengeromyrus knoepffleri SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735269
title: Early Maladaptive Schemas and Self-Stigma in People with Physical Disabilities. The Role of Self-Compassion and Psychological Flexibility

description: Dataset for a research project "Early Maladaptive Schemas and Self-Stigma in People with Physical Disabilities. The Role of Self-Compassion and Psychological Flexibility".
DOI: 10.5281/zenodo.4735268
title: Early Maladaptive Schemas and Self-Stigma in People with Physical Disabilities. The Role of Self-Compassion and Psychological Flexibility

description: Dataset for a research project "Early Maladaptive Schemas and Self-Stigma in People with Physical Disabilities. The Role of Self-Compassion and Psychological Flexibility".
DOI: 10.5517/ccdc.csd.cc26nbdm
title: CCDC 2045330: Experimental Crystal Structure Determination

description: Related Article: Duygu Barut Celepci, Beyhan Yiğit, Murat Yiğit, İsmail Özdemir, Muhittin Aygün|2021|J.Mol.Struct.|1239|130460|doi:10.1016/j.molstruc.2021.130460
DOI: 10.5517/ccdc.csd.cc26nbgp
title: CCDC 2045332: Experimental Crystal Structure Determination

description: Related Article: Duygu Barut Celepci, Beyhan Yiğit, Murat Yiğit, İsmail Özdemir, Muhittin Aygün|2021|J.Mol.Struct.|1239|130460|doi:10.1016/j.molstruc.2021.130460
DOI: 10.5281/zenodo.4735307
title: Brevimyrus niger SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735306
title: Brevimyrus niger SPAdes preassembly

description: .
DOI: 10.6084/m9.figshare.14531607
title: microwave_winGRU_saved_model

description: WindowGRU trained model for Microwave
DOI: 10.5281/zenodo.4729050
title: Supporting data for the manuscript "Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing"

description: Supporting data for the manuscript titled "Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing". The archive includes (i) metaFlye assmeblies and graphs for HiFi and CLR datasets. (ii) HiFi and CLR3 bins/MAGs produced using bin3C / DAS_Tool, (iii) HiFi MAG taxonomy identifications and completeness info.
DOI: 10.5281/zenodo.4735370
title: Brienomyrus brachyistius SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4735369
title: Brienomyrus brachyistius SPAdes preassembly

description: .
DOI: 10.5519/qd.0hkz9geb
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1001 records)
DOI: 10.34740/kaggle/ds/1295752
title: Tree Of Life
DOI: 10.5281/zenodo.4603428
title: Multi-model-median regional means at warming levels for selected indices (CMIP6)

description: Document multi-model-median regional means at warming levels for selected indices (CMIP6).
DOI: 10.5281/zenodo.4603427
title: Multi-model-median regional means at warming levels for selected indices (CMIP6)

description: Document multi-model-median regional means at warming levels for selected indices (CMIP6).
DOI: 10.6084/m9.figshare.12848038
title: Whole-genome resequencing of Dulong Chicken reveal signatures of selection

description: 1. Dulong Chickens (DLCs) live at high altitude (~3000 m) and humidity (~90%), are endemic to the Yunnan province, and have gradually developed unique physiological characteristics, but their genetic basis is still unclear. Using the fixation index (<i>F<sub>ST</sub></i>) approach, based on whole-genome resequencing, DLCs were analysed to uncover the genomic architecture of the population and candidate genes involved in selection during domestication. 2. A total of 469 candidate genes were obtained to be putatively under selection in DLCs. Further investigations revealed the genic footprint for local adaptation (high-altitude and high-humidity) as the genic signatures that are involved in economic traits (related to egg production). 3. Candidate genes were identified that may be associated with disease resistance, aggressiveness, small body size and positive selection of vision in DLCs. 4. These data revealed loci of selective signals that operate during selection for production at high altitude and humidity.
DOI: 10.6084/m9.figshare.12848038.v2
title: Whole-genome resequencing of Dulong Chicken reveal signatures of selection

description: 1. Dulong Chickens (DLCs) live at high altitude (~3000 m) and humidity (~90%), are endemic to the Yunnan province, and have gradually developed unique physiological characteristics, but their genetic basis is still unclear. Using the fixation index (<i>F<sub>ST</sub></i>) approach, based on whole-genome resequencing, DLCs were analysed to uncover the genomic architecture of the population and candidate genes involved in selection during domestication. 2. A total of 469 candidate genes were obtained to be putatively under selection in DLCs. Further investigations revealed the genic footprint for local adaptation (high-altitude and high-humidity) as the genic signatures that are involved in economic traits (related to egg production). 3. Candidate genes were identified that may be associated with disease resistance, aggressiveness, small body size and positive selection of vision in DLCs. 4. These data revealed loci of selective signals that operate during selection for production at high altitude and humidity.
DOI: 10.6084/m9.figshare.13049587
title: Identification of differentially expressed genes and signalling pathways in the ovary of higher and lower laying ducks

description: 1. Ovarian transcriptomic profiling between birds showing high egg number (HEN) and birds of low egg number (LEN) in Longyan Shan-ma ducks at 71 weeks of age was carried out using Illumina Hiseq 2500 technology. 2. A total of 343 differentially expressed genes (DEGs, 269 upregulated and 74 downregulated) were identified between HEN and LEN ovaries. These DEGs were enriched in 30 Gene Ontology terms. Pathway functional analysis found that the DEGs were enriched in 10 metabolic pathways (P Q 3. Three integrin family genes, <i>ITGB2, ITGB5</i> and <i>ITGA8</i> were differentially expressed in the RNA-seq and qPCR experiments. 4. The DEGs and signalling pathways identified in ovarian tissue in this study provide new insights into high egg production in Longyan Shan-ma duck.
DOI: 10.6084/m9.figshare.11566755
title: Identification of key microRNAs affecting melanogenesis of breast muscle in Muchuan black-boned chickens by RNA sequencing

description: 1. Melanin content is considered an important indicator of meat quality in black-boned chickens, which have a high market value. To understand the complex physiological processes underlying muscle melanogenesis in this chicken, differentially expressed miRNAs (DEMs) were detected between black muscle (BM) and white muscle (WM) of chickens using high-throughput sequencing technology. Six small RNA libraries were constructed, and more than 16.75 million clean reads were obtained for each library. 2. A total of 582 known miRNAs and 65 novel miRNAs were identified from the six chicken sequence libraries. A total of 19 DEMs were identified between the two groups, of which nine were upregulated and 10 were downregulated. Furthermore, the DEMs were predicted to target 572 genes. 3. Certain DEMs (such as miR-204, miR-133b, and miR-12 229-3p) and their target genes may play an important role in muscle melanogenesis of chickens. These findings provide a foundation for clarifying the miRNA regulatory mechanisms involved in muscle pigmentation in avian species.
DOI: 10.6084/m9.figshare.13049587.v2
title: Identification of differentially expressed genes and signalling pathways in the ovary of higher and lower laying ducks

description: 1. Ovarian transcriptomic profiling between birds showing high egg number (HEN) and birds of low egg number (LEN) in Longyan Shan-ma ducks at 71 weeks of age was carried out using Illumina Hiseq 2500 technology. 2. A total of 343 differentially expressed genes (DEGs, 269 upregulated and 74 downregulated) were identified between HEN and LEN ovaries. These DEGs were enriched in 30 Gene Ontology terms. Pathway functional analysis found that the DEGs were enriched in 10 metabolic pathways (P Q 3. Three integrin family genes, <i>ITGB2, ITGB5</i> and <i>ITGA8</i> were differentially expressed in the RNA-seq and qPCR experiments. 4. The DEGs and signalling pathways identified in ovarian tissue in this study provide new insights into high egg production in Longyan Shan-ma duck.
DOI: 10.6084/m9.figshare.11566755.v1
title: Identification of key microRNAs affecting melanogenesis of breast muscle in Muchuan black-boned chickens by RNA sequencing

description: 1. Melanin content is considered an important indicator of meat quality in black-boned chickens, which have a high market value. To understand the complex physiological processes underlying muscle melanogenesis in this chicken, differentially expressed miRNAs (DEMs) were detected between black muscle (BM) and white muscle (WM) of chickens using high-throughput sequencing technology. Six small RNA libraries were constructed, and more than 16.75 million clean reads were obtained for each library. 2. A total of 582 known miRNAs and 65 novel miRNAs were identified from the six chicken sequence libraries. A total of 19 DEMs were identified between the two groups, of which nine were upregulated and 10 were downregulated. Furthermore, the DEMs were predicted to target 572 genes. 3. Certain DEMs (such as miR-204, miR-133b, and miR-12229-3p) and their target genes may play an important role in muscle melanogenesis of chickens. These findings provide a foundation for clarifying the miRNA regulatory mechanisms involved in muscle pigmentation in avian species.
DOI: 10.6084/m9.figshare.13318430
title: Proteomic analysis of liver tissue between fat and lean broiler lines

description: 1. The liver is the major site of fatty acid synthesis in chickens. Lipid metabolism in the liver correlates with the deposition of triglycerides in adipose tissue. Northeast Agricultural University broilers lines divergently selected for abdominal fat content (NEAUHLF) provide a unique model to study the mechanisms of fat deposition. 2. In previous studies, differentially expressed genes (DEGs) in the livers of fat and lean broilers were evaluated across different developmental stages. Whether protein expression differences exist between the livers of fat and lean broilers is largely unknown. The current experiment used 2D fluorescence difference gel electrophoresis (2D-DIGE) to screen expressed protein (DEP) spots in the liver tissues of NEAUHLF at one, four and seven weeks of age. 3. Twenty-two DEPs were identified by MALDI-TOF-MS that were involved in lipid, energy, protein and amino acid metabolism, oxidative stress, cytoskeleton, and transport. 4. These data furthered the understanding of the fat and lean phenotypes of broiler chickens.
DOI: 10.6084/m9.figshare.13318430.v2
title: Proteomic analysis of liver tissue between fat and lean broiler lines

description: 1. The liver is the major site of fatty acid synthesis in chickens. Lipid metabolism in the liver correlates with the deposition of triglycerides in adipose tissue. Northeast Agricultural University broilers lines divergently selected for abdominal fat content (NEAUHLF) provide a unique model to study the mechanisms of fat deposition. 2. In previous studies, differentially expressed genes (DEGs) in the livers of fat and lean broilers were evaluated across different developmental stages. Whether protein expression differences exist between the livers of fat and lean broilers is largely unknown. The current experiment used 2D fluorescence difference gel electrophoresis (2D-DIGE) to screen expressed protein (DEP) spots in the liver tissues of NEAUHLF at one, four and seven weeks of age. 3. Twenty-two DEPs were identified by MALDI-TOF-MS that were involved in lipid, energy, protein and amino acid metabolism, oxidative stress, cytoskeleton, and transport. 4. These data furthered the understanding of the fat and lean phenotypes of broiler chickens.
DOI: 10.6084/m9.figshare.13318430.v1
title: Proteomic analysis of liver tissue between fat and lean broiler lines

description: 1. The liver is the major site of fatty acid synthesis in chickens. Lipid metabolism in the liver correlates with the deposition of triglycerides in adipose tissue. Northeast Agricultural University broilers lines divergently selected for abdominal fat content (NEAUHLF) provide a unique model to study the mechanisms of fat deposition. 2. In previous studies, differentially expressed genes (DEGs) in the livers of fat and lean broilers were evaluated across different developmental stages. Whether protein expression differences exist between the livers of fat and lean broilers is largely unknown. The current experiment used 2D fluorescence difference gel electrophoresis (2D-DIGE) to screen expressed protein (DEP) spots in the liver tissues of NEAUHLF at one, four and seven weeks of age. 3. Twenty-two DEPs were identified by MALDI-TOF-MS that were involved in lipid, energy, protein and amino acid metabolism, oxidative stress, cytoskeleton, and transport. 4. These data furthered the understanding of the fat and lean phenotypes of broiler chickens.
DOI: 10.6084/m9.figshare.12906086
title: Molecular cloning, tissue expression and polymorphism analysis of the Caveolin-3 gene in ducks

description: 1. Duck meat is considered a delicacy, but choosing the best meat is problematic. Caveolin-3 (<i>CAV-3</i>) is a muscle-specific protein marker in animals. The goal of the current study was to detect the characteristics of <i>CAV-3</i> gene in ducks. 2. Full-length <i>CAV-3</i> was acquired from ducks (<i>Anas platyrhynchos)</i> using reverse transcriptase PCR and rapid amplification of cDNA ends. DNAMAN software was used for homology comparisons. Quantitative reverse transcription-PCR, PCR-single-strand conformation polymorphism, and sequencing were used to determine <i>CAV-3</i> expression and polymorphism of a single nucleotide, respectively. The study examined four types of ducks, including Jinding, Chaohu, Cherry Valley, and Gaoyou ducks. 3. The study acquired 1066 bp of <i>CAV-3</i> cDNA sequences, including a 456 bp complete open reading frame encoding 151 amino acids. Both coding sequences (CDSs) and translated amino acids exhibited highest homology with <i>Gallus gallus</i> (CDS homology 91.67%, amino acids 94.04%), followed by mammalian species (CDS homology 79.0%, amino acids 78.0%). Single nucleotide polymorphism analysis revealed five mutations in exons (A489G, G501A, A557G, T563A, and A602G), and a C805T mutation in an intron. Among amplified polymorphic loci detected using primer 2, allele frequency was higher for A (489A501G507A563T602A) than B (489G501G507G563T602C) or C (489G501A507G563A602C). The highest occurred in Cherry Valley ducks (0.7587). Using primer 4, the M allele frequency was higher than that of the N allele. <i>CAV-3</i> was most highly expressed in the heart, followed by skeletal muscles. Additionally, <i>CAV-3</i> had higher expression in heart and breast muscle of overfed Muscovy ducks than control ducks, but no difference was seen in thigh muscle. 4. <i>CAV-3</i> in ducks had the highest homology with Gallus gallus <i>CAV-3</i>, and it could be used as a marker for muscle quality in ducks.