cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20009609
title: Modeling the weight gain of freshwater-reared rainbow trout ( Oncorhynchus mykiss ) during the grow-out phase

description: ABSTRACT We used five nonlinear models to calculate the weight gain of rainbow trout (122.11±15.6 g) during the final grow-out phase of 98 days under three different feed types (two commercials diets, A and B, and one experimental diet, C) in triplicate groups. We fitted the von Bertalanffy growth function with allometric and isometric scaling coefficient, Gompertz, Logistic, and Brody functions to weight (g) at age data of 900 fish, distributed in nine tanks. The equations were fitted to the data based on the least squares method using the Marquardt iterative algorithm. The accuracy of the fitted models was evaluated using a model performance metrics, combining mean squared residuals (MSR), mean absolute error (MAE), and Akaike’s Information Criterion corrected for small sample sizes (AICc). All models converged in all cases tested. The evaluation criteria for the Logistic model indicated the best overall fit (0.704) under all different feed types, followed by the Gompertz model (0.148), and the von Bertalanffy-I and von Bertalanffy-A with 0.074 each. The obtained asymptotic values are in agreement with the biological attributes of the species, except for the Brody model, whose values were massively exceeding the biologic traits of rainbow trout in 0.556 of tested cases. Additionally, ∆AICc results identify the Brody model as the only model not substantially supported by the data in any case. All other models are capable of reflecting the effects of various feed types; these results are directly applicable in farm management decisions.
DOI: 10.6084/m9.figshare.20009609.v1
title: Modeling the weight gain of freshwater-reared rainbow trout ( Oncorhynchus mykiss ) during the grow-out phase

description: ABSTRACT We used five nonlinear models to calculate the weight gain of rainbow trout (122.11±15.6 g) during the final grow-out phase of 98 days under three different feed types (two commercials diets, A and B, and one experimental diet, C) in triplicate groups. We fitted the von Bertalanffy growth function with allometric and isometric scaling coefficient, Gompertz, Logistic, and Brody functions to weight (g) at age data of 900 fish, distributed in nine tanks. The equations were fitted to the data based on the least squares method using the Marquardt iterative algorithm. The accuracy of the fitted models was evaluated using a model performance metrics, combining mean squared residuals (MSR), mean absolute error (MAE), and Akaike’s Information Criterion corrected for small sample sizes (AICc). All models converged in all cases tested. The evaluation criteria for the Logistic model indicated the best overall fit (0.704) under all different feed types, followed by the Gompertz model (0.148), and the von Bertalanffy-I and von Bertalanffy-A with 0.074 each. The obtained asymptotic values are in agreement with the biological attributes of the species, except for the Brody model, whose values were massively exceeding the biologic traits of rainbow trout in 0.556 of tested cases. Additionally, ∆AICc results identify the Brody model as the only model not substantially supported by the data in any case. All other models are capable of reflecting the effects of various feed types; these results are directly applicable in farm management decisions.
DOI: 10.6084/m9.figshare.12094476
title: Dietary histidine requirement of grow-out Nile tilapia (Oreochromis niloticus), based on growth performance, muscle development, expression of muscle-growth-related genes, and blood parameters

description: ABSTRACT This research was conducted to determine optimal dietary histidine requirement of grow-out Nile tilapia, Oreochromis niloticus, based on muscle development, expression of muscle-growth-related genes, and blood parameters. Fish (n = 288, initial body weight of 64.17±0.53 g) were fed extruded diets with graded levels of histidine (4.23, 5.44, 7.17, 8.91, and 11.57 g kg−1), containing approximately 289 g kg−1 crude protein and 3565 kcal kg−1 digestible energy. The study followed a completely randomized design with five treatments and four replicates each, for 65 days. There was a quadratic effect of dietary histidine on final body weight, feed conversion, and net protein utilization, and the best values were optimized at 8.09, 7.88, and 7.33 g kg−1, respectively. Feed intake, hepatosomatic index, survival, body composition, and blood parameters of total protein, glucose, triglycerides, cholesterol, hematocrit, and hemoglobin were not affected by dietary treatments. Predominance of hypertrophic growth and higher mRNA levels of myogenin and MyoD were observed in fish fed histidine from 5.44 to 11.57 g kg−1 compared with fish fed histidine at 4.23 g kg−1. The mRNA expression of myostatin was not affected by dietary treatments. The dietary requirement of histidine for grow-out Nile tilapia was determined at 8.09 g kg−1, considering growth performance, muscle development, and gene expression responses.
DOI: 10.6084/m9.figshare.12094476.v1
title: Dietary histidine requirement of grow-out Nile tilapia (Oreochromis niloticus), based on growth performance, muscle development, expression of muscle-growth-related genes, and blood parameters

description: ABSTRACT This research was conducted to determine optimal dietary histidine requirement of grow-out Nile tilapia, Oreochromis niloticus, based on muscle development, expression of muscle-growth-related genes, and blood parameters. Fish (n = 288, initial body weight of 64.17±0.53 g) were fed extruded diets with graded levels of histidine (4.23, 5.44, 7.17, 8.91, and 11.57 g kg−1), containing approximately 289 g kg−1 crude protein and 3565 kcal kg−1 digestible energy. The study followed a completely randomized design with five treatments and four replicates each, for 65 days. There was a quadratic effect of dietary histidine on final body weight, feed conversion, and net protein utilization, and the best values were optimized at 8.09, 7.88, and 7.33 g kg−1, respectively. Feed intake, hepatosomatic index, survival, body composition, and blood parameters of total protein, glucose, triglycerides, cholesterol, hematocrit, and hemoglobin were not affected by dietary treatments. Predominance of hypertrophic growth and higher mRNA levels of myogenin and MyoD were observed in fish fed histidine from 5.44 to 11.57 g kg−1 compared with fish fed histidine at 4.23 g kg−1. The mRNA expression of myostatin was not affected by dietary treatments. The dietary requirement of histidine for grow-out Nile tilapia was determined at 8.09 g kg−1, considering growth performance, muscle development, and gene expression responses.
DOI: 10.6084/m9.figshare.12094527
title: Utilization of rice byproducts as carbon sources in high-density culture of the Pacific white shrimp, Litopenaeus vannamei

description: ABSTRACT This study was conducted to evaluate the effect of rice byproducts on water quality, microbial community, and growth performance of L. vannamei juveniles. Shrimp of 0.98±0.10 g body weight (BW) were reared in 49 tanks of 1.5 m3 under 127 animals m−2 for 77 days. Rice bran, rice grits, and rice hulls were mixed into five different fertilizers varying their fiber content (90, 110, 150, 200, and 250 g kg−1) and compared against sugarcane molasses (MO) and unfertilized tanks (UNF). Rice byproducts and MO were applied in water three times a week at a fixed rate of 4.5 g m−3. Water salinity, pH, temperature, and dissolved oxygen reached 43±2 g L−1, 8.03±0.32, 30.2±0.90 °C, and 5.03±0.53 mg L−1, respectively. Settleable solids (SS) were higher in tanks fertilized with rice byproducts (from 2.5±1.0 to 3.1±1.1 mL L−1) and MO (3.4±1.0 mL L−1). Total ammonia nitrogen (0.19±0.09 mg L−1), nitrite (5.97±2.04 mg L−1), and nitrate (1.29±0.48 mg L−1) were kept low without any significant differences among treatments. The concentration of heterotrophic bacteria and fungi was significantly higher in rice byproducts compared with MO. Water fertilization had no effect on final shrimp survival (85.5±9.5%), weekly growth (0.72±0.11 g), and feed conversion ratio (1.59±0.10). Tanks treated with rice byproducts, except with 90 g kg−1 fiber, resulted in a higher final shrimp BW (from 9.04±1.56 to 9.52±1.89 g) compared with MO (8.75±2.14 g) and UNF (7.74±1.48 g). Gained yield and feed intake were significantly higher for tanks treated with rice byproducts than with UNF. A mix of rice byproducts can be equally or more effective as carbon sources to shrimp culture than MO.
DOI: 10.6084/m9.figshare.12094527.v1
title: Utilization of rice byproducts as carbon sources in high-density culture of the Pacific white shrimp, Litopenaeus vannamei

description: ABSTRACT This study was conducted to evaluate the effect of rice byproducts on water quality, microbial community, and growth performance of L. vannamei juveniles. Shrimp of 0.98±0.10 g body weight (BW) were reared in 49 tanks of 1.5 m3 under 127 animals m−2 for 77 days. Rice bran, rice grits, and rice hulls were mixed into five different fertilizers varying their fiber content (90, 110, 150, 200, and 250 g kg−1) and compared against sugarcane molasses (MO) and unfertilized tanks (UNF). Rice byproducts and MO were applied in water three times a week at a fixed rate of 4.5 g m−3. Water salinity, pH, temperature, and dissolved oxygen reached 43±2 g L−1, 8.03±0.32, 30.2±0.90 °C, and 5.03±0.53 mg L−1, respectively. Settleable solids (SS) were higher in tanks fertilized with rice byproducts (from 2.5±1.0 to 3.1±1.1 mL L−1) and MO (3.4±1.0 mL L−1). Total ammonia nitrogen (0.19±0.09 mg L−1), nitrite (5.97±2.04 mg L−1), and nitrate (1.29±0.48 mg L−1) were kept low without any significant differences among treatments. The concentration of heterotrophic bacteria and fungi was significantly higher in rice byproducts compared with MO. Water fertilization had no effect on final shrimp survival (85.5±9.5%), weekly growth (0.72±0.11 g), and feed conversion ratio (1.59±0.10). Tanks treated with rice byproducts, except with 90 g kg−1 fiber, resulted in a higher final shrimp BW (from 9.04±1.56 to 9.52±1.89 g) compared with MO (8.75±2.14 g) and UNF (7.74±1.48 g). Gained yield and feed intake were significantly higher for tanks treated with rice byproducts than with UNF. A mix of rice byproducts can be equally or more effective as carbon sources to shrimp culture than MO.
DOI: 10.6084/m9.figshare.20009611
title: Population structure and inbreeding of Holstein cattle in southern Brazil

description: ABSTRACT The present investigation aimed to evaluate the population structure and inbreeding of Holstein herds in southern Brazil. To carry out the analysis, the Associação Paranaense de Criadores de Bovinos da Raça Holandesa (APCBRH) in Brazil provided the data, which consisted of a pedigree file of 206,796 animals born between 1970 and 2014. Results regarding the following parameters were determined: pedigree integrity, effective number of founders, effective number of ancestors, generation interval, inbreeding coefficient, realized effective population size, and average relatedness coefficient. POPREP and ENDOG v.4.5 software packages were employed to estimate these parameters. Based on the data set, the mean generation interval was found to be 6.3 years, and the average inbreeding coefficient, related to inbred animals, was 4.99%. Furthermore, the realized effective population size varied throughout the time period, ranging from 22 to 114, whereas the rate of inbreeding in this same period showed a decreasing trend towards the later years in the period until 2014. Upon evaluation, average relatedness coefficient was estimated to be 0.71%. Moreover, the effective number of founders and ancestors were estimated as 418 and 400 animals, respectively. According to the level of inbreeding observed, it could be noticed that genetic diversity remains elevated, which will be important to the genetic progress in the Holstein breeding program in Southern Brazil.
DOI: 10.6084/m9.figshare.20009611.v1
title: Population structure and inbreeding of Holstein cattle in southern Brazil

description: ABSTRACT The present investigation aimed to evaluate the population structure and inbreeding of Holstein herds in southern Brazil. To carry out the analysis, the Associação Paranaense de Criadores de Bovinos da Raça Holandesa (APCBRH) in Brazil provided the data, which consisted of a pedigree file of 206,796 animals born between 1970 and 2014. Results regarding the following parameters were determined: pedigree integrity, effective number of founders, effective number of ancestors, generation interval, inbreeding coefficient, realized effective population size, and average relatedness coefficient. POPREP and ENDOG v.4.5 software packages were employed to estimate these parameters. Based on the data set, the mean generation interval was found to be 6.3 years, and the average inbreeding coefficient, related to inbred animals, was 4.99%. Furthermore, the realized effective population size varied throughout the time period, ranging from 22 to 114, whereas the rate of inbreeding in this same period showed a decreasing trend towards the later years in the period until 2014. Upon evaluation, average relatedness coefficient was estimated to be 0.71%. Moreover, the effective number of founders and ancestors were estimated as 418 and 400 animals, respectively. According to the level of inbreeding observed, it could be noticed that genetic diversity remains elevated, which will be important to the genetic progress in the Holstein breeding program in Southern Brazil.
DOI: 10.6084/m9.figshare.12094317
title: Evaluation of olive leaf extract as a growth promoter on the performance, blood biochemical parameters, and caecal microflora of broiler chickens

description: ABSTRACT The objective of the study was to examine the effects of an alcoholic liquid olive leaf extract (OLE) obtained from fresh leaves on the growth performance, carcass weight, caecal microflora, and some plasma variables, such as triglycerides, total cholesterol, high-density lipoprotein (HDL), and low-density lipoprotein (LDL) cholesterol in broiler chickens. A total of 375 one-day-old male broilers (Ross 308) were randomly divided into five treatments with five replicate pens (15 birds each) per treatment. The birds were fed either a basal diet with no supplement (control), with 75 (OLE75), 150 (OLE150), 300 (OLE300), and 600 (OLE600) mg kg−1 oleuropein, provided by 0.66, 1.33, 2.65, and 5.32 g kg−1 of the OLE. The dietary supplementation of OLE linearly increased daily body weight gain (BWG), feed intake (FI), and carcass weight and improved feed conversion ratio (FCR). Although the OLE600 broilers had the highest daily FI among the treatments, there were significant increases in their BWG and improvements in FCR compared with the control, OLE75, and OLE150 birds. The carcass weights of OLE150, OLE300, and OLE600 birds were higher than those of the control group. The OLE600 diet increased the dressing percentage compared with the OLE75, OLE150, and OLE300 diets. The abdominal fat weight and the plasma HDL concentration of the control broilers were lower than those of all OLE birds. All doses of OLE supplementation decreased the caecal E. coli content. A growth-promoting effect is obtained from the dietary supplementation of 600 mg kg−1 oleuropein due to its beneficial effect on growth performance and caecal microflora populations of broilers.
DOI: 10.6084/m9.figshare.20009614.v1
title: Concerns, attitudes, and opinions of meat buyers in Garanhuns, Pernambuco, Brazil

description: ABSTRACT With the objective of identifying the concerns, attitudes, and opinions of meat buyers and their relationship with their choice of place of purchase (supermarkets, free fair, or butchers), 381 consumers in the city of Garanhuns, Brazil, were interviewed. Data analysis was performed using descriptive statistics and discriminant analysis, complemented by stepwise regression, Wilks’ Lambda test, and Fisher’s linear test. Most of the respondents expressed that inadequate commercialization of meat occurred in free fairs, and the lack of hygiene and the fact that meat was exposed in the environment without refrigeration were the main preoccupations. They also reported that meat consumption without inspection could lead to disease transmission, with pork being considered the most dangerous. Based on the theory of planned behavior, buyers agreed that their attitudes toward the purchase of meat (concern with food safety, price, animal welfare, environment, and slave labor) influenced their purchasing decisions. Regarding the subjective norms, the results indicated that purchase intention could be modulated by the opinion and judgment that other people exercise on the buyer’s choice decision. Regarding perceived control, the respondents said that they were confused at the time of purchase and got irritated after making a purchase that did not satisfy their desires. The factors that differentiated consumers who prefer to buy meat in supermarkets from those who prefer butchers and free fairs are mainly the price of the product, custom/tradition, customer service, and hygiene of the establishment. Buyers who have a lower level of schooling and live in rural areas also tended to buy meat in free fairs.
DOI: 10.6084/m9.figshare.20009614
title: Concerns, attitudes, and opinions of meat buyers in Garanhuns, Pernambuco, Brazil

description: ABSTRACT With the objective of identifying the concerns, attitudes, and opinions of meat buyers and their relationship with their choice of place of purchase (supermarkets, free fair, or butchers), 381 consumers in the city of Garanhuns, Brazil, were interviewed. Data analysis was performed using descriptive statistics and discriminant analysis, complemented by stepwise regression, Wilks’ Lambda test, and Fisher’s linear test. Most of the respondents expressed that inadequate commercialization of meat occurred in free fairs, and the lack of hygiene and the fact that meat was exposed in the environment without refrigeration were the main preoccupations. They also reported that meat consumption without inspection could lead to disease transmission, with pork being considered the most dangerous. Based on the theory of planned behavior, buyers agreed that their attitudes toward the purchase of meat (concern with food safety, price, animal welfare, environment, and slave labor) influenced their purchasing decisions. Regarding the subjective norms, the results indicated that purchase intention could be modulated by the opinion and judgment that other people exercise on the buyer’s choice decision. Regarding perceived control, the respondents said that they were confused at the time of purchase and got irritated after making a purchase that did not satisfy their desires. The factors that differentiated consumers who prefer to buy meat in supermarkets from those who prefer butchers and free fairs are mainly the price of the product, custom/tradition, customer service, and hygiene of the establishment. Buyers who have a lower level of schooling and live in rural areas also tended to buy meat in free fairs.
DOI: 10.6084/m9.figshare.20009480
title: Yamaguchi_Sperm_K4me3rep1

description: 2018 Yamaguchi et al Sperm H3K4me3 chip-seq rep1
DOI: 10.6084/m9.figshare.20009480.v1
title: Yamaguchi_Sperm_K4me3rep1

description: 2018 Yamaguchi et al Sperm H3K4me3 chip-seq rep1
DOI: 10.6084/m9.figshare.20009617
title: Use of quali-quantitative feeding practices criteria in typology of smallholders’ dairy production systems

description: ABSTRACT This study aimed to typify smallholders’ dairy systems using quali-quantitative measures of feeding practices and detect the main discriminatory elements identifying the systems. We collected data from 30 farms distributed in 10 municipalities in the eastern region of Rio Grande do Sul, Brazil, using a survey with semi-structured questions, in addition to bimonthly observations of milking and feeding practices. Multivariate analysis based on principal factors and cluster analysis were performed. Multiple linear regressions were made between the principal factors scores and variables of milk production and composition. Three principal factors with eigenvalues ≥1.0 explained 58.9% of the total variance. The original variables with the highest factor loading values were production scale and feeding practices involving greater quantities of byproducts; use of corn silage and sugarcane; and commercial and farm-made concentrate for principal factor 1, principal factor 2, and principal factor 3, respectively. Milk yield and concentrations of lactose and solids non-fat increased linearly with principal factor 1 and principal factor 3 but decreased linearly with principal factor 2. Observations were grouped into three clusters. Farm area and quantity of corn silage and byproducts were the most important variables to set the clusters. The use of quali-quantitative feeding practices criteria to characterize dairy systems is effective to identify the opportunities for improving milk production and composition. Whereas high inclusion of sugarcane as roughage was detrimental for milk production, moderate supply of concentrate and byproducts enhanced milk yield without compromising milk composition.
DOI: 10.6084/m9.figshare.20009617.v1
title: Use of quali-quantitative feeding practices criteria in typology of smallholders’ dairy production systems

description: ABSTRACT This study aimed to typify smallholders’ dairy systems using quali-quantitative measures of feeding practices and detect the main discriminatory elements identifying the systems. We collected data from 30 farms distributed in 10 municipalities in the eastern region of Rio Grande do Sul, Brazil, using a survey with semi-structured questions, in addition to bimonthly observations of milking and feeding practices. Multivariate analysis based on principal factors and cluster analysis were performed. Multiple linear regressions were made between the principal factors scores and variables of milk production and composition. Three principal factors with eigenvalues ≥1.0 explained 58.9% of the total variance. The original variables with the highest factor loading values were production scale and feeding practices involving greater quantities of byproducts; use of corn silage and sugarcane; and commercial and farm-made concentrate for principal factor 1, principal factor 2, and principal factor 3, respectively. Milk yield and concentrations of lactose and solids non-fat increased linearly with principal factor 1 and principal factor 3 but decreased linearly with principal factor 2. Observations were grouped into three clusters. Farm area and quantity of corn silage and byproducts were the most important variables to set the clusters. The use of quali-quantitative feeding practices criteria to characterize dairy systems is effective to identify the opportunities for improving milk production and composition. Whereas high inclusion of sugarcane as roughage was detrimental for milk production, moderate supply of concentrate and byproducts enhanced milk yield without compromising milk composition.