“Everyday” Knowledge and a New Paradigm of Animal Research

Commentary on Marino and Allen (2017) The Psychology of Cow

Attitudes of Canadian Pig Producers Toward Animal Welfare

As part of a larger study eliciting Canadian producer and non-producer views about animal welfare, open-ended, semi-structured interviews were used to explore opinions about animal welfare of 20 Canadian pig producers, most of whom were involved in confinement-based systems. With the exception of the one organic producer, who emphasized the importance of a ‘‘natural’’ life, participants attached overriding importance to biological health and functioning. They saw their efforts as providing pigs with dry, thermally regulated, indoor environments where animals received abundant feed, careful monitoring and where prospective disease outbreaks could be minimized and controlled. Emphasis was also placed on low-stress handling and agreeable working conditions which were believed to promote good animal care. The fact that pigs tend to respond to such conditions with steady growth reinforced the belief that good welfare was provided. Participants supported the use of sow gestation stalls, but with some reservations, and expressed concern about welfare problems that could occur if sows were grouped. Invasive procedures (castration, tail-docking, teeth clipping) were recognized as painful but were accepted because they were seen as: (1) necessary for sales or management; (2) satisfactory trade-offs to prevent worse welfare problems such as injury or infection; or (3) sufficiently short-term to be relatively unimportant. Participants were adamantly opposed to animal neglect and some welcomed actions of animal protectionists that expose poor care. Producers also welcomed natural-science-based approaches to improving animal welfare. The findings contribute to a broader effort to identify overlapping values among different stakeholder groups as a basis for formulating mutually agreeable, farm animal care and handling polices

Attitudes of Canadian Citizens Toward Farm Animal Welfare: A Qualitative Study

As part of a larger project to determine if there are animal-welfare-related values shared by some commercial food–animal producers and non-producers in Canada, open-ended, semi-structured interviews were conducted to elicit opinions about animal welfare among 24 urban and rural residents not involved in commercial animal production. All participants possessed a self-described interest in food animal well-being and were therefore assumed to represent the views of Canadian non-producers most apt to engage in efforts to shape the animal welfare policies of governments and businesses. Participants described animal welfare in moral or ethical terms, expressed virtually unanimous support for animals having access to “natural” living conditions, and (somewhat less often) linked animal welfare to positive affective states. Maintaining reasonable health and biological functioning was seen as important but was not to take precedence over the benefits of natural living. Participants favoured small family farms and unanimously objected to confinement housing. Participants did, however, offer qualified support for intensive practices and were unanimous in not assigning blame to producers, whom they regarded sympathetically. Predictably perhaps, given our sample, most were critical of industries preoccupied with profits and of consumers who unthinkingly seek cheap food. Recommended ways of improving welfare included instilling in consumers a greater appreciation for the intrinsic value of humanely reared animals, and better education of children regarding the connection between animals and food. Disagreements arose over the welfare implications of organic production and approaches to animal advocacy. Differing demographic backgrounds, experiential involvement with food animals and knowledge of food animal production practices may have influenced the nature or specificity of welfare concerns. Many participants admitted a lack of knowledge about contemporary production practices and some expressed an interest in obtaining additional knowledge. These findings contribute to a broader effort to identify shared values among different stakeholder groups as a basis for formulating widely acceptable, farm animal care and handling polices

"Everyday" Knowledge and a New Paradigm of Animal Research

Commentary on Marino and Allen (2017) The Psychology of Cow

Novel topical fluoride-delivery system for remineralization of dental enamel: optimization studies

Further studies have been conducted on a calcium fluoride delivery system with a view to optimizing its ability to remineralize dental enamel. The influence of particle size and load of calcium fluoride used, as well as treatment time, was evaluated in vitro on prior demineralized bovine enamel. Initial studies with the original singlemembrane system did not allow an unambiguous interpretation of efficacy, due to persistent interference from calcium fluoride particles. To overcome this problem, the system was modified to include a second membrane as protection for the enamel surface. This double-membrane system revealed a marked particle size and load effect on fluoride delivery. The performance of a high load of small size calcium fluoride particles was significantly better than previous results obtained with the system and approached the most effective remineralizing conditions established with solution fluoride.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25203/1/0000642.pd

Measuring the effectiveness of in-hospital and on-base Prevent Alcohol and Risk-related Trauma in Youth (P.A.R.T.Y.) programs on reducing alcohol related harms in naval trainees: P.A.R.T.Y. Defence study protocol

Abstract Background Reducing alcohol related harms in Australian Defence Force (ADF) trainees has been identified as a priority, but there are few evidence-based prevention programs available for the military setting. The study aims to test whether the P.A.R.T.Y. program delivered in-hospital or on-base, can reduce harmful alcohol consumption among ADF trainees. Methods/design The study is a 3-arm randomized controlled trial, involving 953 Royal Australian Navy trainees from a single base. Trainees, aged 18 to 30 years, will be randomly assigned to the study arms: i. in-hospital P.A.R.T.Y.; ii. On-base P.A.R.T.Y.; and iii. Control group. All groups will receive the routine ADF annual alcohol awareness training. The primary outcome is the proportion of participants reporting an Alcohol Use Disorders Identification Test (AUDIT) score of 8 or above at 12 months’ post-intervention. The secondary outcome is the number of alcohol related incidents reported to the Royal Australian Navy (RAN) in the 12 months’ post-intervention. Discussion This is the first trial of the use of the P.A.R.T.Y. program in the military. If the proposed intervention proves efficacious, it may be a useful program in the early education of RAN trainees. Trial registration Australian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12614001332617 , date of registration: 18/12/2014 ‘retrospectively registered’

Drought-Induced, Punctuated Loss of Freshwater Mussels Alters Ecosystem Function Across Temporal Scales

Punctuated, mass mortality events are increasing for many animal taxa and are often related to climatic extremes such as drought. Freshwater mussels are experiencing increased mass mortality events linked to hydrologic drought. Because mussels play important functional roles in rivers it is important to understand the ecosystem effects of these die-offs. Here, we address how mass mortality events of mussels caused by drought may impact stream ecosystem function. We first present a conceptual model, based on the literature, of how mussel mass mortality should affect different ecosystem functions across various ecological time scales, from hours to decades. Next, we highlight two case studies of drought-linked, mussel-mass mortality events from rivers in the southern U.S. We then present the results of an experiment we performed quantifying the ecosystem effects of a punctuated mussel die-off. Finally, we combine our experimental results with field data from a recent mussel die-off to predict how mussel losses will influence ecosystem function. Based on the presented case studies, our mesocosm experiment, and our extrapolated nutrient pulse due to a mussel die-off, we conclude that stream ecosystems are extensively altered following mussel mass mortality events. Mussel loss is governed by drought severity, location within the river network, and species-specific drought tolerances. In the short term, decomposing carrion from mussel die-offs releases a large pulse of nutrients into the water which stimulates food web productivity. In the long term, the overall loss of mussel biomass, and the loss of functional traits as more sensitive species decline, leads to decreases in ecosystem function which may take decades to recover. Drought and human demand for water will make mussel die-offs more likely in the future and it is unlikely that drought sensitive species will recover without changes in water management and restoration of populations through mussel propagation. Our research provides an example of how the loss of an abundant, long-lived organism has cascading and long-term impacts on ecosystems.Open Access fees paid for in whole or in part by the University of Oklahoma LibrariesYe

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Precision medicine in cats:novel niemann-pick type C1 diagnosed by whole-genome sequencing

State-of-the-art health care includes genome sequencing of the patient to identify genetic variants that contribute to either the cause of their malady or variants that can be targeted to improve treatment. The goal was to introduce state-of-the-art health care to cats using genomics and a precision medicine approach. To test the feasibility of a precision medicine approach in domestic cats, a single cat that presented to the University of Missouri, Veterinary Health Center with an undiagnosed neurologic disease was whole-genome sequenced. The DNA variants from the cat were compared to the DNA variant database produced by the 99 Lives Cat Genome Sequencing Consortium. Approximately 25× genomic coverage was produced for the cat. A predicted p.H441P missense mutation was identified in NPC1, the gene causing Niemann-Pick type C1 on cat chromosome D3.47456793 caused by an adenine-to-cytosine transversion, c.1322A>C. The cat was homozygous for the variant. The variant was not identified in any other 73 domestic and 9 wild felids in the sequence database or 190 additionally genotyped cats of various breeds. The successful effort suggested precision medicine is feasible for cats and other undiagnosed cats may benefit from a genomic analysis approach. The 99 Lives DNA variant database was sufficient but would benefit from additional cat sequences. Other cats with the mutation may be identified and could be introduced as a new biomedical model for NPC1. A genetic test could eliminate the disease variant from the population

A New Method for Species Identification via Protein-Coding and Non-Coding DNA Barcodes by Combining Machine Learning with Bioinformatic Methods

Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI) region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS) genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF) to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish) and two representing non-coding ITS barcodes (rust fungi and brown algae). Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ) and Maximum likelihood (ML) methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI) of 99.75–100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62–98.40%) for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60–99.37%) for 1094 brown algae queries, both using ITS barcodes