Nonlinear Mixed Model Research Articles

158 Effects of Increasing Dietary Standardized Ileal Digestible Lysine Levels on Growth Performance of Grow-Finish Pigs That Were Sired by PIC 800 Boars

Abstract A total of 1,092 pigs (PIC 800 × Camborough) were used to investigate the effects of increasing dietary standardized ileal digestible (SID) Lys on growth performance in 4 experiments covering body weight ranges of 25-45 kg (Exp. 1), 45-73 kg (Exp. 2), 74-91 kg (Exp. 3), and 98-120 kg (Exp. 4). Pigs were placed in 1 room and divided into 2 groups with 42 pens/group and 13 pigs/pen (6 or 7 gilts and 7 or 6 barrows, balanced among treatments). Group 1 was used in Exp. 1 and 3; group 2 was used in Exp. 2 and 4. At the beginning of each trial, on-trial pens were blocked by body weight and randomly allotted to one of 6 treatments (85.0, 90.0, 95.0, 100.0, 107.5, or 115.0% of PIC SID Lys recommendations) in a randomized complete block design. Data were analyzed using generalized linear and nonlinear mixed models with pen as the experimental unit. In Exp. 2 to 4, the competing nonlinear models did not fit the data or improve the fitness compared with the linear models. Greater SID Lys linearly increased (P < 0.05) average daily gain in Exp. 1 and 3 (Table 1). Increasing SID Lys tended to increase gain to feed ratio (G:F; quadratic, P < 0.10) in Exp. 1, and broken-line linear and broken-line quadratic models estimated the maximum G:F at 99.9 and 98.5% SID Lys, respectively. In Exp. 2 and 3, increasing SID Lys also increased G:F (linear, P < 0.10). Growth performance did not differ among treatments in Exp. 4. Results indicated that the optimum SID Lys concentration for 25 to 45 kg PIC 800 pigs was between 98.5 and 99.9% of PIC SID Lys recommendations. More research is needed to validate the optimum SID Lys concentrations for pigs above 45 kg.

Integrated Berth and Crane Scheduling Problem Considering Crane Coverage in Multi-Terminal Tidal Ports under Uncertainty

In this work, we study the integrated berth and crane scheduling problem in a tidal port with multiple terminals, considering the uncertainties, tides, maximum coverage of cranes and interference between cranes. For coping with the uncertainties, a certain number of randomly generated samples are used to evaluate the solutions, and slack variables are introduced to reduce the impact caused by the variation in vessel arrival and crane operational efficiency. A novel nonlinear mixed integer programming model is first formulated for the problem to minimize the sum of expectation and variance of costs under all samples. An improved adaptive genetic algorithm, combining a simulated annealing mechanism and greedy construction strategy, is developed and implemented by MATLAB. The feasibility and validity of the algorithm and the benefits of multi-terminal collaborative scheduling strategy under uncertainty are evaluated through numerical experiments. The results show that the algorithm can obtain feasible scheduling solutions with higher quality. Compared to the strategy that considers either the uncertainty or the multi-terminal collaborative mechanism, the resulting solution considering both can effectively reduce the cost and improve the competitiveness of the port.

Massive Paraesophageal Hernia Repair in the Obese Patient Population: Antireflux Gastric Bypass Versus Fundoplication.

Introduction: Obesity is a risk factor for gastroesophageal reflux disease (GERD) and hiatal hernia (HH). Fundoplication is the standard operation for GERD with HH. Roux-en-Y gastric bypass (RYGB) is the procedure of choice for obese patients with either GERD or a large HH, but neither are indications for RYGB. To delineate bypass surgery as a treatment option for obese patients with HH and GERD, we propose new terminology, antireflux gastric bypass (ARGB). ARGB differs from RYGB by utilizing varying efferent limb lengths for GERD treatment. We hypothesized that ARGB would have higher GERD resolution, lower HH recurrence, and improves weight loss when compared with fundoplication. Methods: A retrospective cohort study was performed, evaluating patients undergoing repair of large HH (>5 cm) with obesity from January 2013 to February 2021. The primary outcome was GERD resolution, secondary outcomes include HH recurrence and weight loss. Multivariate logistic regression adjusted for age, body mass index (BMI), and hernia size by nonlinear mixed modeling. Results: Forty patients underwent fundoplication, and 16 patients underwent ARGB. Fundoplication patients had a larger mean hernia size (8.7 × 6.3 cm versus 6.6 × 6.4 cm), whereas ARGB patients had a higher BMI (39.2 versus 34.2 kg/m2). Recurrence showed nonstatistically significant lower incidence with ARGB and no significant difference in GERD resolution. Weight (P < .0001) and excess body weight (P < .0001) loss were superior with ARGB. Conclusions: Obese patients with large HHs and GERD treated with ARGB had similar GERD resolution, lower HH recurrence, and improved weight loss when compared with fundoplication. ARGB is an acceptable treatment option for obese patients with a massive paraesophageal hernia in the setting of GERD.

Robust computationally intensive and asymptotic tests for compound symmetry structure

The covariance matrix with compound symmetry structure is used in many statistical procedures, as in repeated measures design, in mixed linear or non-linear models, as well as in genetic studies. For making inferences about the compound symmetry structure, the classic original likelihood ratio test (OLRT) is commonly used. The main limitation of this test is the difficulty of establishing an exact distribution for test statistic under the null hypothesis in addition to assuming multivariate normality of the sample data, which makes the test not very robust when this condition is violated. This work aims to propose three robust tests named LRTR, PBTR, and PBTC, which are based on robust estimators and parametric bootstrap methods. Besides that, we intended to compare the performance of the three proposed tests with the classic OLRT and robust MCPT tests that already exist in the literature. We also wanted to check if the proposed tests that are based on the Comedian robust estimators performed better than the OLRT and PBTC when considering or not outliers in the data. Finally, the performance of asymptotic tests was compared to those that are computationally intensive tests. The tests were evaluated using the type I error rate and power in Monte Carlo simulations. We concluded that the Comedian robust estimators did not add improvements to the asymptotic tests or the computationally intensive tests. The PBTC and PBTR performed better than the OLRT, LRTR, and MCTP. Therefore, the PBTC and PBTR outperformed the classic OLRT and the robust MCPT.

Performance of specific morphologic features in distinguishing low-grade squamous intraepithelial lesions from high-grade squamous intraepithelial lesions in borderline cases: a College of American Pathologists Cytopathology Committee multiobserver study.

Distinguishing between low-grade squamous intraepithelial lesions (LSIL) and high-grade squamous intraepithelial lesions (HSIL) can be difficult on certain Papanicolaou (Pap) tests, hindering interobserver concordance. We investigated the variables influencing the interpretation of LSIL versus HSIL in Pap test slides rejected from the College of American Pathologists PAP education program. Eleven cytologists, who were unaware of the reference interpretation, examined 21 Pap slides (11 submitted as LSIL and 10 as HSIL) rejected from the PAP education program and recorded the number of LSIL cells, HSIL cells, keratinized dysplastic cells, LSIL clusters with mixed HSIL cells, atypical squamous metaplasia, atypical glandular cells, the presence of inflammation or infectious organisms, and the overall interpretation (LSIL or HSIL). We evaluated the significance of these 11 variables using a nonlinear mixed model analysis. LSIL had greater concordance (92 of 121 responses; 76.0% concordance) than HSIL (68 of 110 responses; 61.8% concordance; P < 0.001). The only predictors of misclassified cases were the number of atypical squamous metaplastic cells and the number of HSIL cells (P < 0.001). The more of these cells identified, the more likely the reviewers were to classify the slide as HSIL. The reproducibility of the diagnosis was fair (Gwet's agreement coefficient, 0.33). Interobserver reproducibility is a challenge for a subset of cases with features intermediate between LSIL and HSIL. Atypical squamous metaplasia and dysplastic nuclei with a nuclear/cytoplasmic ratio greater than one half of the cell volume (HSIL) present on a Pap test influenced the likelihood that a reviewer would interpret the case as HSIL rather than LSIL.

A Longitudinal Study of Quantitative Muscle Strength and Functional Motor Ability in Ambulatory Boys with Duchenne Muscular Dystrophy.

Duchenne muscular dystrophy (DMD) is an X-linked recessive genetic disorder, that is characterized by progressive muscle degeneration and loss of ambulation between 7-13 years of age. Novel pharmacological agents targeting the genetic defects and disease mechanisms are becoming available; however, corticosteroid (CS) therapy remains the standard of care. The purpose of this longitudinal study was to elucidate the effect of CS therapy on the rate of muscle strength and gross motor skill decline in boys with DMD and assess the sensitivity of selected outcome measures. Eighty-four ambulatory boys with DMD (49-180 months), 70 on CS, 14 corticosteroid naïve (NCS), participated in this 8-year multi-site study. Outcomes included; isokinetic dynamometry, the Standing (STD) and Walking/Running/jumping (WRJ) dimensions of the Gross Motor Function Measure (GMFM), and Timed Function Tests (TFTs). Nonlinear mixed modeling procedures determined the rate of change with age and the influence of steroids. Despite CS therapy the rate of decline in strength with age was significant in all muscle groups assessed. CS therapy significantly slowed decline in knee extensor strength, as the NCS group declined at 3x the rate of the CS group. Concurrently, WRJ skills declined in the NCS group at twice the rate of the CS group. 4-stair climb and 10 meter walk/run performance was superior in the boys on CS therapy. CS therapy slowed the rate of muscle strength decline and afforded longer retention of select gross motor skills in boys on CS compared to boys who were NCS. Isokinetic dynamometry, Walk/Run/Jump skills, and select TFTs may prove informative in assessing the efficacy of new therapeutics in ambulatory boys with DMD.

Bitcoin volatility predictability–The role of jumps and regimes

This study mainly focuses on the role of jumps in forecasting Bitcoin volatility using linear and nonlinear mixed data sampling models. The results provide strong evidence that using a forecasting model that incorporates continuous-time jump and two-stage regimes can significantly improve predictive accuracy and achieve high economic gains. Interestingly, the superior forecasting ability of the model with a continuous-time jump is reflected in highly volatile periods, especially in the period of a Black Swan event.

Development of a decision-making application for optimum soybean and maize fertilization strategies in Mato Grosso

Mato Grosso accounts for 25 and 31% of soybean and maize grain production in Brazil, respectively. Despite the importance of this region, there is limited information to optimize fertilization management decisions for these crops. Our objectives were to i) quantify soybean and maize yield response to fertilization, ii) develop prediction algorithms to prescribe recommendations based on site characteristics, and iii) incorporate these algorithms in a decision-making application. A total of 37 soybean and 27 maize field trials (year by site combinations) were conducted to test yield responses of soybean to phosphorus (P) and potassium (K), and maize responses to nitrogen (N) and K. Soybean and maize showed significant yield increments to applied P and N, respectively, but K fertilization showed minor yield effects in both crops (and was not considered further). Yield responses to P and N in soybean and maize, respectively, were highly variable across environments, and non-linear mixed model analysis was used to test co-variates to optimize yield response predictions. Including soil pH and initial soil P for soybean, and planting date and soil clay for maize, helped reduce a significant fraction of the site-to-site random variation. Soybean yield response to P increased in soils with higher pH values, agreeing with the concept of more mineral P retention in acidic soils. Maize showed lower N fertilization yield responses in later plantings dates, agreeing with higher water stress typical of late plantings. Out-of-sample relative root mean square error (rRMSE) of predictions were 15.9 and 19.5% for soybean and maize, respectively, showing the model has adequate accuracy to predict crop yield responses to nutrient fertilizations across the region. These algorithms were incorporated in a user-friendly web application to facilitate utilization, and dynamically calculates optimum fertilization rates including economic inputs such as grain and fertilizer prices. Our field results provide basic information to optimize fertilization rates for soybean and maize in Mato Grosso and are available for management decisions through a web application.

Optimizing Resource‐Constrained Project Scheduling Problem considering the Reliability Function

Resource‐constrained project scheduling has been a significant and practical problem in recent decades. In this research, besides previous assumptions and models regarding scheduling, the reliability function with a novel approach is included in the model. A new look at the project scheduling problem is pursued by studying the probability of access to renewable resources. The mentioned problem programming model is a mixed nonlinear mathematical model that uses the properties of an exponential function to become a linear programming model, exact optimization software is used to solve it in smaller dimensions, and a genetic algorithm is used to solve it in NP‐hard dimensions. The algorithms and statistical analysis results at a 95% confidence level show the proper performance of the genetic algorithm; therefore, this algorithm is more efficient for the proposed model. Using the provided mathematical model, this research leads to decreasing time and lags, decreasing costs, and increasing reliability in multimode activities.

Optimal pricing and seat allocation schemes in passenger railway systems

This paper examines optimal pricing and seat allocation schemes in passenger railway systems, where ticket pricing and seat allocation (or capacity allocation) are both Origin-Destination specific. We consider that the demand is sensitive to the ticket price, and a non-concave and non-linear mixed integer optimization model is then formulated for the ticket pricing and seat allocation problem to maximize the railway ticket revenue. To find the optimal solution of the ticket revenue maximization problem effectively, the proposed non-concave and non-linear model is reformulated such that the objective function and constraints are linear with respect to the decision variables or the logarithms of the decision variables. The linearized model is then further relaxed as a mixed-integer programing problem (MILP). Based on the above linearization and relaxation techniques, a globally optimal solution can be obtained by iteratively solving the relaxed MILP and adopting the range reduction scheme. Two numerical examples are presented for illustration.

Simultaneous optimization of quality and censored reliability characteristics with constrained randomization experiment

ABSTRACT Product quality and reliability characteristics are important considerations for all manufacturers in the product and process design. Industrial experiments may include both quality and reliability characteristics with the goal to obtain a compromise optimization of the two responses. In many cases, such experiments do not use a completely randomized design. Instead, they involve a more complicated experimental protocol, for example, subsampling, blocking, and split-plot structure. This paper presents a framework for the simultaneous optimization of quality and reliability characteristics with random effects. The paper provides a linear mixed model for quality characteristic and a nonlinear mixed model for Type I censored lifetime to incorporate random effects in the analysis. Subsequently, the desirability function approach is used to obtain a trade-off between the quality and reliability characteristics. The mixed models in this paper can incorporate information from all censored test stands and random effects. The proposed framework provides engineers with an appropriate approach to simultaneously optimize the quality and reliability characteristics with random effects. The paper used a case study to illustrate the proposed framework. A simulation study is also considered to present the necessary of incorporating random effects in the modelling stage.

Performance of Bos indicus beef cattle supplemented with mineral or with concentrates in tropical Urochloa decumbens pastures: A meta-regression approach

Models are useful to predict responses of beef cattle to supplementation and its interactions with pasture quality. Therefore, this study was conducted to quantitatively understand variables that influence the performance of cattle under grazing, with or without supplementation, in the tropics by using a meta-analytical approach. The database was composed of individual data of 577 heifers and 194 young bulls from 18 experiments. Information collected included: sex (male or female), total dry matter intake, supplement dry matter intake, forage crude protein (CPforage), forage indigestible neutral detergent fiber (iNDFforage), forage neutral detergent fiber, neutral detergent insoluble protein, crude protein intake from supplement (CPIsupp), metabolizable energy intake from supplement (MEIsupp), initial body weight (BW), final BW and average daily gain (ADG). Additionally, the intakes of rumen degradable protein (RDP), rumen undegradable protein (RUP), and metabolizable protein (MP) from the supplement of each study were calculated. To model animal performance, values within each experiment were divided into two components: ADG-pasture (ADG of non-supplemented animals) and ADG-supplement (differential ADG in relation to non-supplemented animals). Data were evaluated using a meta-analysis approach to estimate fixed and random effects of experiment using linear and nonlinear mixed models. There was no correlation between ADG-pasture and initial BW or final BW. The CPforage was positively correlated, and iNDFforage was negatively correlated with ADG-pasture. Therefore, two equations were developed to predict ADG-pasture, as follows: ADG-pasturemales (kg/day) = 0.007434 × CPforage – 0.001044 × iNDFforage; ADG-pasturefemales (kg/day) = 0.01445 × CPforage – 0.0000642 × CPforage2 – 0.001598 × iNDFforage. There was no correlation between ADG-supplement and total dry matter intake, initial BW, or final BW. The ADG-supplement was positively correlated with CPIsupp and MEIsupp. An exponential model was chosen to fit ADG-supplement. Equations to predict ADG-supplement were composed of three exponential compartments based on ADG-pasture, CPIsupp (or RDP, RUP or MP intakes from supplement), and MEIsupp. The replacement of CPIsupp by RDP, RUP or MP intakes from supplement demonstrated that all protein components could be used to predict the performance of grazing animals. Still, the best fit was observed when RUP intake from supplement was used. The validation process through cross-validation analyses demonstrated that all equations had high accuracy and moderate precision. In conclusion, our results indicate that ADG-pasture can be estimated from CPforage, iNDFforage. The ADG-supplement can be estimated from ADG-pasture, MEIsupp, and protein components intake in grazing heifers and young bulls.

Polymorphism in the BIEC2-808543 locus and its association with growth curve in Brasileiro de Hipismo horse breed

Our objective was to evaluate whether the single nucleotide polymorphism (SNP) BIEC2-808543, identified in some horse breeds, also occurs in the Brasileiro de Hipismo (BH) breed. In addition, we verified if this SNP is related to the growth curve profile of these animals for the variables body mass, height at withers, and height at croup, using nonlinear mixed models. For the DNA isolation, we collected blood samples from 167 young BH horses. We obtained the genotypes of these animals [...]

Optimal station locations for en-route charging of electric vehicles in congested intercity networks: A new problem formulation and exact and approximate partitioning algorithms

This paper addresses a new electricity-charging station location problem for congested intercity or regional networks, in which electric vehicles with a limited driving range require recharges for their long-distance trips. When the distribution of charging stations does not sufficiently cover all used routes, some drivers may take a detour to find charging opportunities (or switch to another transportation mode). The goal of this station location problem is to find, under a limited construction budget, an optimal set of charging station locations such that all vehicles finish their trips by choosing a self-optimal route with necessary charging opportunities while the overall network congestion caused by possible detours is minimized. The problem is written as a bi-level mixed nonlinear integer programming model, where the upper level of the model is set to regulate the selection of station locations subject to the construction budget while the lower level is used to characterize the equilibrium flow pattern of electric vehicles with the charging requirement. Selected exact and approximate algorithms, namely, the branch-and-bound algorithm and the nested partitions algorithm are adopted to solve this station location problem. While both algorithms imply a divide-and-conquer strategy, the branch-and-bound algorithm poses a deterministic, exact procedure that utilizes the bounding mechanism to prune impossible solution subspaces, whereas the nested partitions algorithm performs a stochastic search and selection process in terms of the optimality probability for near-optimal solutions. To get numerical insights on the algorithmic performance and solution behavior, we test these algorithms through a couple of benchmark network instances. A performance comparison of the algorithms indicates that, the branch-and-bound algorithm can quickly obtain the global optimum when the driving range is relatively low, while the nested partitions algorithm can find optimal solutions or extremely near-optimal solutions in all cases and typically spend on average only one fourth of the computing time of the branch-and-bound algorithm. The network flow solutions clearly show, compared to gasoline vehicle drivers, how an insufficient driving range or number of charging stations may significantly reduce the number of feasible paths and force electric vehicle drivers to choose more costly paths, which thus reshapes flow patterns and possibly increases congestion levels.

Genetic Profile and Associated Characteristics of 150 Korean Patients with Retinitis Pigmentosa.

Purpose Retinitis pigmentosa (RP) shows great diversity between genotypes and phenotypes, and it is important to identify the causative genes. This study aimed to analyze the molecular profiles, associated ocular characteristics, and progression of RP in Korean patients. Methods All the genetic variants in patients with RP, identified using targeted next-generation sequencing (NGS) with a panel of 88 RP-related genes between November 2018 and November 2019, were retrospectively reviewed. All the patients underwent comprehensive ophthalmological evaluations, and their clinical and family histories were recorded. The best-corrected visual acuity (BCVA) deterioration and photoreceptor disruption progression rates were determined based on the major causative mutational genes using nonlinear mixed models, and the differences among them were investigated using the interaction effect. Results Among the 144 probands, 82 variants in 24 causative genes were identified in 77 families (53.5%). Most of the RP cases were associated with autosomal recessive variants (N = 64 (44.4%)), followed by autosomal dominant (N = 10 (6.9%)) and X-linked variants (N = 3 (2.1%)). The four most frequently affected genes were EYS (N = 15 (10.4%)), USH2A (N = 12 (8.3%)), PDE6B (N = 9 (6.3%)), and RP1 (N = 8 (5.6%)). Epiretinal membranes and cystoid macular edema were frequently noted in the patients with USH2A (75.0%) and PDE6B (50.0%) variants, respectively. During the follow-up period, the BCVA and photoreceptor disruption changes were significantly different among the patients carrying the four common causative genes (P=0.014 and 0.034, resp.). Patients with PDE6B variants showed faster BCVA changes (0.2 LogMAR/10 years), and those with USH2A variants showed the fastest ellipsoid zone disruptions (−170.4 µm/year). Conclusion In conclusion, our genetic analysis using targeted NGS provides information about the prevalence of RP-associated mutations in Korean patients. Delineating clinical characteristics according to genetic variations may help clinicians identify subtype features and predict the clinical course of RP.

Effects of a Dominant Species on the Functional Diversity of Coexisting Species in Temperate Deciduous Understorey.

The herb layer plays a significant role in maintaining forest functions, and its community composition is determined by various abiotic factors and biotic interactions. This study attempted to investigate the interspecific plant–plant biotic interactions using a functional traits approach. Specifically, the effects of a dominant species coverage on the functional diversity of coexisting species in the temperate forest understory were studied. Species coverage and soil moisture data were collected using a 1 m2 quadrat couplet (2 × 1 m2) from six sites alongside a 20 m linear transect encompassing a cover gradient of Allium ursinum in southwest Hungary. Major plant functional dimensions i.e., aboveground, and clonal functional traits were considered. Linear and nonlinear mixed models to quantify the effects of biotic interaction on the functional diversity of every single trait and multiple traits were employed. Both aboveground traits and clonal traits of persistent clonal growth organs responded positively to the A. ursinum L., cover gradient. The coexistence of understory species in the presence of a monodominant species seems to be mainly influenced by aboveground traits as compared to the clonal traits suggesting, a role of niche differentiation. The consistent impact of A. ursinum coverage on coexisting species dynamics highlights a need for similar in-depth studies in various forest settings.

Architecture of broiler breeder energy partitioning models

A robust model that estimates the ME intake over broiler breeder lifetime is essential for formulating diets with optimum nutrient levels. The experiment was conducted as a randomized controlled trial with 40 Ross 708 broiler breeder pullets reared on 1 of 10 target growth trajectories, which were designed with 2 levels of cumulative BW gain in prepubertal growth phase and 5 levels of timing of growth around puberty. This study investigated the effect of growth pattern on energy efficiency of birds and tested the effects of dividing data into daily, 4-d, weekly, 2-wk, and 3-wk periods and the inclusion of random terms associated with individual maintenance ME and ADG requirements, and age on ME partitioning model fit and predictive performance. Model [I] was: MEId = a × BWb + c × ADGp + d × ADGn + e × EM + ε, where MEId was daily ME intake (kcal/d); BW in kg; ADGp was positive ADG; ADGn was negative ADG (g/d); EM was egg mass (g/d); ε was the model residual. Models [II to IV] were nonlinear mixed models based on the model [I] with inclusion of a random term for individual maintenance requirement, age, and ADG, respectively. Model [II] – 3 wk was chosen as the most parsimonious based on lower autocorrelation bias, closer fit of the estimates to the actual data (lower model MSE and closer R2 to 1), and greater predictive performance among the models. Estimated ME partitioned to maintenance in model [II] – 3 wk was 100.47 ± 7.43 kcal/kg0.56, and the ME requirement for ADGp, ADGn, and EM were 3.49 ± 0.37; 3.16 ± 3.91; and 2.96 ± 0.13 kcal/g, respectively. Standard treatment had lower residual heat production (RHP; -0.68 kcal/kg BW0.56) than high early growth treatment (0.79 kcal/kg BW0.56), indicating greater efficiency in utilizing the ME consumed. Including random term associated with individual maintenance ME in a 3-wk chunk size provided a robust, biologically sound life-time energy partitioning model for breeders.

Genome-Wide Association Studies for Growth Curves in Meat Rabbits Through the Single-Step Nonlinear Mixed Model.

Growth is a complex trait with moderate to high heritability in livestock and must be described by the longitudinal data measured over multiple time points. Therefore, the used phenotype in genome-wide association studies (GWAS) of growth traits could be either the measures at the preselected time point or the fitted parameters of whole growth trajectory. A promising alternative approach was recently proposed that combined the fitting of growth curves and estimation of single-nucleotide polymorphism (SNP) effects into single-step nonlinear mixed model (NMM). In this study, we collected the body weights at 35, 42, 49, 56, 63, 70, and 84 days of age for 401 animals in a crossbred population of meat rabbits and compared five fitting models of growth curves (Logistic, Gompertz, Brody, Von Bertalanffy, and Richards). The logistic model was preferably selected and subjected to GWAS using the approach of single-step NMM, which was based on 87,704 genome-wide SNPs. A total of 45 significant SNPs distributed on five chromosomes were found to simultaneously affect the two growth parameters of mature weight (A) and maturity rate (K). However, no SNP was found to be independently associated with either A or K. Seven positional genes, including KCNIP4, GBA3, PPARGC1A, LDB2, SHISA3, GNA13, and FGF10, were suggested to be candidates affecting growth performances in meat rabbits. To the best of our knowledge, this is the first report of GWAS based on single-step NMM for longitudinal traits in rabbits, which also revealed the genetic architecture of growth traits that are helpful in implementing genome selection.

Site-specific modelling of short-term soil carbon mineralization in central Argentina

Soil organic carbon (SOC) mineralization is essential for nutrient cycling; however, it also increases carbon emission as CO2 to the atmosphere (CO2-C). Therefore, detailed information is required to design land use practices promoting positive C balances and soil health. Short-term SOC mineralization is sensitive to soil properties. Short-term soil C mineralization at a landscape scale has been poorly describe, despite the need to understand the variability of C dynamics among environments. The objectives of this work were to 1) estimate the parameters of short-term soil C mineralization kinetics in different locations within a region and 2) explore correlations among site-specific kinetic parameters and edaphoclimatic properties of sampled sites. The study involved 150 sites with different soil and climatic characteristics sampled from a 165,000 km2 area in central Argentina. CO2-C data were obtained from 28-day laboratory incubation experiments of the 150 soil samples. We tested three models (exponential, hyperbolic and power), which depend non-linearly on their parameters, to describe the population average cumulative CO2-C. Using nonlinear mixed models, we tested the significance of random site effects to explain variability in curve parameters among soils. Random forest was used to explain C mineralization parameters from edaphoclimatic properties. The best fit was provided by the power model with random effects on two parameters: initial C mineralization rate and mineralization rate coefficient. The results indicate heterogeneous C mineralization processes across central Argentina. The observed cumulative CO2-C after 28 days of soil incubation ranged between 250 and 1693 mg C kg−1 soil with an average of 826 mg C kg soil−1. Lower amounts of CO2-C (800 mg C kg−1 soil) are expected at 28 days of mineralization in sandy loam soils with lower organic matter than in rich loam soils (more than 1000 mg C kg−1 soil). A relational study explaining site-specific C mineralization from soil, climatic and management variables indicated a significantly higher short-term C mineralization in soils with high organic matter and soil chemical fertility, with soil properties being more important process drivers than climatic variables. Thus, short-term C mineralization kinetics can be predicted from soil properties at the large scale.

Longitudinal changes in energy cost during walking in boys with Duchenne Muscular Dystrophy (DMD).

In boys with DMD, muscle weakness progresses in a proximal to distal pattern, leading to compensatory gait strategies, including hyperlordosis and equinus, that increase energy cost and accelerate the loss of walking capacity. The purpose of this study was to determine the changes in the energy cost of walking that occur with disease progression and to determine the optimal normalization scheme for the longitudinal assessment of the energy cost of walking in boys with DMD. Energy cost was assessed with the COSMED K4b2. Three normalization schemes were examined: gross energy cost (EC), net non-dimensional oxygen cost (NNcost) and speed-matched control energy cost (SMC-EC). Nonlinear mixed modeling procedures determined the rate of change with age. Linear regression was used to asses the relationship between each normalization scheme and age and body height. 74 boys with DMD were assessed for the energy cost of walking. Velocity decreased at a significant rate (-.00245/month, p = .03) across time; (Fig. 2), while gross EC (.003248/month, p = 0.0026), NNcost (.006155/month, p < 0.0001) and SMC-EC (.001690/month, p = 0.03) all increased significantly. Age and height were significantly associated with NNcost and SMC-EC. The sensitivity of NNcost and SMC-EC to age over time were similar, while SMC-EC was less sensitive to changes in height over time than NNcost. In contrast to able-bodied peers, boys with DMD decrease their velocity while all walking energy cost measures increased over time. Both SMC-EC and NNcost proved appropriate normalization schemes for boys with DMD. Compared to gross EC, both NNcost and SMC-EC were less sensitive to changes in age over time, while SMC-EC was less sensitive to changes in height than NNcost. Therefore, both NNCost and SMC-EC are suggested normalization schemes for the longitudinal assessment of energy cost in boys with DMD.