Kalman filter with impulse noised outliers: a robust sequential algorithm to filter data with a large number of outliers.

Impulse noised outliers are data points that differ significantly from other observations. They are generally removed from the data set through local regression or the Kalman filter algorithm. However, these methods, or their generalizations, are not well suited when the number of outliers is of the same order as the number of low-noise data (often called nominal measurement). In this article, we propose a new model for impulsed noise outliers. It is based on a hierarchical model and a simple linear Gaussian process as with the Kalman Filter. We present a fast forward-backward algorithm to filter and smooth sequential data and which also detects these outliers. We compare the robustness and efficiency of this algorithm with classical methods. Finally, we apply this method on a real data set from a Walk Over Weighing system admitting around 60 % of outliers. For this application, we further develop an (explicit) EM algorithm to calibrate some algorithm parameters.

Short-term responses of meat ewes facing an acute nutritional challenge in early-mid lactation.

Simulating a consequence of a climate change event on feed availability, responses of Mediterranean meat ewes facing an acute undernutritional challenge (CHA; i.e., fed only low nutritional value cereal straw) were evaluated at a sensitive physiological stage (i.e., early suckling). Forty Romane ewes were chosen at early-mid pregnancy (around 2 mo) according to parity (20 primiparous, PRIM; 20 multiparous, MULT); feed efficiency genetic line of their sires (residual feed intake [RFI]; efficient, RFI-, n = 10 per parity; inefficient, RFI+, n = 10 per parity); litter size (i.e., bearing twins, diagnosed by ultrasonography); body weight (BW, kg) and body condition score (BCS) (initial BW and BCS [mean ±â€…SD]: 51.6 ±â€…7.41 kg; 2.5 ±â€…0.20, respectively; representing flock' averages per parity). Effects on dry matter intake (DMI), ewes' BW and BCS, subcutaneous dorsal fat thickness (DFT), energy metabolism (plasma non-esterified fatty acids [NEFA], ß-hydroxybutyrate (ß-OHB), glucose, urea, triiodothyronine [T3]), and lambs' growth (BW and average daily gain [ADG]; g/d) were examined before, during and after CHA. Individuals' profiles of the response-recovery to CHA were described using a piecewise mixed-effects model. The fixed effect of parity and genetic line and the random effect of individual (ewe) were considered. A linear mixed-effects model was fitted to explore the effects on lambs' growth. The 2-d straw-only CHA had significant effects on most of the recorded parameters. Meaningful drops and recoveries were observed on ewes' DMI, BW, and DFT with effect on postchallenge levels. BW, BCS, DFT, or DMI were also affected by parity (MULT > PRIM) but not by genetic line. Plasma NEFA, ß-OHB, glucose, urea, and T3 responded well to CHA with drops in T3, urea, and glucose levels, whereas NEFA and ß-OHB significantly increased after CHA. MULT ewes presented sharper ß-OHB recovery from CHA than PRIM (P ≤ 0.05). With this study, we provide tangible and necessary data for an emerging field of research. Our results give new insights into how such a short and abrupt CHA affects some key zootechnical and physiological parameters, and to what extent the impacts of CHA and the ewes' response-recovery are influenced. It also revealed potential between-individual differences in the adaptive capacities of ewes, which require further exploration.

Genome-wide analyses reveal a strong association between LEPR gene variants and body fat reserves in ewes.

BACKGROUND: Among the adaptive capacities of animals, the management of energetic body reserves (BR) through the BR mobilization and accretion processes (BR dynamics, BRD) has become an increasingly valuable attribute for livestock sustainability, allowing animals to cope with more variable environments. BRD has previously been reported to be heritable in ruminants. In the present work, we conducted genome-wide studies (GWAS) in sheep to determine genetic variants associated with BRD. BR (i.e. levels) and BRD (i.e. changes over time) were obtained through body condition score measurements at eight physiological stages throughout each productive cycle in Romane ewes (n = 1034) and were used as phenotypes for GWAS. After quality controls and imputation, 48,593 single nucleotide polymorphisms (SNP) were included in the GWAS. RESULTS: Among the 23 QTL regions identified, a major QTL associated with BR during pregnancy and lactation was identified on chromosome 1. In this region, several significant SNPs mapped to the leptin receptor gene (LEPR), among which one SNP mapped to the coding sequence. The point mutation induces the p.P1019S substitution in the cytoplasmic domain, close to tyrosine phosphorylation sites. The frequency of the SNP associated with increased BR levels was 32%, and the LEPR genotype explained up to 5% of the variance of the trait. Higher fatness levels in ewes carrying the LEPR p.P1019S mutation were observed all along the productive cycle. CONCLUSIONS: These results provide strong evidences for involvement of LEPR in the regulation of BR in sheep and highlight it as a major candidate gene for improving adaptive capacities by genetic selection.

Residual Feed Intake in Dairy Ewes: An Evidence of Intraflock Variability.

This study examined the intraflock variability of feed efficiency in dairy ewes, through monitoring residual feed intakes (RFI). Primiparous lactating ewes (n = 43; 57.7 ± 0.91 kg body weight [BW] at lambing), representative of a French Lacaune dairy flock, were allocated in an equilibrated 2 × 2 factorial design experiment, lasting for 63 days during mid-lactation and combining 2 litter sizes (singletons, SING or twins, TWIN) and 2 daily milking frequencies (once, ONE or twice, TWO). Weaning occurred, and milking started, at 35 days after lambing (DIM). Ewes were individually fed a diet based on ryegrass silage, local hay, and supplements. Individual DMI was recorded daily and further used to evaluate (and compare) differences in RFI between ewes at 42, 49, 56, 63, 70, 77, 84, 91, and 98. Average individual RFI were calculated weekly since the first week (i.e., 35-42 DIM). Total (BW) and metabolic (BW0.75) body weight, body condition score (BCS), milk yield, and plasma non-esterified fatty acids (NEFA) were monitored weekly. Differences in DMI were mainly due to the lactation stage and litter size and were 11% higher in ewes with TWIN compared to SING. This was positively correlated to milk yield and consistent with differences in RFI which varied due to litter size and to the milking frequency × lactation stage interaction. Ewes that lambed SING showed higher feed efficiency (-0.08 ± 0.018 vs. 0.13 ± 0.014 kg DM/ewe/d of RFI in SING vs. TWIN, respectively), whereas there were no differences in BW or BCS. Milking frequency did not affect DMI but milk yields were higher in TWO, which was related to a higher feed efficiency in this group (0.115 ± 0.016 vs. -0.07 ± 0.016 kg DM/ewe/d of RFI in ONE vs. TWO, respectively). Average RFI was affected (p < 0.0001) by the ewe, thus allowing a ranking among individuals to be established. High (n = 22) or low (n = 21) feed efficiency ewes averaged -0.17 ± 0.09 or 0.18 ± 0.09 kg DM/d RFI, respectively. Estimates of RFI were not correlated to the individual milk production potential. Even if no differences in BW, BW0.75, or BCS were detected, high-efficiency ewes mobilized 1.5 times their body reserves (0.30 vs. 0.20 mmol NEFA/L of plasma) when compared to the low-efficiency group. The observed intraflock variability in feed efficiency of this dairy ewes' flock was affected by litter size and milking frequency but also by evident differences between individuals' physiologies.

Short-, Medium- and Long-Term Metabolic Responses of Adult Meat Ewes Subjected to Nutritional and ß-Adrenergic Challenges.

Shortage and refeeding situations lead to switches in metabolic pathways induced by undernutrition and body energy reserve (BR) replenishment cycles. In a 122-d experiment, 36 adult Merinos d'Arles ewes were chosen and first accustomed to diet ingredients (i.e., wheat straw, pelleted alfalfa and sugar beet pulp) and the facility environment for 22 d. Then, ewes were randomly assigned to one of three "diet challenge" treatments during 50 d, (control, underfed and overfed; 12 ewes each) corresponding to 100%, 70% or 160% of energy requirements allowances, respectively. Then, a "refeeding challenge" was applied the last 50 d (i.e., diets adjusted with the same ingredients). An individual monitoring of body weight (BW), body condition score (BCS) and energy metabolism was carried out. The last day, a "ß-adrenergic challenge" was applied. Anabolic or catabolic responses were accompanied by synchronized metabolic regulations, leading to contrasting metabolic and BR profiles. Average BW and BCS were higher and lower in overfed and underfed ewes, respectively, which was proportional to lower and higher BR mobilization dynamics. Higher plasma free fatty acids (FFA) were accompanied by lower blood insulin, leptin and glucose levels. After refeeding, a rebound in BW and BCS were observed, and FFA were drastically reduced in underfed ewes. No differences were detected in plasma FFA at the end of the study, but the lipolytic activity was different and contrasted with the adipose tissue mass.

Indirect measures of methane emissions of Sahelian zebu cattle in West Africa, role of environment and management.

In Northern Senegal, traditional cattle management systems (TRAD) which depend on natural forages coexist with intensified systems (INT) which rely on periodic supplementation with crop residues and local concentrates. This study aims to estimate the effects of seasons and management systems on the methane emissions of Gobra zebu, in relation to the diet's chemical composition and feed intake. Six Gobra zebu cows per management system were individually monitored over 10 months, diet and faeces were sampled each season and their chemical composition and dry matter intake (DMI) were predicted by near infrared spectroscopy. Each diet was fermented in vitro to assess methane production and volatile fatty acid concentration. The DMI and digestible organic matter intake (DOMI) decreased (P < 0.0001) during the dry seasons for both systems in the same range, but INT improved the crude protein of the diets (P < 0.0001). Enteric methane production (mmol.g-1 dry matter) was lower for TRAD than INT, except during the rainy season when TRAD cows experienced a higher increase (P = 0.002). The methanogenic potential (methane production in vitro × DMI) varied with the seasons and the system with more accentuated variations for TRAD (P < 0.0001). Methanogenic potential shows true reflection of the effects of the seasons and management systems. The results highlight that enteric methane emissions varied with seasonal changes and that intensifying the diet induced no mitigating effect.

Relationships between body reserve dynamics and rearing performances in meat ewes1.

The main objective of this work was to study the relationships between body reserve (BR) dynamics and rearing performance (PERF) traits in ewes from a Romane meat sheep flock managed extensively on "Causse" rangelands in the south of France. Flock records were used to generate data sets covering 14 lambing years (YR). The data set included 1,146 ewes with 2 ages of first lambing (AGE), 3 parities (PAR), and 4 litter sizes (LS). Repeated measurements of the BW and BCS were used as indicators of BR. The ewe PERF traits recorded were indirect measurements for maternal abilities and included prolificacy, litter weight and lamb BW at lambing and weaning, ADG at 1, 2, and 3 mo after lambing, and litter survival from lambing to weaning. The effects of different BW and BCS trajectories (e.g., changes in BW and BCS across the production cycle), previously been characterized in the same animals, on PERF traits were investigated. Such trajectories reflected different profiles at the intraflock level in the dynamics of BR mobilization-accretion cycles. Genetic relationships between BR and PERF traits were assessed. All the fixed variables considered (i.e., YR, AGE, PAR, LS, and SEX ratio of the litter) have significant effects on the PERF traits. Similarly, BW trajectories had an effect on the PERF traits across the 3 PARs studied, particularly during the first cycle (PAR 1). The BCS trajectories only affected prolificacy, lamb BW at birth, and litter survival. Most of the PERF traits considered here showed moderate heritabilities (0.17-0.23) except for prolificacy, the lamb growth rate during the third month and litter survival which showed very low heritabilities. With exception of litter survival and prolificacy, ewe PERF traits were genetically, strongly, and positively correlated with BW whatever the physiological stage. A few weak genetic correlations were found between BCS and PERF traits. As illustrated by BW and BCS changes over time, favorable genetic correlations were found, even if few and moderate, between BR accretion or mobilization and PERF traits, particularly for prolificacy and litter weight at birth. In conclusion, our results show significant relationships between BR dynamics and PERF traits in ewes, which could be considered in future sheep selection programs aiming to improve robustness.

Genetic analysis of robustness in meat sheep through body weight and body condition score changes over time.

Animal robustness may be defined as a complex trait characterizing the ability of an individual to be adapted, productive and healthy under contrasted and fluctuating environmental situations. Such a trait is now considered an essential criterion in order to meet the more ambitious goals of farming sustainability. In ruminants, one of the key mechanisms via which robustness is expressed is the capacity to mobilize or restore body reserves (BR) to cope with the challenges of negative energy balances. The objectives of this work were as follows: 1) to estimate the genetic parameters related to BR dynamics in ewes over successive production cycles and 2) to investigate BR management relationships between different physiological stages. For this, historical individual BW and BCS data from 2,920 phenotyped ewes were used for genetic analysis. The changes in BW (∆BW) and BCS (∆BCS) over time were analyzed. Eight physiological stages were considered to investigate these changes over time: mating, early pregnancy, mid-pregnancy, lambing, early suckling, mid-suckling, weaning, and postweaning. The estimated heritability were low for both ∆BW (h2 = 0.13 to 0.18) and ∆BCS (h2 = 0.04 to 0.16). Moderate to high positive genetic correlations (from 0.48 to 0.91) were obtained between BR mobilization phases and between BR accretion phases. Similarly, moderate to high negative genetic correlations (from -0.36 to -0.75) were estimated between the BR mobilization and accretion periods, suggesting that mechanisms driving BR mobilization and accretion processes were genetically correlated. This is the first study in ruminants that demonstrate that the extent and temporal changes in profiles of BR mobilization and accretion are heritable and genetically linked, indicating that such traits could be considered in genetic programs aimed at improving robustness. Nevertheless, further research is needed for a more comprehensive understanding of BR dynamics, notably by including other physiological parameters (i.e., metabolites and hormones) and additional information on the productive and reproductive life of the ewe.

Indigenous sheep breeds in Brazil: potential role for contributing to the sustainability of production systems.

Brazil has vocation for food production, both vegetable and animal, with the sheep industry having an expanding activity. However, productivity rates are often bellowing the possibilities of the country. Here, the roles the native breeds may develop in this expanding activity are described. Breeds considered are the hair breeds Santa Inês, Morada Nova, Somális Brasileira, Cariri, and Rabo Largo, and the wool breeds Bergamácia Brasileira, Crioula Lanada, and Pantaneira. These breeds have arisen in environments that may be considered difficult for other (exotic) breeds, less adapted to the local conditions. The hair breeds emerged in a semi-arid environment, a hot and with low rainfall region, of the Northeast of Brazil. The Crioula Lanada is the only breed that originated in the South, in a subtropical region with cold winters. The genetic group Pantaneira had its origin in an environment with higher humidity, especially soil moisture. The Bergamácia Brasileira derived from the Italian Bergamasca breed, which was first introduced in northeastern Brazil. Animals from these breeds have been regarded as robust, with lower requirements for maintenance, resistant to worms, and easy to handle. On the other side, as they are generally smaller than the exotic breeds used for meat production, they are often considered as less productive. In this literature review, a possibility of valorizing them, both as purebred or in crossbreeding programs, especially for meat production is addressed. These breeds are part of the genetic, historical, and cultural heritage of Brazil, and if used properly, according to the different environments and production systems, they can also be very important in the development of the sheep industry.

Integrating banana and ruminant production in the French West Indies.

Using a mechanistic model, we compared five alternative farming systems with the purpose of transforming monoculture (MON) banana farms into mixed farming systems (MFS) with ruminants feeding banana by-products (leaves, pseudostems and nonmarketable fruits) and forage from the fallow land. The paper presents the main structure of the model (land surface changes, available biomass for animals, stocking rates, productive or reproductive indicators), and impact assessment (change in farm productivity) is discussed. Five MFS with typical local ruminant production systems were used to compare MON to the strategies using forage from fallow and/or integrating Creole cattle (CC), Creole goats (CG) or Martinik sheep (MS) into banana farming. One hectare MON shifted into an MFS allows a stocking rate of 1,184, 285, and 418 kg of live weight per hectare for CC, CG and MS, respectively. Banana by-products seem to be better valorized by the CC scenario. However, parameters such as length of the cycle, local prices for cattle, goat and sheep meat, work time and farmer's skills in ruminant management may have been taken into account by the farmer when choosing the ruminant species to rear.