Reporting flock patterns

Data representing moving objects is rapidly getting more available, especially in the area of wildlife GPS tracking. It is a central belief that information is hidden in large data sets in the form of interesting patterns. One of the most common spatio-temporal patterns sought after is flocks. A flock is a large enough subset of objects moving along paths close to each other for a certain pre-defined time. We give a new definition that we argue is more realistic than the previous ones, and by the use of techniques from computational geometry we present fast algorithms to detect and report flocks. The algorithms are analysed both theoretically and experimentally

The epidemiology of avian influenza in the Mekong River Delta of Viet Nam : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University

Between December 2003 and December 2012 a total of 4,349 commune-level outbreaks of highly pathogenic avian influenza (HPAI) H5N1 were recorded in domestic poultry flocks throughout Viet Nam. Throughout the same period there were 123 cases of HPAI H5N1 virus infection in humans, 61 of which were fatal. The studies presented in this thesis are largely based on data collected from a prospective cohort study of domestic poultry in 157 flocks in the Mekong River Delta of Viet Nam between December 2008 and April 2010. The first research chapter (Chapter 3) provides a description of the components and design features of an animal health decision support system for use in Viet Nam. While not explicitly used for the prospective cohort study, the motivation for development of this system was to provide a means for recording and storing animal health data so as to minimise duplication of data collection efforts. A feature of the system is the inclusion of a flexible reporting tool that provides system users with the capability of developing reports to deal with virtually any animal health issue, not just avian influenza. The intent of this system is that it will allow the Vietnamese Department of Animal Health to identify and respond to existing and emerging threats to animal health in a timely and cost-effective manner. Our descriptive analyses (Chapter 4) show that the overall incidence rate of influenza Type A and H5 virus infection in village poultry was relatively high throughout the 17-month follow up period of the prospective cohort study. This implies that interventions such as vaccination, movement controls and biosecurity measures need to be carried out continuously throughout the year rather than focusing only on the established high risk periods. Broiler ducks had an incidence rate of influenza H5 virus infection that was approximately four times greater than that of layer ducks and in-contact species. This indicates that broiler ducks should be the focus of disease surveillance and control strategies. Survival analyses, accounting for the intermittent sampling of birds throughout the follow-up period of the prospective cohort study (by interval censoring) and for the hierarchical structure of the data set were used to determine the duration of immunity to H5N1 following vaccination (Chapter 5). After adjusting for the effect of known confounders and unmeasured variation at the flock level the duration of immunity to H5N1 following vaccination was estimated to be in the order of 56 (95% CI 51 – 61) days, considerably shorter than the duration of immunity previously reported in laboratory-based studies. A multilevel logistic regression analysis carried out to identify risk factors for influenza Type A virus infection in the prospective cohort study poultry population found that the relative contribution of unmeasured flock- and bird-level factors on influenza Type A virus infection risk were approximately equal (Chapter 6). Most of the significant fixed-effects were flock-level exposures indicating that interventions to reduce the maintenance and transmission of influenza Type A virus in domestic poultry in this area of Viet Nam should be applied at the individual bird and individual flock level. Chapter 7 presents the results of a study of poultry movement events that occurred in the south of Viet Nam between September 2009 and June 2010. Poultry were more likely to be moved between communes with provincial roads and between communes with more than 1,000 poultryowning households. Assuming a causal relationship exists between a commune-to-commune poultry movement activity and HPAI H5N1 risk, a conclusion from this study was that communes more likely to be connected to others as a result of movement should be targeted for disease control and surveillance. The findings presented in each of these chapters of this thesis have broadened our knowledge of the epidemiology of not only the HPAI H5N1 subtype, but influenza Type A viruses in poultry in general. It should be stressed that the methodological techniques that have been used in this thesis can be applied to a wide range of animal health issues, not just HPAI H5N1

Reduction in livestock losses following placement of livestock guarding dogs and the impact of herd species and dog sex

Livestock guarding dogs have been placed on South African farms by the not-for-profit organisation, Cheetah Outreach Trust, since 2005, and have been proven to be an efficient form of non-lethal predator control against jackal, caracal, leopards, cheetahs and other predators found in South Africa. However, the impact that herd species (sheep, goat, cattle or mixed) or the sex of the dog may have on the observed reduction in livestock losses following placement of a livestock guarding dogs has not been investigated. To address this, the reduction in livestock losses following placement of an Anatolian livestock guarding dogs was measured in two South African provinces over a nine year period and data simultaneously collected on herd type and dog sex. Dogs comprised of 78 males and 49 females. Farms consisted of 68 sheep, 37 goats, 23 cattle, and two exotic game farms. Effectiveness was measured as the difference between farmer-reported livestock losses before and after the placement of a dog and was calculated as percentage change in stock loss after introduction of a livestock guarding dog according herd species and dog sex. This study determined the impact of herd type or dog sex on the difference between livestock loss before versus after livestock guarding dog s placement. This study indicates that the use of this breed of livestock guarding dog is an effective means of reducing perceived livestock losses due to predation, regardless of dog sex, and may be used with equal effectiveness with a range of herd species

Modeling highly pathogenic avian influenza transmission in wild birds and poultry in West Bengal, India.

Wild birds are suspected to have played a role in highly pathogenic avian influenza (HPAI) H5N1 outbreaks in West Bengal. Cluster analysis showed that H5N1 was introduced in West Bengal at least 3 times between 2008 and 2010. We simulated the introduction of H5N1 by wild birds and their contact with poultry through a stochastic continuous-time mathematical model. Results showed that reducing contact between wild birds and domestic poultry, and increasing the culling rate of infected domestic poultry communities will reduce the probability of outbreaks. Poultry communities that shared habitat with wild birds or those indistricts with previous outbreaks were more likely to suffer an outbreak. These results indicate that wild birds can introduce HPAI to domestic poultry and that limiting their contact at shared habitats together with swift culling of infected domestic poultry can greatly reduce the likelihood of HPAI outbreaks

Do Birds of a Feather Flock Together? Speculator Herding in the World Oil Market

This paper looks at speculative behavior in the international oil market. Much of the blame for oil-market turbulence has been placed on speculators, particularly hedge funds. Speculative capital has been characterized as “hot money,” with capital flows driven by “herding,” “flocking,” and “contagion.” Policies to deal with volatility by weakening, or even disabling speculation, have been based largely on anecdote, convenience (speculators have long served as scapegoats for various problems), and ideology, rather than careful analysis. Part of the problem arises from the secrecy with which speculators operate. Because speculative trading cannot easily be observed, it is difficult to assess speculators’ contribution, if any, to volatility. The paper utilizes a large, detailed database on individual trader positions in crude-oil and heating-oil futures markets. The paper is exploratory, with focus on measuring and assessing the tendency of speculators to herd (trade in the same direction as a group) and flock (trade in the same direction by subgroups of speculators).oil, speculation, volatility, herding, derivatives, futures

Hazard Analysis of Critical Control Points Assessment as a Tool to Respond to Emerging Infectious Disease Outbreaks

Highly pathogenic avian influenza virus (HPAI) strain H5N1 has had direct and indirect economic impacts arising from direct mortality and control programmes in over 50 countries reporting poultry outbreaks. HPAI H5N1 is now reported as the most widespread and expensive zoonotic disease recorded and continues to pose a global health threat. The aim of this research was to assess the potential of utilising Hazard Analysis of Critical Control Points (HACCP) assessments in providing a framework for a rapid response to emerging infectious disease outbreaks. This novel approach applies a scientific process, widely used in food production systems, to assess risks related to a specific emerging health threat within a known zoonotic disease hotspot. We conducted a HACCP assessment for HPAI viruses within Vietnam’s domestic poultry trade and relate our findings to the existing literature. Our HACCP assessment identified poultry flock isolation, transportation, slaughter, preparation and consumption as critical control points for Vietnam’s domestic poultry trade. Introduction of the preventative measures highlighted through this HACCP evaluation would reduce the risks posed by HPAI viruses and pressure on the national economy. We conclude that this HACCP assessment provides compelling evidence for the future potential that HACCP analyses could play in initiating a rapid response to emerging infectious diseases

Modularity-Based Clustering for Network-Constrained Trajectories

We present a novel clustering approach for moving object trajectories that are constrained by an underlying road network. The approach builds a similarity graph based on these trajectories then uses modularity-optimization hiearchical graph clustering to regroup trajectories with similar profiles. Our experimental study shows the superiority of the proposed approach over classic hierarchical clustering and gives a brief insight to visualization of the clustering results.Comment: 20-th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN 2012), Bruges : Belgium (2012

Bacteriological and epidemiological studies of campylobacter spp. in Swedish broilers

Campylobacter jejuni is the most frequently reported cause of bacterial gastrointestinal illness in humans in Sweden. Chicken products are considered an important risk factor for human infection. This thesis analyses and identifies sources and risk factors for colonisation of Campylobacter spp. in broilers at both farm level and slaughter. Slaughter groups with a low within-group prevalence were identified, split slaughter was confirmed as a risk factor and contamination of carcasses was shown to occur both during transport and during the slaughter process. Environmental campylobacter load was comparable on high and low incidence farms, indicating that hygiene regime is of greater importance than environmental load. Slaughter groups with a high within-flock prevalence had significantly higher campylobacter load in carcasses at slaughter than slaughter groups with a low degree of colonisation Campylobacter jejuni is the Campylobacter sp. predominantly found in broilers. Strain characterisation below species level, so-called subtyping, is a helpful tool in epidemiological studies, e.g. in determination of transmission routes. Certain subtypes were shown to be common in Sweden and may have a higher ability to survive in the environment around broiler houses. The results from phylogenetic analysis indicated that typing based on 16S rRNA sequencing is not always sufficient for differentiating between C. jejuni and C. coli. However, nine different 16S rRNA types were identified among 47 Swedish campylobacter isolates from broilers. About one-third of Swedish broiler producers seldom deliver any campylobacter-positive broilers to slaughter, demonstrating that it is possible to produce campylobacter-free chickens in Sweden. The factors identified as carrying the highest risk of producing campylobacter-positive broilers in Sweden were (i) insufficient general tidiness on the farm, (ii) split slaughter, (iii) an in-line position of the doors between the outside and access into broiler houses instead of an angled position. Furthermore, (iv) high risk farms often had other livestock such as cattle and pigs, and (v) high risk farms were more frequently situated in groves than in forest. Reducing the proportion of campylobacter-infected broiler flocks and the numbers of campylobacter on broiler carcasses would considerably lower the risk for consumers

How to be a great dad: Parental care in a flock of greater flamingo (Phoenicopterus roseus)

In the last years, studies on captive greater flamingos have increased. Research on zoo animals is important to improve the knowledge on these species and to improve their ex-situ and in-situ conservation. The aim of the present study was to investigate the parental behaviour of a captive colony of greater flamingo hosted at Parco Natura Viva, an Italian zoological garden, to improve the knowledge on this species in zoos. In particular, the present study investigated and compared the parental care of females and males in 35 breeding pairs of greater flamingos. For each pair, we collected durations of parental care behaviour of both females and males, recording their position in relation to the nest (near the nest, on the nest, away from the nest) and individual and social behaviours performed. First, both partners were involved in parental care and displayed species-specific behaviours reported in the wild. The main results were that males spent more time than females on the nest (P = 0.010) and near it (P = 0.0001) and were more aggressive toward other flamingos than females, both when sitting on the nest (P = 0.003) and when near the nest (P = 0.0003). Therefore, male flamingos seem to be more involved in incubation duties and nest protection than females. This kind of research is important not only to expand the knowledge on bird species such as flamingos, but also to improve their husbandry and breeding in controlled environment. Indeed, understanding animal behaviour allows us to gain insights into their individual and social needs, addressing potential animal welfare issues