cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20013036
title: Additional file 3 of Complete genome sequences and genomic characterization of five plasmids harbored by environmentally persistent Cronobacter sakazakii strains ST83 H322 and ST64 GK1025B obtained from powdered infant formula manufacturing facilities

description: Additional file 3: Table S3. BLAST analysis of 683 Cronobacter genomes housed in a local database for the presnece of phage-plasmid pH322_1.
DOI: 10.6084/m9.figshare.20013055
title: Estimation of genetic and environmental relationships between milk yield and different measures of mastitis and hyperkeratosis in Holstein cows

description: ABSTRACT In this research, records of milk yield, mastitis occurrence and teats hyperkeratosis of 453 Holstein cows from a large herd with calving dates from December 2012 to December 2014 was used to estimate genetic and environmental correlations between milk yield, mastitis and hyperkeratosis. The highest and the lowest number of mastitis occurrence were in winter (January to March) and spring (April to June), respectively. Also, the highest and the lowest averages of days in milk at the time of mastitis occurrence were observed in winter and spring, respectively (162.53 vs. 29.67 days). The total number of mastitis occurrence was 151 times and in average a sick cow was infected 1.649 times. Obtained results showed low heritabilities for measures of mastitis (ranging from 0.048 to 0.134). Genetic correlations between measures of mastitis and milk yield were negative (from -0.502 to -0.183). Genetic correlation between hyperkeratosis and mastitis was positive which showed that selection for udder type traits would decrease mastitis occurrence. The results of this study can provide a background about the relationships between aforementioned traits and serve as a starting point for further study on these traits.
DOI: 10.6084/m9.figshare.20013055.v1
title: Estimation of genetic and environmental relationships between milk yield and different measures of mastitis and hyperkeratosis in Holstein cows

description: ABSTRACT In this research, records of milk yield, mastitis occurrence and teats hyperkeratosis of 453 Holstein cows from a large herd with calving dates from December 2012 to December 2014 was used to estimate genetic and environmental correlations between milk yield, mastitis and hyperkeratosis. The highest and the lowest number of mastitis occurrence were in winter (January to March) and spring (April to June), respectively. Also, the highest and the lowest averages of days in milk at the time of mastitis occurrence were observed in winter and spring, respectively (162.53 vs. 29.67 days). The total number of mastitis occurrence was 151 times and in average a sick cow was infected 1.649 times. Obtained results showed low heritabilities for measures of mastitis (ranging from 0.048 to 0.134). Genetic correlations between measures of mastitis and milk yield were negative (from -0.502 to -0.183). Genetic correlation between hyperkeratosis and mastitis was positive which showed that selection for udder type traits would decrease mastitis occurrence. The results of this study can provide a background about the relationships between aforementioned traits and serve as a starting point for further study on these traits.
DOI: 10.6084/m9.figshare.20013075
title: Patterns of use of time by heifers with or without supplementation at different phenological stages of winter grasses

description: ABSTRACT A joint data analysis was performed to characterize forage intake rate and patterns of use of time by grazing heifers in cold season pastures. Heifers received or not energetic supplementation at different phenological stages of grasses (vegetative, pre-flowering and flowering). Experiments involved 360 heifers with initial age of eight months and average body weight of 145 ± 17 kg, on continuous grazing method and variable number of animals. Supplementaed heifers consumed 17.0% less forage and 22.2% less leaf blades than heifers exclusively on pasture. Grazing activity was concentrated in the afternoon shift, regardless of the feeding system and phenological stages evaluated, with the longest event of rumination during the night. Forage intake rate is similar, regardless of supplement intake and phenological stages of grasses.
DOI: 10.6084/m9.figshare.20013075.v1
title: Patterns of use of time by heifers with or without supplementation at different phenological stages of winter grasses

description: ABSTRACT A joint data analysis was performed to characterize forage intake rate and patterns of use of time by grazing heifers in cold season pastures. Heifers received or not energetic supplementation at different phenological stages of grasses (vegetative, pre-flowering and flowering). Experiments involved 360 heifers with initial age of eight months and average body weight of 145 ± 17 kg, on continuous grazing method and variable number of animals. Supplementaed heifers consumed 17.0% less forage and 22.2% less leaf blades than heifers exclusively on pasture. Grazing activity was concentrated in the afternoon shift, regardless of the feeding system and phenological stages evaluated, with the longest event of rumination during the night. Forage intake rate is similar, regardless of supplement intake and phenological stages of grasses.
DOI: 10.6084/m9.figshare.20013096.v1
title: Performance of Japanese quails fed diets with low-protein and isoleucine

description: ABSTRACT. Aiming to assess isoleucine levels in low protein diets for laying Japanese quails, 648 quails of 182 days of age were distributed in experimental block design with six treatments and six replicates of 18 birds each. Treatments consisted of a basal level corresponding to 0.672% isoleucine and supplemented with isoleucine to the levels of 0.816, 0.960; 1.104; 1.248%. The experimental diets were compared to a control diet containing 20% CP. The parameters studied were: performance, egg quality, total solids and nitrogen in the excreta. There was a linear increase only for isoleucine intake with increasing levels of isoleucine in the diets. The comparison of mean values of each combination of isoleucine levels for diets with 16% CP with the control with 20% CP showed that the intake of CP and isoleucine, egg weight, nitrogen excretion and yolk color were significantly affected. For Japanese quail fed diets with 16% CP, with isoleucine level at 0.672%, meets the requirements for obtaining satisfactory performance and egg quality and promoted a reduction in nitrogen excretion.
DOI: 10.6084/m9.figshare.20013096
title: Performance of Japanese quails fed diets with low-protein and isoleucine

description: ABSTRACT. Aiming to assess isoleucine levels in low protein diets for laying Japanese quails, 648 quails of 182 days of age were distributed in experimental block design with six treatments and six replicates of 18 birds each. Treatments consisted of a basal level corresponding to 0.672% isoleucine and supplemented with isoleucine to the levels of 0.816, 0.960; 1.104; 1.248%. The experimental diets were compared to a control diet containing 20% CP. The parameters studied were: performance, egg quality, total solids and nitrogen in the excreta. There was a linear increase only for isoleucine intake with increasing levels of isoleucine in the diets. The comparison of mean values of each combination of isoleucine levels for diets with 16% CP with the control with 20% CP showed that the intake of CP and isoleucine, egg weight, nitrogen excretion and yolk color were significantly affected. For Japanese quail fed diets with 16% CP, with isoleucine level at 0.672%, meets the requirements for obtaining satisfactory performance and egg quality and promoted a reduction in nitrogen excretion.
DOI: 10.6084/m9.figshare.20013109
title: Aquatic microbiota diversity in the culture of Nile tilapia ( Oreochromis niloticus ) using bioflocs or periphyton: virulence factors and biofilm formation

description: ABSTRACT The following research isolated and identified the main bacterial groups present in the culture of juvenile Nile tilapia in the presence of bioflocs and/or periphyton. The strains were also tested for the production of exoenzymes, indicative of potential virulence factors, and ability to form biofilm. The water samples were taken from tilapia cultured in the presence of bioflocs (T1), in the presence of bioflocs and periphyton (T2), from traditional culture (T3) and from culture in the presence of periphyton (T4). In the growth and selection of the bacterial groups, pour plate method was used, along with the following media: Plate Count Agar (PCA - DIFCO), Aero Pseudo Selective Agar (GSP - Himedia) and Nutrient Agar (AN - Merck). 46 strains were isolated in the following distribution: T1 (n = 12); T2 (n = 10); T3 (n = 14) and T4 (n = 10). Among the isolates, the most frequent genera were: Pseudomonas spp., Aeromonas spp., Staphylococcus spp., Bacillus spp., Mycobacterium spp., Micrococcus spp., and Corybacterium spp. Bacterial isolates in treatments T1 and T3 tested positive for five virulence profiles each, while those isolated from T2 and T4 for two and three virulence profiles, respectively. Treatments in bioflocs and periphyton (T2) or only periphyton (T4) yielded bacteria of less pathogenic potentials. In relation to the fish growth, T1 and T4 resulted in a higher final weight.
DOI: 10.6084/m9.figshare.20013109.v1
title: Aquatic microbiota diversity in the culture of Nile tilapia ( Oreochromis niloticus ) using bioflocs or periphyton: virulence factors and biofilm formation

description: ABSTRACT The following research isolated and identified the main bacterial groups present in the culture of juvenile Nile tilapia in the presence of bioflocs and/or periphyton. The strains were also tested for the production of exoenzymes, indicative of potential virulence factors, and ability to form biofilm. The water samples were taken from tilapia cultured in the presence of bioflocs (T1), in the presence of bioflocs and periphyton (T2), from traditional culture (T3) and from culture in the presence of periphyton (T4). In the growth and selection of the bacterial groups, pour plate method was used, along with the following media: Plate Count Agar (PCA - DIFCO), Aero Pseudo Selective Agar (GSP - Himedia) and Nutrient Agar (AN - Merck). 46 strains were isolated in the following distribution: T1 (n = 12); T2 (n = 10); T3 (n = 14) and T4 (n = 10). Among the isolates, the most frequent genera were: Pseudomonas spp., Aeromonas spp., Staphylococcus spp., Bacillus spp., Mycobacterium spp., Micrococcus spp., and Corybacterium spp. Bacterial isolates in treatments T1 and T3 tested positive for five virulence profiles each, while those isolated from T2 and T4 for two and three virulence profiles, respectively. Treatments in bioflocs and periphyton (T2) or only periphyton (T4) yielded bacteria of less pathogenic potentials. In relation to the fish growth, T1 and T4 resulted in a higher final weight.
DOI: 10.6084/m9.figshare.20013114
title: Chemical composition of lipids from native and exotic fish in reservoirs of the state of Ceará, Brazil

description: ABSTRACT Current study analyzes the chemical composition of lipids in fish commonly found in the dams of the state of Ceará, Brazil, namely Pterygoplichthys pardalis (bodó), Hoplias malabaricus (traira), Cichla ocellaris (tucunaré), Prochilodus brevis (curimatã) and Oreochomis niloticus (tilapia). The animals were collected during the summer and Folch extraction procedure was used for the extraction of lipids, whilst Iupac methodology (International Union of Pure and Applied Chemistry [Iupac], 1987) was used to methylate the fatty acids. Methyl esters were analyzed by GC/MS and the different components in fish oil were identified. Palmitic acid, C16:0 (35.71-45.02%), was the saturated fatty acid with the highest percentage, while oleic acid, C18:1Δ9 (10.62-25.29%) had the highest percentage among the unsaturated fatty acids. The chemical composition of analyzed freshwater fish lipids revealed low levels of polyunsaturated fatty acids.
DOI: 10.6084/m9.figshare.20013114.v1
title: Chemical composition of lipids from native and exotic fish in reservoirs of the state of Ceará, Brazil

description: ABSTRACT Current study analyzes the chemical composition of lipids in fish commonly found in the dams of the state of Ceará, Brazil, namely Pterygoplichthys pardalis (bodó), Hoplias malabaricus (traira), Cichla ocellaris (tucunaré), Prochilodus brevis (curimatã) and Oreochomis niloticus (tilapia). The animals were collected during the summer and Folch extraction procedure was used for the extraction of lipids, whilst Iupac methodology (International Union of Pure and Applied Chemistry [Iupac], 1987) was used to methylate the fatty acids. Methyl esters were analyzed by GC/MS and the different components in fish oil were identified. Palmitic acid, C16:0 (35.71-45.02%), was the saturated fatty acid with the highest percentage, while oleic acid, C18:1Δ9 (10.62-25.29%) had the highest percentage among the unsaturated fatty acids. The chemical composition of analyzed freshwater fish lipids revealed low levels of polyunsaturated fatty acids.
DOI: 10.6084/m9.figshare.20013111
title: Additional file 3 of Gorham-Stout case report: a multi-omic analysis reveals recurrent fusions as new potential drivers of the disease

description: Additional file3: Table S1. Table of gene fusions detected and selected for validation including chromosome information and the number of reads in DNA and RNA level.
DOI: 10.6084/m9.figshare.20013111.v1
title: Additional file 3 of Gorham-Stout case report: a multi-omic analysis reveals recurrent fusions as new potential drivers of the disease

description: Additional file3: Table S1. Table of gene fusions detected and selected for validation including chromosome information and the number of reads in DNA and RNA level.
DOI: 10.6084/m9.figshare.20013120
title: Additional file 5 of Gorham-Stout case report: a multi-omic analysis reveals recurrent fusions as new potential drivers of the disease

description: Additional file5: Table S2. Table results of the gene set expression analysis for lymphangiogenesis showing the affected genes in the RNA-seq expression and their contribution to the pathway.
DOI: 10.6084/m9.figshare.20013120.v1
title: Additional file 5 of Gorham-Stout case report: a multi-omic analysis reveals recurrent fusions as new potential drivers of the disease

description: Additional file5: Table S2. Table results of the gene set expression analysis for lymphangiogenesis showing the affected genes in the RNA-seq expression and their contribution to the pathway.
DOI: 10.6084/m9.figshare.20013123
title: Additional file 6 of Gorham-Stout case report: a multi-omic analysis reveals recurrent fusions as new potential drivers of the disease

description: Additional file6: Table S3. Table results of the gene set expression analysis for osteolysis showing the affected genes in the RNA-seq expression and their contribution to the pathway.
DOI: 10.6084/m9.figshare.20013123.v1
title: Additional file 6 of Gorham-Stout case report: a multi-omic analysis reveals recurrent fusions as new potential drivers of the disease

description: Additional file6: Table S3. Table results of the gene set expression analysis for osteolysis showing the affected genes in the RNA-seq expression and their contribution to the pathway.
DOI: 10.6084/m9.figshare.20013135.v1
title: Forage mass and nutritive value of bermuda grass mixed to forage peanut or common vetch

description: ABSTRACT Three pasture-based systems (PS) with bermuda grass (BG) + forage peanut + 75 kg of N ha-1; BG + common vetch + 75 kg of N ha-1 and BG + 150 kg of N ha-1 were evaluated. Lactating Holstein cows were used for evaluation and the experimental design was completely randomized. Forage mass, botanical and structural composition, daily dry matter accumulation rate and stocking rate were evaluated. Samples were collected by hand-plucking method to analyze crude protein (CP), neutral detergent fiber (NDF), (ISDMD), in situ organic matter digestibility (ISOMD) and total digestible nutrients (TDN). Average forage production and stocking rate were 13.8; 15.3 and 16.1 t ha-1 and 5.6; 6.4 and 5.5 UA ha-1 day-1 for PS respectively. Average CP and NDF were 16.4; 22.2 and 15.3%; 68.3; 65.7 and 66.3%; for ISDMD, ISOMD and TDN were 68.5; 70.3 and 66.4%; 64.3; 63.2 and 65.3%; 57.3; 58.3 and 57.5%, for PS respectively. Best results were reported on bermuda grass mixed with common vetch.
DOI: 10.6084/m9.figshare.20013135
title: Forage mass and nutritive value of bermuda grass mixed to forage peanut or common vetch

description: ABSTRACT Three pasture-based systems (PS) with bermuda grass (BG) + forage peanut + 75 kg of N ha-1; BG + common vetch + 75 kg of N ha-1 and BG + 150 kg of N ha-1 were evaluated. Lactating Holstein cows were used for evaluation and the experimental design was completely randomized. Forage mass, botanical and structural composition, daily dry matter accumulation rate and stocking rate were evaluated. Samples were collected by hand-plucking method to analyze crude protein (CP), neutral detergent fiber (NDF), (ISDMD), in situ organic matter digestibility (ISOMD) and total digestible nutrients (TDN). Average forage production and stocking rate were 13.8; 15.3 and 16.1 t ha-1 and 5.6; 6.4 and 5.5 UA ha-1 day-1 for PS respectively. Average CP and NDF were 16.4; 22.2 and 15.3%; 68.3; 65.7 and 66.3%; for ISDMD, ISOMD and TDN were 68.5; 70.3 and 66.4%; 64.3; 63.2 and 65.3%; 57.3; 58.3 and 57.5%, for PS respectively. Best results were reported on bermuda grass mixed with common vetch.
DOI: 10.6084/m9.figshare.20013142.v1
title: Fermentation kinetics and in vitro degradation rates of grasses of the genus Cynodon

description: ABSTRACT The present study aimed to evaluate the fermentation kinetics and degradation rates of Cynodon grasses estimated by semi-automated technique of in vitro gas production. The forages were: Coastcross, Tifton 85 and Tifton 68. Pressure readings were taken at 0, 2, 4, 6, 8, 10, 12, 15, 19, 24, 30, 36, 48, 72 and 96 hours. Dry matter degradability (DMD) was obtained by the percentage of dry matter (DM) remaining after 0, 6, 12, 24, 48 and 96 hours of fermentation. Tifton 85 showed a higher total gas production (p &lt;0.05). Higher fermentation rates were found at the beginning of fermentation followed by subsequent reduction (p &lt;0.05) over time. Tifton 85 and Tifton 68 showed higher values (p &lt; 0.05) for soluble fraction, potentially degradable insoluble fraction, insoluble fraction, potential and effective degradability of dry matter in relation to Coastcross grass. Higher gas production during in vitro incubation of dry matter was observed for Tifton 85 g.
DOI: 10.6084/m9.figshare.20013142
title: Fermentation kinetics and in vitro degradation rates of grasses of the genus Cynodon

description: ABSTRACT The present study aimed to evaluate the fermentation kinetics and degradation rates of Cynodon grasses estimated by semi-automated technique of in vitro gas production. The forages were: Coastcross, Tifton 85 and Tifton 68. Pressure readings were taken at 0, 2, 4, 6, 8, 10, 12, 15, 19, 24, 30, 36, 48, 72 and 96 hours. Dry matter degradability (DMD) was obtained by the percentage of dry matter (DM) remaining after 0, 6, 12, 24, 48 and 96 hours of fermentation. Tifton 85 showed a higher total gas production (p &lt;0.05). Higher fermentation rates were found at the beginning of fermentation followed by subsequent reduction (p &lt;0.05) over time. Tifton 85 and Tifton 68 showed higher values (p &lt; 0.05) for soluble fraction, potentially degradable insoluble fraction, insoluble fraction, potential and effective degradability of dry matter in relation to Coastcross grass. Higher gas production during in vitro incubation of dry matter was observed for Tifton 85 g.
DOI: 10.6084/m9.figshare.20013162
title: Additional file 1 of Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment

description: Additional file 1: Figure S1. Nucleotide sequences (FeSOD-A and FeSOD-B genes) of the datasets used in this study.
DOI: 10.6084/m9.figshare.20013162.v1
title: Additional file 1 of Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment

description: Additional file 1: Figure S1. Nucleotide sequences (FeSOD-A and FeSOD-B genes) of the datasets used in this study.
DOI: 10.6084/m9.figshare.20013165
title: Additional file 2 of Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment

description: Additional file 2: Figure S2. Alignment of sequences of potential T. cruzi FeSOD-C.
DOI: 10.6084/m9.figshare.20013165.v1
title: Additional file 2 of Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment

description: Additional file 2: Figure S2. Alignment of sequences of potential T. cruzi FeSOD-C.
DOI: 10.6084/m9.figshare.20013171
title: Additional file 4 of Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment

description: Additional file 4: Figure S4. Nucleotide sequence alignment of the datasets used in this study. Alignments were performed in MUSCLE as implemented in MEGA and edited by visual inspection. Different types of sites identified in each alignment are indicated in Table S1. Each edited alignment was further used for phylogenetic reconstruction.
DOI: 10.6084/m9.figshare.20013174
title: Additional file 5 of Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment

description: Additional file 5: Figure S5. Alignment of sequences of the trees reconstructed in this study (FeSOD-A and FeSOD-B sequences), Tulahuen gene sequences (FeSOD-A and FeSOD-B sequences) and FeSOD-C genes (used to determine the copy number in the T. cruzi CL-Brener genome).
DOI: 10.6084/m9.figshare.20013171.v1
title: Additional file 4 of Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment

description: Additional file 4: Figure S4. Nucleotide sequence alignment of the datasets used in this study. Alignments were performed in MUSCLE as implemented in MEGA and edited by visual inspection. Different types of sites identified in each alignment are indicated in Table S1. Each edited alignment was further used for phylogenetic reconstruction.
DOI: 10.6084/m9.figshare.20013174.v1
title: Additional file 5 of Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment

description: Additional file 5: Figure S5. Alignment of sequences of the trees reconstructed in this study (FeSOD-A and FeSOD-B sequences), Tulahuen gene sequences (FeSOD-A and FeSOD-B sequences) and FeSOD-C genes (used to determine the copy number in the T. cruzi CL-Brener genome).
DOI: 10.6084/m9.figshare.20013177
title: Additional file 6 of Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment

description: Additional file 6: Table S4. Information of sequences of the trees reconstructed in this study (FeSOD-A and FeSOD-B sequences) and FeSOD-C genes (used to determine the copy number in the T. cruzi CL-Brener genome).
DOI: 10.6084/m9.figshare.20013177.v1
title: Additional file 6 of Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment

description: Additional file 6: Table S4. Information of sequences of the trees reconstructed in this study (FeSOD-A and FeSOD-B sequences) and FeSOD-C genes (used to determine the copy number in the T. cruzi CL-Brener genome).
DOI: 10.6084/m9.figshare.20013180
title: Additional file 7 of Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment

description: Additional file 7: Figure S6. Trees of the datasets used in this study. Trees were reconstructed in MrBayes and PhyML.