Time Series Classification: Lessons Learned in the (Literal) Field while Studying Chicken Behavior

Poultry farms are a major contributor to the human food chain. However, around the world, there have been growing concerns about the quality of life for the livestock in poultry farms; and increasingly vocal demands for improved standards of animal welfare. Recent advances in sensing technologies and machine learning allow the possibility of monitoring birds, and employing the lessons learned to improve the welfare for all birds. This task superficially appears to be easy, yet, studying behavioral patterns involves collecting enormous amounts of data, justifying the term Big Data. Before the big data can be used for analytical purposes to tease out meaningful, well-conserved behavioral patterns, the collected data needs to be pre-processed. The pre-processing refers to processes for cleansing and preparing data so that it is in the format ready to be analyzed by downstream algorithms, such as classification and clustering algorithms. However, as we shall demonstrate, efficient pre-processing of chicken big data is both non-trivial and crucial towards success of further analytics.Comment: arXiv admin note: text overlap with arXiv:1811.0314

Bluetongue virus infection creates light averse Culicoides vectors and serious errors in transmission risk estimates.

BackgroundPathogen manipulation of host behavior can greatly impact vector-borne disease transmission, but almost no attention has been paid to how it affects disease surveillance. Bluetongue virus (BTV), transmitted by Culicoides biting midges, is a serious disease of ruminant livestock that can cause high morbidity and mortality and significant economic losses. Worldwide, the majority of surveillance for Culicoides to assess BTV transmission risk is done using UV-light traps. Here we show that field infection rates of BTV are significantly lower in midge vectors collected using traps baited with UV light versus a host cue (CO2).MethodsWe collected Culicoides sonorensis midges in suction traps baited with CO2, UV-light, or CO2 + UV on three dairies in southern California to assess differences in the resulting estimated infection rates from these collections. Pools of midges were tested for BTV by qRT-PCR, and maximum likelihood estimates of infection rate were calculated by trap. Infection rate estimates were also calculated by trapping site within a dairy. Colonized C. sonorensis were orally infected with BTV, and infection of the structures of the compound eye was examined using structured illumination microscopy.ResultsUV traps failed entirely to detect virus both early and late in the transmission season, and underestimated virus prevalence by as much as 8.5-fold. CO2 + UV traps also had significantly lower infection rates than CO2-only traps, suggesting that light may repel infected vectors. We found very high virus levels in the eyes of infected midges, possibly causing altered vision or light perception. Collecting location also greatly impacts our perception of virus activity.ConclusionsBecause the majority of global vector surveillance for bluetongue uses only light-trapping, transmission risk estimates based on these collections are likely severely understated. Where national surveillance programs exist, alternatives to light-trapping should be considered. More broadly, disseminated infections of many arboviruses include infections in vectors' eyes and nervous tissues, and this may be causing unanticipated behavioral effects. Field demonstrations of pathogen-induced changes in vector behavior are quite rare, but should be studied in more systems to accurately predict vector-borne disease transmission

Detection and isolation of exotic Newcastle disease virus from field-collected flies.

Flies were collected by sweep net from the vicinity of two small groups of "backyard" poultry (10-20 chickens per group) that had been identified as infected with exotic Newcastle disease virus (family Paramyxoviridae, genus avulavirus, ENDV) in Los Angeles County, CA, during the 2002-2003 END outbreak. Collected flies were subdivided into pools and homogenized in brain-heart infusion broth with antibiotics. The separated supernatant was tested for the presence of ENDV by inoculation into embryonated chicken eggs. Exotic Newcastle disease virus was isolated from pools of Phaenicia cuprina (Wiedemann), Fannia canicularis (L.), and Musca domestica L., and it was identified by hemagglutination inhibition with Newcastle disease virus antiserum. Viral concentration in positive pools was low (<1 egg infectious dose50 per fly). Isolated virus demonstrated identical monoclonal antibody binding profiles as well as 99% sequence homology in the 635-bp fusion gene sequence compared with ENDV recovered from infected commercial egg layer poultry during the 2002 outbreak

VetPestX: Finally! An Online, Searchable, Pesticide Label Database Just for Pests of Animals

Almost all online pesticide databases contain crop-specific product labels; very few include products labeled for animal use. A single online location for veterinary pesticide labels was needed. Led by Alec Gerry of the University of California at Riverside (UCR), veterinary entomologists from California, Washington, New Mexico, and Oklahoma contributed information on animal pesticide products registered in five western states (CA, WA, OR, ID, NM) and OK to a new, online, searchable, veterinary pesticide labels database named VetPestX, developed and maintained on UC Riverside\u27s website. Animal producers and owners requesting pesticide information to manage pests are now routinely directed to VetPestX

Laboratory evaluation of stable isotope labeling of Culicoides (Diptera: Ceratopogonidae) for adult dispersal studies.

BackgroundStable isotope labeling is a promising method for use in insect mark-capture and dispersal studies. Culicoides biting midges, which transmit several important animal pathogens, including bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV), are small flies that develop in various semi-aquatic habitats. Previous Culicoides dispersal studies have suffered from the limitations of other labeling techniques, and an inability to definitively connect collected adult midges to specific immature development sites.ResultsAdult C. sonorensis were successfully labeled with 13C and 15N stable isotopes as larvae developing in a semi-aquatic mud substrate in the laboratory. High and low-dose isotope treatments for both elements significantly enriched midges above the background isotope levels of unenriched controls. Enrichment had no effect on C. sonorensis survival, though a slight (~ 5 day) delay in emergence was observed, and there was no significant effect of pool size on 13C or 15N enrichment levels.ConclusionsStable isotope labeling is life-long, and does not interfere with natural insect behaviors. Stable isotope enrichment using 13C or 15N shows promise for Culicoides dispersal studies in the field. This method can be used to identify adult dispersal from larval source habitat where a midge developed. It may be possible to detect a single enriched midge in a pool of unenriched individuals, though further testing is needed to confirm the sensitivity of this method

Parasitic mites alter chicken behaviour and negatively impact animal welfare.

The northern fowl mite, Ornithonyssus sylviarum, is one of the most common and damaging ectoparasites of poultry. As an obligate blood feeding mite, the northern fowl mite can cause anaemia, slower growth, and decreased egg production of parasitized birds. However, the impact of mites or other ectoparasites on hen behaviour or welfare is not well studied. Here, we use activity sensors (three-axis accelerometers) affixed to individual birds to continuously record hen movement before, during, and after infestation with mites. Movements recorded by sensors were identified to specific bird behaviours through a previously trained algorithm, with frequency of these behaviours recorded for individual birds. Hen welfare was also determined before, during, and after mite infestation of hens using animal-based welfare metrics. Northern fowl mites significantly increased hen preening behaviour and resulted in increased skin lesions of infested birds

Seasonal variation and impact of waste-water lagoons as larval habitat on the population dynamics of Culicoides sonorensis (Diptera:Ceratpogonidae) at two dairy farms in northern California.

The Sacramento (northern Central) Valley of California (CA) has a hot Mediterranean climate and a diverse ecological landscape that is impacted extensively by human activities, which include the intensive farming of crops and livestock. Waste-water ponds, marshes, and irrigated fields associated with these agricultural activities provide abundant larval habitats for C. sonorensis midges, in addition to those sites that exist in the natural environment. Within this region, C. sonorensis is an important vector of bluetongue (BTV) and related viruses that adversely affect the international trade and movement of livestock, the economics of livestock production, and animal welfare. To characterize the seasonal dynamics of immature and adult C. sonorensis populations, abundance was monitored intensively on two dairy farms in the Sacramento Valley from August 2012- to July 2013. Adults were sampled every two weeks for 52 weeks by trapping (CDC style traps without light and baited with dry-ice) along N-S and E-W transects on each farm. One farm had large operational waste-water lagoons, whereas the lagoon on the other farm was drained and remained dry during the study. Spring emergence and seasonal abundance of adult C. sonorensis on both farms coincided with rising vernal temperature. Paradoxically, the abundance of midges on the farm without a functioning waste-water lagoon was increased as compared to abundance on the farm with a waste-water lagoon system, indicating that this infrastructure may not serve as the sole, or even the primary larval habitat. Adult midges disappeared from both farms from late November until May; however, low numbers of parous female midges were detected in traps set during daylight in the inter-seasonal winter period. This latter finding is especially critical as it provides a potential mechanism for the "overwintering" of BTV in temperate regions such as northern CA. Precise documentation of temporal changes in the annual abundance and dispersal of Culicoides midges is essential for the creation of models to predict BTV infection of livestock and to develop sound abatement strategies