Pairwise ratio-based differential abundance analysis of infant microbiome 16S sequencing data.

Differential abundance analysis of infant 16S microbial sequencing data is complicated by challenging data properties, including high sparsity, extreme dispersion and the relative nature of the information contained within the data. In this study, we propose a pairwise ratio analysis that uses the compositional data analysis principle of subcompositional coherence and merges it with a beta-binomial regression model. The resulting method provides a flexible and easily interpretable approach to infant 16S sequencing data differential abundance analysis that does not require zero imputation.

Longitudinal study on the prevalence of extended spectrum cephalosporins-resistant Escherichia coli colonization in Dutch veal farms.

A longitudinal study was performed to investigate the prevalence of Extended-Spectrum Cephalosporin-Resistant (ESC-R) Escherichia coli colonization in Dutch veal farms. Rectal swabs from 683 calves born in 13 Dutch dairy farms were collected one day prior to transportation to the veal farm at 14 or 28 days of age, and at 5 different time points 8 Dutch veal farms. In addition, characteristics of the calf, cows, and farm management were collected.

Housing and personality effects on judgement and attention biases in dairy cows.

Affective states can be inferred from responses to ambiguous and threatening stimuli, using Judgement Bias Tasks (JBTs) and Attention Bias Tasks (ABTs). We investigated the separate and interactive effects of personality and housing conditions on dairy cattle affective states. We assessed personality in 48 heifers using Open-Field, Novel-Object and Runway tests.

Developing a feasible and sensitive judgement bias task in dairy cows.

Judgement bias tasks (JBTs) are used to assess the influence of farm practices on livestock affective states. The tasks must be adjusted to the species and age group of focus. In cattle, most JBTs were designed for calves instead of adult cows.

Effects of pre-transport diet, transport duration and transport condition on immune cell subsets, haptoglobin, cortisol and bilirubin in young veal calves.

The aim of this study was to investigate effects of pre-transport diets, transport durations and transport conditions on immune cell subsets, haptoglobin, cortisol and bilirubin of young calves upon arrival at the veal farm. An experiment was conducted with a 2 × 2 × 2 factorial arrangement with 3 factors: 1) provision of rearing milk or electrolytes at the collection center (CC); 2) transport duration (6 or 18 hours) and 3) transport condition (open truck or conditioned truck). Holstein-Friesian and cross-bred calves were used (N = 368; 18 ± 4 days; 45.

Transport of Young Veal Calves: Effects of Pre-transport Diet, Transport Duration and Type of Vehicle on Health, Behavior, Use of Medicines, and Slaughter Characteristics.

The aim of this study was to investigate effects of different early life transport-related factors on health, behavior, use of medicines and slaughter characteristics of veal calves. An experiment was conducted with a 2 × 2 × 2 factorial arrangement with 3 factors: (1) provision of rearing milk or electrolytes before transport, (2) transport duration (6 or 18 h), and (3) type of vehicle (open truck or conditioned truck). The study included male Holstein-Friesian and cross-bred calves ( = 368; 18 ± 4 days; 45.

Human spatial memory implicitly prioritizes high-calorie foods.

All species face the important adaptive problem of efficiently locating high-quality nutritional resources. We explored whether human spatial cognition is enhanced for high-calorie foods, in a large multisensory experiment that covertly tested the location memory of people who navigated a maze-like food setting. We found that individuals incidentally learned and more accurately recalled locations of high-calorie foods - regardless of explicit hedonic valuations or personal familiarity with foods.

Correcting fresh grass allowance for rejected patches due to excreta in intensive grazing systems for dairy cows.

Dairy farms with intensive grazing systems combine grazing with supplemental feeding, which can be challenging because an incorrect balance between fresh grass allowance and feed supplementation results in inefficient use of the pasture, lower feed efficiency, and potential decreases in animal production. When estimating fresh grass allowance, we currently do not correct for the formation of rejected patches (RP) surrounding excreta, which can lead to overestimation of the potential fresh grass intake and hampers optimal grazing. In this study, therefore, we aim to quantify the formation of RP in intensive grazing systems and improve the quantification of fresh grass allowance.

The effect of intensive grazing systems on the rising plate meter calibration for perennial ryegrass pastures.

The rising plate meter (RPM) is used to measure grass height, which subsequently is used in a calibration equation to estimate herbage mass (HM), an important parameter for optimization of feed management in grazing systems. The RPM is placed on the sward and measures the resistance of the sward toward the plate, which depends not only on grass length, but also on sward structure. The accuracy of the calibration equation for the RPM to estimate HM across grazing systems, however, has not yet been evaluated.

Study of potential health effects of electromagnetic fields of telephony and Wi-Fi, using chicken embryo development as animal model.

The objective of this study is to investigate possible biological effects of radiofrequency electromagnetic fields (RF-EMF) as used in modern wireless telecommunication in a well-controlled experimental environment using chicken embryo development as animal model. Chicken eggs were incubated under continuous experimental exposure to GSM (1.8 GHz), DECT (1.

Feeding guild of non-host community members affects host-foraging efficiency of a parasitic wasp.

Interactions between predator and prey, or parasitoid and host, are shaped by trait- and density-mediated processes involving other community members. Parasitoids that lay their eggs in herbivorous insects locate their hosts through infochemicals such as herbivore-induced plant volatiles (HIPVs) and host-produced kairomones. Hosts are frequently accompanied by non-host herbivores that are unsuitable for the parasitoid.

Marker-based estimation of heritability in immortal populations.

Heritability is a central parameter in quantitative genetics, from both an evolutionary and a breeding perspective. For plant traits heritability is traditionally estimated by comparing within- and between-genotype variability. This approach estimates broad-sense heritability and does not account for different genetic relatedness.

Chopped or long roughage: what do calves prefer? Using cross point analysis of double demand functions.

The present study aimed to quantify calves' (Bos taurus) preference for long versus chopped hay and straw, and hay versus straw, using cross point analysis of double demand functions, in a context where energy intake was not a limiting factor. Nine calves, fed milk replacer and concentrate, were trained to work for roughage rewards from two simultaneously available panels. The cost (number of muzzle presses) required on the panels varied in each session (left panel/right panel): 7/35, 14/28, 21/21, 28/14, 35/7.

Assessment of performance of selected serological tests for diagnosing brucellosis in pigs.

Swine brucellosis due to Brucella suis is considered an emerging zoonotic disease whose control is based on serological testing and the subsequent culling of seropositive animals or the full depopulation of affected flocks. Here we assessed the performance of several serological tests (Rose Bengal Test [RBT], indirect ELISA [i-ELISA], blocking ELISA [b-ELISA], and two competitive ELISAs [c-ELISA]) for diagnosing swine brucellosis caused by B. suis biovar 2.

Actinobacillus pleuropneumoniae is impaired by the garlic volatile allyl methyl sulfide (AMS) in vitro and in-feed garlic alleviates pleuropneumonia in a pig model.

Decomposition products of ingested garlic are to a certain extent excreted via the lungs. If the supposed health-supporting capacities associated with garlic extend to these exhaled sulfurous compounds, they could have an effect on the course of pneumonia. In this study, the garlic-derived volatile allyl methyl sulfide (AMS) as a lead compound of volatile garlic metabolites was shown to exhibit an antibacterial effect against the pig pathogen Actinobacillus pleuropneumoniae serotype 9.

Breeding with resistant rams leads to rapid control of classical scrapie in affected sheep flocks.

Susceptibility to scrapie, a transmissible spongiform encephalopathy in sheep, is modulated by the genetic make-up of the sheep. Scrapie control policies, based on selecting animals of resistant genotype for breeding, have recently been adopted by the Netherlands and other European countries. Here we assess the effectiveness of a breeding programme based on selecting rams of resistant genotype to obtain outbreak control in classical scrapie-affected sheep flocks under field conditions.

Scrapie prevalence in sheep of susceptible genotype is declining in a population subject to breeding for resistance.

Background: Susceptibility of sheep to scrapie infection is known to be modulated by the PrP genotype of the animal. In the Netherlands an ambitious scrapie control programme was started in 1998, based on genetic selection of animals for breeding. From 2002 onwards EU regulations required intensive active scrapie surveillance as well as certain control measures in affected flocks.

Validation of diagnostic tests for detection of avian influenza in vaccinated chickens using Bayesian analysis.

Vaccination is an attractive tool for the prevention of outbreaks of highly pathogenic avian influenza in domestic birds. It is known, however, that under certain circumstances vaccination may fail to prevent infection, and that the detection of infection in vaccinated birds can be problematic. Here, we investigate the characteristics of three serological tests (immunofluorescent antibody test (iIFAT), neuraminidase inhibition (NI) assay, and NS1 ELISA) that are able to differentiate infected from vaccinated animals.

Serodiagnosis of Mycobacterium avium infections in pigs.

The aim of this study is the development and evaluation of a serodiagnostic assay for Mycobacterium avium (MA). After screening MA lipid fractions in an ELISA format, a polar lipid fraction was selected as antigen because of its superior recognition by serum antibodies in experimentally infected pigs. The resulting MA-ELISA was evaluated as an alternative for detection of MA infection by traditional pathological examination of pig lymph nodes for granulomatous lesions by meat inspectors.

Expert opinion as 'validation' of risk assessment applied to calf welfare.

Background: Recently, a Risk Assessment methodology was applied to animal welfare issues in a report of the European Food Safety Authority (EFSA) on intensively housed calves.

Methods: Because this is a new and potentially influential approach to derive conclusions on animal welfare issues, a so-called semantic-modelling type 'validation' study was conducted by asking expert scientists, who had been involved or quoted in the report, to give welfare scores for housing systems and for welfare hazards.

Results: Kendall's coefficient of concordance among experts (n = 24) was highly significant (P < 0.

A Bayesian evaluation of six diagnostic tests for foot-and-mouth disease for vaccinated and non-vaccinated cattle.

The sensitivity and specificity of six ELISA tests for foot-and-mouth disease (FMD) to discriminate between sero-converted (for non-structural FMD virus proteins) and non-sero-converted cattle were evaluated for vaccinated and unvaccinated cattle. Since none of the tests could be considered as a proper reference test and for about half of the tested sera the true status (sero-converted or not for non-structural proteins, i.e.

Evaluation of a new antibody-based enzyme-linked immunosorbent assay for the detection of bovine leukemia virus infection in dairy cattle.

The objective of this study was to validate a new blocking enzyme-linked immunosorbent assay (ELISA) (designated M108 for milk and S108 for serum samples) for detecting bovine leukemia virus (BLV) infection in dairy cattle. Milk, serum, and ethylenediaminetetraacetic acid-blood samples were collected from 524 adult Holstein cows originating from 6 dairy herds in Central Argentina. The M108 and S108 were compared with agar gel immunodiffusion (AGID), polymerase chain reaction and a commercial ELISA.

Detection of extracellular factor-positive Streptococcus suis serotype 2 strains in tonsillar swabs of live sows by PCR.

In this study, the sensitivity (Se) and specificity (Sp) of a PCR for the detection of EF-positive Streptococcus suis serotype 2 strains in tonsillar swabs of live sows were assessed. We sampled 471 sows originating from four farrow-to-finish farms by tonsillar swabbing and collected their tonsils after slaughter. On these specimens, a PCR, a bacterial examination (BE) or both were performed for the detection of EF-positive S.