Improved estimation of trawling tracks using cubic Hermite spline interpolation of position registration data

For control and enforcement purposes, all fishing vessels operating in European waters are equipped with satellite-based Vessel Monitoring by Satellite systems (VMS) recording their position at regular time intervals. VMS data are increasingly used by scientists to study spatial and temporal patterns of fishing activity and thus fishing impact (e.g. surface of sea bed trawled during a fishing trip). However, due to their low resolution (2 h basis), these data may provide a biased perception of fishing impact. We present here a method aiming at interpolating vessel trajectories from VMS data points to obtain higher-resolution data on vessel trajectories which in turn should provide improved estimates of the spatial and temporal patterns of fishing activity and hence fishing impact. This method is based on a spline interpolation technique, the cubic Hermite spline (cHs), using position, heading and speed to interpolate the trawl track of a vessel between two succeeding VMS data points. To take uncertainty of the interpolated track into account, the method also determines a confidence interval, which represents the spatial distribution of vessel presence probability between two successive VMS positions. The cHs method was compared to the straight line interpolation technique using a reference data set with intervals of 6 min which was assumed to represent the real trawl tracks. The results showed that the cHs method approximates the real trawl track markedly better than a straight line interpolation. The cHs method should therefore be preferred to the conventional straight line approach to interpolate vessel tracks in studies aiming at estimating fishing impact from VMS data.     

Latent entry and spread of Colletotrichum acutatum (species complex) in strawberry fields

Anthracnose, caused by Colletotrichum acutatum (species complex), has become a troublesome problem in strawberry production worldwide. This paper reports (i) an optimized sampling method combined with a real‐time PCR technique to detect the latent presence of C. acutatum in cold‐stored strawberry plants used as planting material in several European countries, and (ii) a study of the spread of C. acutatum following a point inoculation under field conditions. Screening of different parts of planting material suggested that C. acutatum is most likely to be present on runners and old petioles. In addition, in seven out of nine batches of planting material from different nurseries, latent infection by C. acutatum was detected in at least one of five replicate samples. Field experiments in 2009 and 2010 showed extensive latent within‐field spread of the pathogen on strawberry leaves, with a within‐row dispersal distance up to at least 1·75 m in 1 week. A straw ground cover between the rows did not decrease C. acutatum spread, probably because introduced (and/or subsequent) inoculum was confined to the plant bed (within the row) and was not present between the beds. Moreover, the number of C. acutatum spores on the symptomless leaves, as estimated using a real‐time PCR method, was significantly (P < 0·05) correlated with the incidence of fruit rot at harvest and post‐harvest (r = 0·56–0·66). These results illustrate the importance of detecting latent infections in planting material and strawberry leaves in the field.     

Cryotolerance of Bovine Blastocysts is Affected by Oocyte Maturation in Media Containing Palmitic or Stearic Acid

In this study, non-esterified fatty acids (NEFAs) were added during in vitro maturation at concentrations measured previously in follicular fluid (FF) of high-producing dairy cows in a negative energy status to evaluate their subsequent effect on the embryos cryotolerance. Oocytes were matured for 24 h in serum-free media with or without (negative control) the addition of NEFAs dissolved in ethanol or ethanol alone (positive control). Matured oocytes were fertilized and cultured for 7 days in synthetic oviduct fluid medium supplemented with 5% FCS. Embryos that had at least reached the blastocyst stage were vitrified by open pulled straw (OPS) vitrification. Addition of palmitic (C16 : 0) or stearic acid (C18 : 0) during oocyte maturation had significant negative effects on embryo cryotolerance, whereas ethanol or oleic acid (C18 : 1) had no effect. These in vitro results suggest that high NEFA concentrations in FF during a period of negative energy balance in high-yielding dairy cows can have carry-over effects on embryo quality.     

How to Evaluate and Quantify the Influence of Coincidence on Fertility and Herd Health Parameters? A Practical Overview of Frequently Used and Abused Statistical Techniques in Research and Practice

In this article, frequently encountered statistical questions and methods used both in research and in daily practice are described and explained. First, the concepts of variability and uncertainty are explained and illustrated. From this, it is explained how variation can be quantified and how the limits of what can be expected as a result of normal variation are determined both for continuous and binary data. Based on the basic concepts of probability theory, an introduction to risk assessment was given. Finally it is explained how to test whether individual observations lie outside the normal range or the test whether populations are different from each other. All these are carried out avoiding theory and formulas as much as possible and illustrated with real examples from reproduction and herd health.     

Type and frequency of contacts between Belgian pig herds

Knowledge of the frequency of direct and indirect contacts between pig herds is a requirement for understanding the potential between-herd transmission of pathogens. Our aim was to investigate the different contacts between Belgian pig herds. We obtained data by conducting a postal survey on 421 pig herds in August 2005 and by analysis of available information on livestock movements in the national identification-and-registration database (18-months period in 2004-2006). Direct contacts included transports of pigs by onto-farm, off-farm and between-farm movements. Indirect contacts included vehicles entering the herd and visitors entering the stables. The median number of direct contacts per herd made by onto-farm movements was 0.2/month (Q1: 0; Q3: 0.5). About 1.2% of herds had > or = 3 onto-farm movements/month. We used a zero-inflated negative-binomial regression model to describe differences in the number of onto-farm movements according to herd size and herd type. Piglet multipliers followed by finishing herds were predicted to have the most onto-farm movements. Farrow-to-finishing herds made less movements compared to breeding herds. A median of 3997 between-farm movements/month was made in Belgium; these mainly concerned piglets. The median number of origin herds during an 8-month period for between-farm movements was 4 (Q1: 2; Q3: 8). For a typical 1-month period, we constructed directed graphs of between-farm piglet and replacement stock movements, illustrating potential receivers and distributors of infection. Of these between-farm movements, many were made over a short distance (median straight-line distance 19 km (Q1: 8; Q3: 36)). The median number of vehicles entering a herd and visitors entering the stables was 8/month (Q1: 6; Q3: 13) and 3/month (Q1: 2; Q3: 6) respectively. The number of indirect contacts by vehicles and persons were associated with herd size (Spearman's r: 0.7 and 0.2), herd type and other factors. Skewness of both direct and indirect contacts, illustrated that there was a wide variety in contact structure between pig herds in Belgium. Infection control might benefit by accounting for this variation in contacts and by targeting 'high-risk' herds in case of animal-disease emergencies.     

经人工授精传播的猪病及其预防措施

猪人工授精技术（Artificial insemination,AI）已在集约化养猪生产国中得到了广泛应用。人工授精是一种将优秀基因引入母猪群中的非常有效的工具,并能够将疾病传播的风险降至最小。然而,受到病原体污染的精液对生产实际的危害是巨大的。在已经从公猪精液中检测到的微生物中,大部分是非致病性的,但有一些是有名的病原体,如猪繁殖与呼吸综合症病毒,这部分病原体能给养猪业造成重大的经济损失。精液受到微生物的污染可能是由于公猪全身性感染和/或泌尿生殖道感染所致,或可能发生在精液采集、处理和存储过程中。这会导致精液品质下降,胚胎或胎儿死亡,以及受体母猪的子宫内膜炎和全身性感染和/或发病。用于从精液中分离细菌和病毒的常规技术因受多种原因的影响并不总是能获得理想的结果,这些原因包括所用技术缺乏敏感性和检测速度慢、对检测结果难以进行解释。近年来,PCR技术得到了普遍的应用,它们具有很高的敏感性,能很快获得检测结果,并且适合对大样本的检测。防止通过人工授精传播疾病的最佳方法是使用无特定病原体的公猪、对它们及其精液进行定期检测以及维持极高的生物安全水平。其它方法则应该侧重于利用合适的抗菌剂对精液进行处理,以及重点减少在采集、处理和存储过程中精液所受到的污染。     

IUCN Red List of freshwater fishes and lampreys in Flanders (north Belgium)

Red Lists are used to assess the extinction risk of species. Regional IUCN criteria were applied to categorise 42 indigenous freshwater fish species in Flanders into Red List categories. As such, three species are assessed as Regionally Extinct, eight as Critically Endangered, two as Endangered and eight as Vulnerable. A further five species are considered Near Threatened, 15 species as Least Concern and one species is Data Deficient. Five species disappeared from the Regionally Extinct category compared with the previous Red List (1988) as a consequence of improved water quality of estuaries and reintroduction programmes. In total, 62% of the freshwater fish species in Flanders was considered extinct or threatened. This is higher than neighbouring regions and Europe as a whole (44%). This new Red List of freshwater fishes in Flanders can be used to inform conservation actions.     

Fast and sensitive on-site isothermal assay (LAMP) for diagnosis and detection of three fruit tree phytoplasmas

Over the years, real-time PCR outflanked endpoint PCR in phytopathogen diagnostics, mainly because of the increase in sensitivity and timesaving aspects of the technique. However, a time consuming 16S rRNA-based nested PCR method is still the gold standard for phytoplasma diagnosis. This is also the case for phytoplasma detection in Malus, Pyrus and Prunus, the three main host plants of apple proliferation (AP), pear decline (PD) and European stone fruit yellows (ESFY) phytoplasma, respectively. The last decade, loop-mediated isothermal amplification (LAMP) (Notomi et al. 2000) is gaining a lot in significance and is also for phytoplasmas expected to become a widely used reliable diagnostic tool. High specificity and sensitivity which also requires a less stringent need for DNA purification, and the short analysis time and the limited equipment requirements makes the LAMP method a fast and affordable alternative with great point-of-care diagnostic potential. In this paper, we present a LAMP primer set for the ribosomal group 16SrX, containing the important fruit tree phytoplasmas AP, PD and ESFY. The primers were developed and validated for fast and sensitive detection and general use for diagnosis. We foresee that the LAMP technique will also have its application in on-site diagnosis of the fruit tree phytoplasmas during inspections and surveys.     

Effect of host factors on the susceptibility of Rhododendron to Phytophthora ramorum

Phytophthora ramorum causes sudden oak death (SOD) in western coastal forests of the USA. In Europe, the pathogen is mainly present in the nursery industry, particularly on Rhododendron. Because of the primary role of Rhododendron as a host and potentially as a vector, the effect of Rhododendron host factors on P. ramorum susceptibility and sporulation was investigated. Inoculation methods using either wounded or non‐wounded detached leaves were applied to 59 Rhododendron cultivars and 22 botanical species, replicated in three separate years. All Rhododendron species and cultivars were susceptible when using wounded leaves, but not when using non‐wounded leaves, suggesting a resistance mechanism operating at the level of leaf penetration. Using a regression tree analysis, the cultivars and species were split into four susceptibility classes. Young leaves were more susceptible than mature leaves when wounded, but less susceptible when non‐wounded. This effect was not correlated with leaf hydrophobicity or the number of leaf hairs. The presence or the type of rootstock did not affect the cultivar susceptibility level. Sporangia and chlamydospore production in the leaf lesions varied widely among Rhododendron cultivars and was not correlated with the susceptibility level. The susceptibility to P. ramorum correlated well with the susceptibility to P. citricola and P. hedraiandra × cactorum, suggesting that the resistance mechanisms against these species are non‐specific. Susceptibility to P. kernoviae was low for most cultivars. These findings have implications for detection, spread and disease control, and are therefore important in pest risk assessment.