The South Island dairy lameness group project

Lameness is an important issue wherever dairy production occurs. It is consistently placed after infertility and mastitis in the top three cow health issues for farmers both internationally and in New Zealand (NZ). It has been a commonly held view in the South Island (SI) industry that there is more lameness here than in the North Island (NI), and that the problem has been growing in recent years. There are strong opinions in the SI industry suggesting there are important local influences on lameness. This is often explained in reference to differences between the NI and SI climate, herds, and management. The current SI herd has a cluster of features linked to the recent history of dairying here. In the past 15 years there has been strong expansion of the NZ dairy industry into the SI, where cheaper land and the availability of extensive, dependable irrigation have enabled a sustained increase in the number of dairy farms and cows (Anonymous, 2006). Despite the obvious similarities of grass based dairying between the NI and SI, there are several observed differences. The average farm in the SI has a greater herd size and greater per cow and per hectare production, and this high production is particularly pronounced in some regions (eg. Canterbury). Over the period of expansion there has often been emphasis on increasing herd size, which can reduce options around culling of cows. Many SI farms are conversions and irrigation along with intensive, recent pasture refurbishment are common features. Pasture management is often a top tier priority, and very intensive systems, to increase utilisation and maintain high quality (high energy, low fibre) across the season are commonplace. In addition, the long daylight hours and cooler nights are thought to promote higher sugar content in the pastures. Against that background, the origins of the most common and longstanding explanations within the SI industry for high lameness - particularly the role of nutrition - can be better understood. In brief summary, the popular idea of the influence of nutrition, the high energy and low fibre pastures are thought to induce rumen dysfunction resulting in secondary weakness in the hooves

Rumen function and lameness in South Island cows

A large part of the rumen research we use here in NZ is drawn from work done overseas, routinely on cows fed lots of grain, while there is perishingly little hard data on the high production, grass based rumens that are the direction NZ dairy appears to be heading in. Despite this, or maybe because of this, there are a considerable number of loud and strong opinions around rumen function here in NZ, and particularly about the high producing cow. Although it seems there are a lot of issues around rumen function spoken about, in reality there is just one central theme that is most commonly discussed, and this is just recycled in different forms. This paper will look at what we know, and don’t know, about rumen function in grass based dairy cows under NZ conditions, and outline the results of the three years of rumen research on the Lincoln University Dairy Farm (LUDF), and what this tells us about the role of the rumen in lameness here in the South Island

Dehydration accelerates reductions in cerebral blood flow during prolonged exercise in the heat without compromising brain metabolism

Dehydration hastens the decline in cerebral blood flow (CBF) during incremental exercise, while the cerebral metabolic rate for oxygen (CMRO2) is preserved. It remains unknown whether CMRO2 is also maintained during prolonged exercise in the heat and whether an eventual decline in CBF is coupled to fatigue. Two studies were undertaken. In study 1, ten male cyclists cycled in the heat for ~2 h with (control) and without fluid replacement (dehydration) while internal (ICA) and external (ECA) carotid artery blood flow and core and blood temperature were obtained. Arterial and internal jugular venous blood samples were assessed with dehydration to evaluate the CMRO2. In study 2 (8 males), middle cerebral artery blood velocity (MCA Vmean) was measured during prolonged exercise to exhaustion in both dehydrated and euhydrated states. After a rise at the onset of exercise, ICA flow declined to baseline with progressive dehydration (P < 0.05). However, cerebral metabolism remained stable through enhanced oxygen and glucose extraction (P < 0.05). ECA flow increased for one hour but declined prior to exhaustion. Fluid ingestion maintained cerebral and extra-cranial perfusion throughout non-fatiguing exercise. During exhaustive exercise, however, euhydration delayed but did not prevent the decline in cerebral perfusion. In conclusion, during prolonged exercise in the heat dehydration accelerates the decline in CBF without affecting CMRO2 and also restricts extra-cranial perfusion. Thus fatigue is related to reduction in CBF and extra-cranial perfusion rather than in CMRO2.The study was supported by a grant from the Gatorade Sports Science Institute, PepsiCo Inc, USA

Ammonia emissions from cattle urine and dung excreted on pasture

Twelve cattle were kept for three days in a circular area of 16 m radius on short pasture and fed with freshly-cut pasture. Ammonia (NH₃) emissions from the urine and dung excreted by the cattle were measured with a micrometeorological mass-balance method, during the cattle presence and for 10 subsequent days. Daily-integrated emission rates peaked on Day 3 of the experiment (last day of cattle presence) and declined steadily for five days thereafter. Urine patches were the dominant sources for these emissions. On Day 9, a secondary emissions peak occurred, with dung pats likely to be the main sources. This interpretation is based on simultaneous observations of the pH evolution in urine patches and dung pats created next to the circular plot. Feed and dung samples were analysed to estimate the amounts of nitrogen (N) ingested and excreted. Total N volatilised as NH₃ was 19.8 (± 0.9)% of N intake and 22.4 (± 1.3)% of N excreted. The bimodal shape of the emissions time series allowed to infer separate estimates for volatilisation from urine and dung, respectively, with the result that urine accounted for 88.6 (± 2.6)% of the total NH₃ emissions. The emissions from urine represented 25.5 (± 2.0)% of the excreted urine-N, while the emissions from dung amounted to 11.6 (± 2.7)% of the deposited dung-N. Emissions from dung may have continued after Day 13 but were not resolved by the measurement technique. A simple resistance model shows that the magnitude of the emissions from dung is controlled by the resistance of the dung crust. © Author(s) 2013

QES-Fire: A dynamically coupled fast-response wildfire model

A microscale wildfire model, QES-Fire, that dynamically couples the fire front to microscale winds was developed using a simplified physics rate of spread (ROS) model, a kinematic plume-rise model and a mass-consistent wind solver. The model is three-dimensional and couples fire heat fluxes to the wind field while being more computationally efficient than other coupled models. The plume-rise model calculates a potential velocity field scaled by the ROS model\u27s fire heat flux. Distinct plumes are merged using a multiscale plume-merging methodology that can efficiently represent complex fire fronts. The plume velocity is then superimposed on the ambient winds and the wind solver enforces conservation of mass on the combined field, which is then fed into the ROS model and iterated on until convergence. QES-Fire\u27s ability to represent plume rise is evaluated by comparing its results with those from an atmospheric large-eddy simulation (LES) model. Additionally, the model is compared with data from the FireFlux II field experiment. QES-Fire agrees well with both the LES and field experiment data, with domain-integrated buoyancy fluxes differing by less than 17% between LES and QES-Fire and less than a 10% difference in the ROS between QES-Fire and FireFlux II data

A methodology for projecting hospital bed need: a Michigan case study

Michigan's Department of Community Health (MDCH) is responsible for managing hospitals through the utilization of a Certificate of Need (CON) Commission. Regulation is achieved by limiting the number of beds a hospital can use for inpatient services. MDCH assigns hospitals to service areas and sub areas by use patterns. Hospital beds are then assigned within these Hospital Service Areas and Facility Sub Areas. The determination of the number of hospital beds a facility subarea is authorized to hold, called bed need, is defined in the Michigan Hospital Standards and published by the CON Commission and MDCH. These standards vaguely define a methodology for calculating hospital bed need for a projection year, five years ahead of the base year (defined as the most recent year for which patient data have been published by the Michigan Hospital Association). MDCH approached the authors and requested a reformulation of the process. Here we present a comprehensive guide and associated code as interpreted from the hospital standards with results from the 2011 projection year. Additionally, we discuss methodologies for other states and compare them to Michigan's Bed Need methodology

Identification of plasma lipid biomarkers for prostate cancer by lipidomics and bioinformatics

Background: Lipids have critical functions in cellular energy storage, structure and signaling. Many individual lipid molecules have been associated with the evolution of prostate cancer; however, none of them has been approved to be used as a biomarker. The aim of this study is to identify lipid molecules from hundreds plasma apparent lipid species as biomarkers for diagnosis of prostate cancer. Methodology/Principal Findings: Using lipidomics, lipid profiling of 390 individual apparent lipid species was performed on 141 plasma samples from 105 patients with prostate cancer and 36 male controls. High throughput data generated from lipidomics were analyzed using bioinformatic and statistical methods. From 390 apparent lipid species, 35 species were demonstrated to have potential in differentiation of prostate cancer. Within the 35 species, 12 were identified as individual plasma lipid biomarkers for diagnosis of prostate cancer with a sensitivity above 80%, specificity above 50% and accuracy above 80%. Using top 15 of 35 potential biomarkers together increased predictive power dramatically in diagnosis of prostate cancer with a sensitivity of 93.6%, specificity of 90.1% and accuracy of 97.3%. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) demonstrated that patient and control populations were visually separated by identified lipid biomarkers. RandomForest and 10-fold cross validation analyses demonstrated that the identified lipid biomarkers were able to predict unknown populations accurately, and this was not influenced by patient's age and race. Three out of 13 lipid classes, phosphatidylethanolamine (PE), ether-linked phosphatidylethanolamine (ePE) and ether-linked phosphatidylcholine (ePC) could be considered as biomarkers in diagnosis of prostate cancer. Conclusions/Significance: Using lipidomics and bioinformatic and statistical methods, we have identified a few out of hundreds plasma apparent lipid molecular species as biomarkers for diagnosis of prostate cancer with a high sensitivity, specificity and accuracy

Depredation influences anglers’ perceptions on coastal shark management and conservation in the United States Gulf of Mexico

Overfishing, habitat degradation, and climate change have caused declines in shark populations throughout the world’s oceans. However, in the United States Gulf of Mexico (GoM), populations of several coastal shark species are starting to stabilize following decades of successful regulations and enforcement. The stabilization of coastal shark populations, coupled with increases in recreational fishing effort, has the potential to escalate human-wildlife interactions. The most often reported conflict is shark depredation, the partial or complete removal of a hooked species by a shark. Reported increases in shark depredation within the last several years have begun to erode angler support for shark conservation, potentially undermining decades of previous work. To address these concerns, we implemented a GoM-wide online survey to characterize the impact of depredation on recreational reef fish anglers’ fishing satisfaction and perceptions of shark management and conservation. Our results revealed that most recreational anglers in the GoM have witnessed depredation but have not changed their fishing behaviors. In contrast, anglers’ viewpoints on managing shark populations were split between reducing population sizes and maintaining current population levels. As coastal shark populations in the GoM continue to recover, shark depredation is likely to increase. Consequently, efforts to characterize anglers’ satisfaction and perceptions are a critical component of future shark conservation initiatives

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought

Additional rare variant analysis in Parkinson's Disease cases with and without known pathogenic mutations: evidence for oligogenic inheritance

Oligogenic inheritance implies a role for several genetic factors in disease etiology. We studied oligogenic inheritance in Parkinson’s (PD) by assessing the potential burden of additional rare variants in established Mendelian genes and/or GBA, in individuals with and without a primary pathogenic genetic cause in two large independent cohorts totaling 7,900 PD cases and 6,166 controls. An excess (≥30%) of cases with a recognized primary genetic cause had ≥1 additional rare variants in Mendelian PD genes, as compared with no known mutation PD cases (17%) and unaffected controls (16%), supporting our hypothesis. Carriers of additional Mendelian gene variants have younger ages at onset (AAO). The effect of additional Mendelian variants in LRRK2 G2019S mutation carriers, of which ATP13A2 variation is particularly common, may account for some of the variation in penetrance. About 10% of no known mutation PD cases harbor a rare GBA variant compared to known pathogenic mutation PD cases (8%) and controls (5%), with carriers having earlier AAOs. Together, the data suggest that the oligogenic inheritance of rare Mendelian variants may be important in patient with a primary pathogenic cause, whereas GBA increases risk across all forms of PD. This study highlights potential genetic complexity of Mendelian PD. The identification of potential modifying variants provides new insights into disease mechanisms by potentially separating relevant from benign variants and by the interaction between genes in specific pathways. In the future this may be relevant to genetic testing and counselling of PD patients and their families