Bootstrap Confidence intervals for the Shannon biodiversity index: A simulation study

Biodiversity determination at any organization level is a heuristic tool in environmental management. The Shannon biodiversity index stands out among the various available indexes that combine both components of the concept: species number and their relative abundance. Whatever the index used, an aspect that has received little attention in the study of biodiversity is the uncertainty quantification, precluding hypothesis testing. Applying standard bootstrap methods to estimate the index allows us to build confidence bounds, but it yields underestimated indexes due to unsampled species. This article explores the empirical mean coverage of confidence intervals for the Shannon biodiversity index when the total number of species in the sample itself is subject to random variation. I analyze their dependence on evenness, total abundance, and number of species within the community. Very low empirical coverages of bootstrap confidence intervals were obtained using the standard and bias-corrected techniques. I propose a new technique using the difference of the original sample and each bootstrap replication to build an empirical, adjustment for the bias, and get an adjusted point estimator and corresponding confidence interval. An example based on field data, is considered.     

Definition of apparent, true, and standardized ileal digestibility of amino acids in pigs

Measures of ileal digestibility (ID) are used routinely as estimates of amino acid (AA) bio-availability in pig feed ingredients. Values for ID may be expressed as apparent (AID), standardized (SID), or true (TID). Values for AID are calculated by deducting the total ileal outflow of AA (the sum of endogenous losses (IAA_end) and non-digested dietary AA) from dietary AA intake. The IAA_end may be separated into basal losses, which are not influenced by feed ingredient composition, and specific losses induced by feed ingredient characteristics such as anti-nutritional factors and dietary fiber. If the AID values are corrected for total IAA_end, then values for TID are calculated. Lack of additivity of AID values in feed formulation may be overcome by correcting AID values for basal IAA_end only, which yields SID values. Until reliable procedures for the routine measurement of specific IAA_end become available, it is suggested that SID values are used for feed formulation. It is advisable that basal IAA_end are measured in digestibility experiments and that these losses are reported with SID values.     

Understanding veterinary practitioners' decision-making process: implications for veterinary medical education

Understanding how veterinary practitioners make clinical decisions, and how they use scientific information to inform their decisions, is important to optimize animal care, client satisfaction, and veterinary education. We aimed to develop an understanding of private practitioners' process of decision making. On the basis of a grounded-theory qualitative approach, we conducted a telephone survey and semi-structured face-to-face interviews. We identified a decision-making framework consisting of two possible processes to make decisions, five steps in the management of a clinical case, and three influencing factors. To inform their decision, veterinary surgeons rarely take the evidence-based medicine (EBM) approach. They consult first-opinion colleagues, specialists, laboratories, and the Internet rather than scientific databases and peer-reviewed literature, mainly because of limited time. Most interviewees suggested the development of educational interventions to better develop decision-making skills in veterinary schools. Adequate information and EBM tools are needed to optimize the time spent in query and assessment of scientific information, and practitioners need to be trained in their use.     

A Case of Atypical Psoroptic Mange in a Domestic Rabbit

A female checkered giant cross rabbit (Oryctolagus cuniculus) was presented with skin lesions on the perineal region. The cutaneous lesions extended 2 cm from the vulva and perineal glands. They were moist and erythematous, with abundant greasy yellowish scabs. Skin scrapings from the lesions were mounted in Amman’s chloral-lactophenol on microscope slides and examined at ×10 and ×40 magnification. Numerous mites were observed and identified as Psoroptes cuniculi, a common causal agent of otitis externa in rabbits. The rabbit was treated successfully with ivermectin. This case of psoroptic mange is atypical owing to the perineal location, apparent absence of auricular lesions, and the lack of contagion despite close contact with several other rabbits.     

Energy and protein retention in holoxenic,axenig and gnotoxenig chickens monoassociated with Lactobacillus SPP

1. Axenic, holoxenic and monoxenic chickens (strains LEM 220 or LEM 206 of lactobacilli isolated from the crop of the cockerel) were fed ad libitum on semi‐purified diets containing 180 or 200 g protein and 30 g long (LCD) or short (SCD) chain dextrins/kg. Energy and protein retentions were determined from 0 to 3 weeks of age by carcass analysis.

2. Energy retained as a proportion of gross energy intake was only influenced by the microflora in birds receiving 180 g protein/kg and nitrogen retention followed a similar pattern, but differences were less marked: total flora always depressed retentions, but in monoxenic birds the action of the microflora varied with changes in the carbohydrate composition of the diet, the lowest retentions occurring when the diet contained carbohydrates (SCD) which allowed rapid lactate production in the crop.     

Induction of a barrier membrane to facilitate reconstruction of massive segmental diaphyseal bone defects: an ovine model

OBJECTIVES: To report an ovine model that can be used to evaluate the efficacy of bone substitutes for repair of segmental diaphyseal bone defects. STUDY DESIGN: Experimental study. ANIMALS: Eleven 2-year-old Pré-Alpes Sheep. METHODS: Mid-diaphyseal metatarsal bone defects (25 mm long) were stabilized by a dynamic compression plate over a polymethylmethacrylate (PMMA) cement spacer, and by external coaptation. The PMMA spacer was removed at 6 weeks by incising the encapsulating membrane. The defect remained unfilled (Group 1; n=5) or was filled with morselized autologous corticocancellous graft (Group 2; n=6), the membrane sutured closed, and external coaptation applied for 6 months, when healing was evaluated. RESULTS: Radiographic, computed tomographic, and histologic examinations at 6 months after the 2nd surgery revealed non-union in ungrafted defects whereas grafted defects showed bone healing. The induced membrane had blood vessels, CBFA1+ cells, and very few macrophages entrapped in a collagenous tissue positive for type I collagen. CONCLUSION: This ovine metatarsal defect model resulted in a critical-size defect (non-union) that healed when grafted. The PMMA-induced membrane constrained the graft, was well vascularized, and may have osteogenic properties. CLINICAL RELEVANCE: This model may be useful to evaluate new strategies in bone tissue engineering because the PMMA-induced membrane may help confine bone morphogenetic proteins, skeletal stem cells, or other agents to the defect cavity where they could be useful to enhance bone formation.     

The effect of grinding and pelleting of wheat and maize on amino acids true ileal digestibility and endogenous losses in growing pigs

Two experiments were performed in order to test the effects of grinding and pelleting wheat (experiment 1) or maize (experiment 2) on amino acids (AA) standardized (SID) and true (TID) ileal digestibility. Basal ileal endogenous losses (IEL), used to calculate SID from apparent digestibility, were determined by feeding a protein-free diet. Total IEL required to calculate TID were estimated as the difference between total and dietary losses determined according to the isotope dilution technique using ¹⁵N-labeled crops. Wheat and maize were ground to compare two different mean particle sizes (d₅₀ 500 μm and 1000 μm). Then, a fraction of the 500-μm mash was further pelleted through two dies of different thicknesses (16 vs. 20 mm for wheat and 16 vs. 24 mm for maize), holes diameter 4 mm in both cases. Cereals were incorporated in 4 isoproteic diets either in mash form (fine vs. coarse mash) or in pelleted form (thin vs. thick die). In experiment 1, wheat was associated with rapeseed meal diets, while in experiment 2, maize was associated with soybean meal. The reduction of wheat particle size affected neither AA SID nor TID. In contrast, the pelleting treatment significantly improved protein and most AA SID and TID. In addition, total IEL of protein and several AA were significantly reduced when the thicker die was used. Numeric improvements of protein and AA SID were observed with reduction of maize particle size and this was associated with a significant decrease in total IEL so that TID was not modified. Further improvements of AA SID and TID occurred with pelleting of maize, without significant effect on IEL regardless of die thickness.