Short-term associations between ambient ammonia concentrations and growing-finishing pig performance and health.

Using sensors, the health and welfare of growing-finishing pigs can be continuously monitored by detecting deviations from pigs' normal behaviour, but the validity of such algorithms requires improvement. As changes in the environment influence pig behaviour, monitoring temporal changes in environmental factors may help identify periods with a higher risk of welfare issues. The real-time relationships between pig welfare and many environmental factors are, however, not well-understood.

Light intensity preferences of broiler chickens is affected by breed, age, time of day and behaviour.

Light is an important aspect of broiler husbandry and management as it influences behaviour and welfare. However, a lot remains unknown regarding broiler preferences for light intensities, especially for slower-growing broilers which are increasingly used in broiler production systems in the EU. We identified preferences of fast (F)- and slower (S)-growing broilers for intensities in relation to behaviour, age and time of day.

Effects of breed and early feeding on intestinal microbiota, inflammation markers, and behavior of broiler chickens.

Recently, the Netherlands has shifted toward more welfare-friendly broiler production systems using slower-growing broiler breeds. Early post-hatch feeding (EF) is a dietary strategy that is currently used in commercial broiler production to modulate the gut microbiota and improve performance and welfare. However, there is a knowledge gap in how both breed and EF and their interplay affect gut microbiota composition and diversity, inflammatory status, and broiler behavior.

Corrigendum: Animal-based factors prior to infection predict histological disease outcome in porcine reproductive and respiratory syndrome virus- and -infected pigs.

[This corrects the article DOI: 10.3389/fvets.2021.

Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance.

Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance.

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.

Pitfalls in the statistical analysis of microbiome amplicon sequencing data.

Microbiome data are characterized by several aspects that make them challenging to analyse statistically: they are compositional, high dimensional and rich in zeros. A large array of statistical methods exist to analyse these data. Some are borrowed from other fields, such as ecology or RNA-sequencing, while others are custom-made for microbiome data.

Effect of Type of Cow-Calf Contact on Health, Blood Parameters, and Performance of Dairy Cows and Calves.

Prolonged cow-calf contact (CCC) could potentially improve dairy calf welfare. However, it is currently unknown how different types of CCC affect animals' biological functions. We evaluated health and performance parameters of dairy calves and their dams, where calves: (i) had no contact with their dam (NC), in which the calf was removed from the dam directly after birth ( = 10); (ii) were allowed to have partial contact (PC) with their dam, in which the calf was housed in a calf pen adjacent to the cow area allowing physical contact on the initiative of the dam but no suckling ( = 18); (iii) were allowed to have full contact (FC) with their dam, including suckling, in which calves were housed together with their dams in a free-stall barn ( = 20).

Animal-Based Factors Prior to Infection Predict Histological Disease Outcome in Porcine Reproductive and Respiratory Syndrome Virus- and -Infected Pigs.

A large variety of clinical manifestation in individual pigs occurs after infection with pathogens involved in porcine respiratory disease complex (PRDC). Some pigs are less prone to develop respiratory disease symptoms. The variation in clinical impact after infection and the recovery capacity of an individual animal are measures of its resilience.

Species Identity, Life History, and Geographic Distance Influence Gut Bacterial Communities in Lab-Reared and European Field-Collected Culicoides Biting midges.

Bacteria are part of the insect gut system and influence many physiological traits of their host. Gut bacteria may even reduce or block the transmission of arboviruses in several species of arthropod vectors. Culicoides biting midges are important arboviral vectors of several livestock and wildlife diseases, yet limited information is available on their gut bacterial communities.

Chitin- and Keratin-Rich Soil Amendments Suppress Rhizoctonia solani Disease via Changes to the Soil Microbial Community.

Enhancing soil suppressiveness against plant pathogens or pests is a promising alternative strategy to chemical pesticides. Organic amendments have been shown to reduce crop diseases and pests, with chitin products the most efficient against fungal pathogens. To study which characteristics of organic products are correlated with disease suppression, an experiment was designed in which 10 types of organic amendments with different physicochemical properties were tested against the soilborne pathogen in sugar beet seedlings.

Log-ratio analysis of microbiome data with many zeroes is library size dependent.

Microbiome composition data collected through amplicon sequencing are count data on taxa in which the total count per sample (the library size) is an artefact of the sequencing platform, and as a result, such data are compositional. To avoid library size dependency, one common way of analysing multivariate compositional data is to perform a principal component analysis (PCA) on data transformed with the centred log-ratio, hereafter called a log-ratio PCA. Two aspects typical of amplicon sequencing data are the large differences in library size and the large number of zeroes.

Outcome prediction of head and neck squamous cell carcinoma by MRI radiomic signatures.

Objectives: Head and neck squamous cell carcinoma (HNSCC) shows a remarkable heterogeneity between tumors, which may be captured by a variety of quantitative features extracted from diagnostic images, termed radiomics. The aim of this study was to develop and validate MRI-based radiomic prognostic models in oral and oropharyngeal cancer.

Materials And Methods: Native T1-weighted images of four independent, retrospective (2005-2013), patient cohorts (n = 102, n = 76, n = 89, and n = 56) were used to delineate primary tumors, and to extract 545 quantitative features from.

Learning from a lot: Empirical Bayes for high-dimensional model-based prediction.

Empirical Bayes is a versatile approach to "learn from a lot" in two ways: first, from a large number of variables and, second, from a potentially large amount of prior information, for example, stored in public repositories. We review applications of a variety of empirical Bayes methods to several well-known model-based prediction methods, including penalized regression, linear discriminant analysis, and Bayesian models with sparse or dense priors. We discuss "formal" empirical Bayes methods that maximize the marginal likelihood but also more informal approaches based on other data summaries.

Improved high-dimensional prediction with Random Forests by the use of co-data.

Background: Prediction in high dimensional settings is difficult due to the large number of variables relative to the sample size. We demonstrate how auxiliary 'co-data' can be used to improve the performance of a Random Forest in such a setting.

Results: Co-data are incorporated in the Random Forest by replacing the uniform sampling probabilities that are used to draw candidate variables by co-data moderated sampling probabilities.

Heterosubtypic cross-reactivity of HA1 antibodies to influenza A, with emphasis on nonhuman subtypes (H5N1, H7N7, H9N2).

Epidemics of influenza A vary greatly in size and age distribution of cases, and this variation is attributed to varying levels of pre-existing immunity. Recent studies have shown that antibody-mediated immune responses are more cross-reactive than previously believed, and shape patterns of humoral immunity to influenza A viruses over long periods. Here we quantify antibody responses to the hemagglutinin subunit 1 (HA1) across a range of subtypes using protein microarray analysis of cross-sectional serological surveys carried out in the Netherlands before and after the A/2009 (H1N1) pandemic.

The FA/BRCA Pathway Identified as the Major Predictor of Cisplatin Response in Head and Neck Cancer by Functional Genomics.

Patients with advanced stage head and neck squamous cell carcinoma (HNSCC) are often treated with cisplatin-containing chemoradiation protocols. Although cisplatin is an effective radiation sensitizer, it causes severe toxicity and not all patients benefit from the combination treatment. HNSCCs expectedly not responding to cisplatin may better be treated with surgery and postoperative radiation or cetuximab and radiation, but biomarkers to personalize chemoradiotherapy are not available.

Joint modelling of serological and hospitalization data reveals that high levels of pre-existing immunity and school holidays shaped the influenza A pandemic of 2009 in the Netherlands.

Obtaining a quantitative understanding of the transmission dynamics of influenza A is important for predicting healthcare demand and assessing the likely impact of intervention measures. The pandemic of 2009 provides an ideal platform for developing integrative analyses as it has been studied intensively, and a wealth of data sources is available. Here, we analyse two complementary datasets in a disease transmission framework: cross-sectional serological surveys providing data on infection attack rates, and hospitalization data that convey information on the timing and duration of the pandemic.

Estimation of the serial interval of pertussis in Dutch households.

Increasing incidence has led to the re-appearance of pertussis as a public health problem in developed countries. Pertussis infection is usually mild in vaccinated children and adults, but it can be fatal in infants who are too young for effective vaccination (≤3 months). Tailoring of control strategies to prevent infection of the infant hinges on the availability of estimates of key epidemiological quantities.

Driving factors of influenza transmission in the Netherlands.

Influenza epidemics in temperate regions show a characteristic seasonal pattern with peak incidence occurring in winter. Previous research has shown that low absolute humidity and school holidays can both affect influenza transmission. During an epidemic, transmission is strongly influenced by the depletion of susceptibles (i.

Estimating the generation interval of influenza A (H1N1) in a range of social settings.

A proper understanding of the infection dynamics of influenza A viruses hinges on the availability of reliable estimates of key epidemiologic parameters such as the reproduction number, intrinsic growth rate, and generation interval. Often the generation interval is assumed to be similar in different settings although there is little evidence justifying this. Here we estimate the generation interval for stratifications based on age, cluster size, and social setting (camp, school, workplace, household) using data from 16 clusters of Novel Influenza A (H1N1) in the Netherlands.

Risk based culling for highly infectious diseases of livestock.

The control of highly infectious diseases of livestock such as classical swine fever, foot-and-mouth disease, and avian influenza is fraught with ethical, economic, and public health dilemmas. Attempts to control outbreaks of these pathogens rely on massive culling of infected farms, and farms deemed to be at risk of infection. Conventional approaches usually involve the preventive culling of all farms within a certain radius of an infected farm.

Effectiveness of personal protective equipment and oseltamivir prophylaxis during avian influenza A (H7N7) epidemic, the Netherlands, 2003.

We analyzed the effectiveness of personal protective equipment and oseltamivir use during the 2003 avian influenza A (H7N7) epidemic in the Netherlands by linking databases containing information about farm visits, human infections, and use of oseltamivir and personal protective equipment. Using a stringent case definition, based on self-reported conjunctivitis combined with a positive hemagglutination-inhibition assay, we found that prophylactic treatment with oseltamivir significantly reduced the risk for infection per farm visit from 0.145 (95% confidence interval [CI] 0.