Automated body condition scoring of dairy cattle : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Engineering at Massey University, Manawatū, New Zealand

This research demonstrates the development and implementation of an automatic body condition scoring system for dairy cattle that can operate in a real-world environment. Body condition scoring is a subjective method used for measuring changes in energy reserves in many animals, including dairy cattle. These energy reserves can be measured by analysing specific regions on the cow to estimate the amount of fat the animal is carrying. This information allows for greater management of the herd by adjusting the feeding strategies to ensure that each cow is at an optimal condition score. Maintaining an optimal condition throughout the year has implications for milk yield, reproductive performance, animal welfare, and overall farm profits. Current condition scoring methods are manual and are highly subjective, time consuming, expensive, and require a high level of training and competency. These limitations have created a demand for an accurate and objective scoring system. This research presents an automated system that utilises a single camera to be placed above the path of the cow at the entrance or exit to a milking platform or weigh scale. When the cow passes in view of the camera, the features are automatically extracted and converted to a conditions score. Tests have shown that the system successfully predicted the condition score within half a point of the true score for 83% of the 710 cows scored, and 96% within one point

Functionally different PIN proteins control auxin flux during bulbil development in Agave tequilana

In Agave tequilana, reproductive failure or inadequate flower development stimulates the formation of vegetative bulbils at the bracteoles, ensuring survival in a hostile environment. Little is known about the signals that trigger this probably unique phenomenon in agave species. Here we report that auxin plays a central role in bulbil development and show that the localization of PIN1-related proteins is consistent with altered auxin transport during this process. Analysis of agave transcriptome data led to the identification of the A. tequilana orthologue of PIN1 (denoted AtqPIN1) and a second closely related gene from a distinct clade reported as ‘Sister of PIN1’ (denoted AtqSoPIN1). Quantitative real-time reverse transcription–PCR (RT-qPCR) analysis showed different patterns of expression for each gene during bulbil formation, and heterologous expression of the A. tequilana PIN1 and SoPIN1 genes in Arabidopsis thaliana confirmed functional differences between these genes. Although no free auxin was detected in induced pedicel samples, changes in the levels of auxin precursors were observed. Taken as a whole, the data support the model that AtqPIN1 and AtqSoPIN1 have co-ordinated but distinct functions in relation to auxin transport during the initial stages of bulbil formation

Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle

peer-reviewedPeriodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10-20) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10-20) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10-20) and solid (ρ = 0.69, P = <1x10-20) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.This study was supported by the Science Foundation Ireland (http://www.sfi.ie) (Contract number SFI 09/RFP/GEN2447-awarded to SMW) and Teagasc Walsh Fellowship Funding (www.teagasc.ie) (Teagasc project RMIS 6341-awarded to SMW)

Drivers and Seasonal Variability of Redox-Sensitive Metal Chemistry in a Shallow Subterranean Estuary

The subterranean estuary (STE) has been historically defined in terms of the mixing of saline and fresh water, in an analogy to surface estuaries. However, redox gradients are also a defining characteristic of the STE and influence its role as a source or sink for metals in the environment. Approaching the STE from a redox-focused biogeochemical perspective (e.g., considering the role of microbial respiration and availability of organic matter) provides the ability to quantify drivers of metal transport across spatial and temporal scales. This study measured the groundwater composition of a shallow STE over 2 years and used multiple linear regression to characterize the influence of salinity and redox chemistry on the behavior of redox-sensitive metals (RSMs) including Mo, U, V, and Cr. Molybdenum and uranium were both supplied to the STE by surface water, but differed in their removal mechanisms and seasonal behavior. Molybdenum showed non-conservative removal by reaction with sulfide in all seasons. Sulfide concentrations at this site were consistently higher than required for quantitative reaction with Mo (10 µM sulfide), evidently leading to quantitative removal at the same depth regardless of season. In contrast, U appeared to depend directly on microbial activity for removal, and showed more extensive removal at shallower depths in summer. Both V and Cr were elevated in meteoric groundwater (2.5–297 nM and 2.6–236 nM, respectively), with higher endmember concentrations in summer. Both V and Cr also showed non-conservative addition within the STE relative to conservative mixing among the observed endmembers. The mobility of V and Cr in the STE, and therefore their supply to the coastal ocean, was controlled by the availability of dissolved organic matter and Fe, suggesting V and Cr were potentially complexed in the colloidal fraction. Complexation by different organic matter pools led to seasonal variations in V but greater interannual variability of Cr. These results reveal distinct behaviors of RSMs in response to seasonal biogeochemical processes that drive microbial activity, organic matter composition, and complexation by inorganic species

Environmental forcing by submarine canyons: Evidence between two closely situated cold-water coral mounds (Porcupine Bank Canyon and Western Porcupine Bank, NE Atlantic)

Within the Porcupine Bank Canyon (NE Atlantic), cold-water coral (CWC) mounds are mostly found clustered along the canyon lip, with individual disconnected mounds occurring nearby on the western Porcupine Bank. Remotely operated vehicle-mounted vibrocoring was utilized to acquire cores from both of these sites. This study is the first to employ this novel method when aiming to precisely sample two closely situated areas. Radiometric ages constrain the records from the early to mid-Holocene (9.1 to 5.6 ka BP). The cores were then subjected to 3D segmented computer tomography to capture mound formation stages. The cores were then further examined using stable isotopes and benthic foraminiferal assemblages, to constrain the paleoenvironmental variation that influenced CWC mound formation of each site. In total, mound aggradation rate in the Porcupine Bank Canyon and western Porcupine Bank was comparable to other Holocene CWC mounds situated off western Ireland. Results derived from multiproxy analysis, show that regional climatic shifts define the environmental conditions that allow positive coral mound formation. In addition, the aggradation rate of coral mounds is higher adjacent to the Porcupine Bank Canyon than on the western Porcupine Bank. Benthic foraminifera assemblages and planktic foraminiferal δ13C reveal that higher quality organic matter is more readily available closer to the canyon lip. As such, we hypothesize that coral mound formation in the region is likely controlled by an interplay between enhanced shelf currents and the existence of the Eastern North Atlantic Water-Mediterranean Outflow Water-Transition Zone. The geomorphology of the canyon promotes upwelling of these water masses that are enriched in particles, including food and sediment supply. The higher availability of these particles support the development and succession of ecological hotspots along the canyon lip and adjacent areas of the seafloor. These observations provide a glimpse into the role that submarine canyons play in influencing macro and micro benthic fauna distributions and highlights the importance of their conservation

Using novel methods to track British and Irish Ice Sheet dynamics since the Late Pleistocene, along the west Porcupine Bank, NE Atlantic

Extensive research has been undertaken to elucidate the glacial history of the British Irish Ice Sheet (BIIS) in the NE Atlantic. BRITICE-CHRONO has compiled terrestrial and marine based evidence, to provide an empirical reconstruction of ice sheet expansion and retreat during the Late Pleistocene. Across the Irish margin, particular focus has been given to seafloor sediments which contain ice-rafted debris (IRD). However, there are few publications on IRD from areas proximal to the maximum extent of the BIIS, which would offer further insights on the behaviour of the ice sheet during (de)glacial events. Previous exploratory surveys of the west Porcupine Bank (wPB) visually identified IRD on the seafloor and these present a new study site to investigate the extent of the BIIS and the course of its icebergs. Moreover, there are uncertainties about the effects of icebergs on the marine life and cold-water corals occupying the nearby Porcupine Bank Canyon. Assessing a sediment core containing an IRD analogue for the wPB would thus, have a dual purpose. In the past however, coring missions of the wPB using traditional coring methods (i.e. piston and gravity cores) were unsuccessful. Here, we utilized a novel ROV-mounted vibrocoring procedure to capture a 0.75 m IRD-bearing sediment core from the wPB. Then further novel analytical methods (computed tomography-based IRD-detection) were used to quantify IRD every 0.02 cm to provide the highest resolution record of BIIS related IRD to date. From this, several fluxes of IRD deposition onto the wPB between 31.6 and 9 ka BP were revealed and corroborated by other published records from across the NE Atlantic. It was shown that the wPB IRD fluxes occur simultaneously with other parts of the margin. The IRD signal also shows that iceberg calving occurred on the wPB during the Younger Dryas. Grain-size analysis of the core allowed for a reconstruction and interpretation of the palaeoenvironmental conditions during these IRD flux events and shows that BIIS-derived glaciers had a major impact on hydrodynamic conditions in the wPB. Subsequently, intensive scouring led to a major hiatus in the core during 27.3â 17.2 ka BP. These results are a useful addition to BIIS literature on this part of the shelf. Furthermore, it shows that bottom currents were influenced by (de)glacial events, an important finding when considering the presence of nearby current-dependant benthos

Irish primary school teachers’ experiences, training and knowledge in first aid

Injury and illness can occur in children. Since children spend a considerable amount of time in school, teachers must have the ability to assist when required. However, no research to date has examined Irish primary school teachers’ experiences, training and knowledge in first aid. An online survey (n = 587) examined Irish male and female primary school teachers previous first aid experiences, training and knowledge. Respondents generally showed high levels of both previous first aid training and exposure to events requiring first aid. In addition, most teachers knew the location of the school’s first aid equipment and were aware of their school’s first aid policy. However, many felt ill equipped to deal with these situations, particularly for serious incidents and over a third of teachers were not currently certified in first aid. While teachers displayed good overall knowledge, gaps were evident. The findings demonstrate the need to develop a multilevel school strategy to ensure teacher proficiency and school preparedness in managing situations requiring first aid

Quantifying Drug-Induced Bone Marrow Toxicity Using a Novel Haematopoiesis Systems Pharmacology Model.

Haematological toxicity associated with cancer therapeutics is monitored by changes in blood cell count, and their primary effect is on proliferative progenitors in the bone marrow. Using observations in rat bone marrow and blood, we characterize a mathematical model that comprises cell proliferation and differentiation of the full haematopoietic phylogeny, with interacting feedback loops between lineages in homeostasis as well as following carboplatin exposure. We accurately predicted the temporal dynamics of several mature cell types related to carboplatin-induced bone marrow toxicity and identified novel insights into haematopoiesis. Our model confirms a significant degree of plasticity within bone marrow cells, with the number and type of both early progenitors and circulating cells affecting cell balance, via feedback mechanisms, through fate decisions of the multipotent progenitors. We also demonstrated cross-species translation of our predictions to patients, applying the same core model structure and considering differences in drug-dependent and physiology-dependent parameters