PRNP Haplotype Associated with Classical BSE Incidence in European Holstein Cattle

Background: Classical bovine spongiform encephalopathy (BSE) is an acquired prion disease of cattle. The bovine prion gene (PRNP) contains regions of both high and low linkage disequilibrium (LD) that appear to be conserved across Bos taurus populations. The region of high LD, which spans the promoter and part of intron 2, contains polymorphic loci that have been associated with classical BSE status. However, the complex genetic architecture of PRNP has not been systematically tested for an association with classical BSE. Methodology/Principal Findings: In this study, haplotype tagging single nucleotide polymorphisms (htSNPs) within PRNP were used to test for association between PRNP haplotypes and BSE disease. A combination of Illumina goldengate assay, sequencing and PCR amplification was used to genotype 18 htSNPs and 2 indels in 95 BSE case and 134 control animals. A haplotype within the region of high LD was found to be associated with BSE unaffected animals (p-value = 0.000114). Conclusion/Significance: A PRNP haplotype association with classical BSE incidence has been identified. This result suggests that a genetic determinant in or near PRNP may influence classical BSE incidence in cattle

Implications of Storing Urinary DNA from Different Populations for Molecular Analyses

Molecular diagnosis using urine is established for many sexually transmitted diseases and is increasingly used to diagnose tumours and other infectious diseases. Storage of urine prior to analysis, whether due to home collection or bio-banking, is increasingly advocated yet no best practice has emerged. Here, we examined the stability of DNA in stored urine in two populations over 28 days.Urine from 40 (20 male) healthy volunteers from two populations, Italy and Zambia, was stored at four different temperatures (RT, 4 degrees C, -20 degrees C & -80 degrees C) with and without EDTA preservative solution. Urines were extracted at days 0, 1, 3, 7 and 28 after storage. Human DNA content was measured using multi-copy (ALU J) and single copy (TLR2) targets by quantitative real-time PCR. Zambian and Italian samples contained comparable DNA quantity at time zero. Generally, two trends were observed during storage; no degradation, or rapid degradation from days 0 to 7 followed by little further degradation to 28 days. The biphasic degradation was always observed in Zambia regardless of storage conditions, but only twice in Italy.Site-specific differences in urine composition significantly affect the stability of DNA during storage. Assessing the quality of stored urine for molecular analysis, by using the type of strategy described here, is paramount before these samples are used for molecular prognostic monitoring, genetic analyses and disease diagnosis

Impacts of Poultry House Environment on Poultry Litter Bacterial Community Composition

Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly Gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens

Population ecology of the sea lamprey (Petromyzon marinus) as an invasive species in the Laurentian Great Lakes and an imperiled species in Europe

The sea lamprey Petromyzon marinus (Linnaeus) is both an invasive non-native species in the Laurentian Great Lakes of North America and an imperiled species in much of its native range in North America and Europe. To compare and contrast how understanding of population ecology is useful for control programs in the Great Lakes and restoration programs in Europe, we review current understanding of the population ecology of the sea lamprey in its native and introduced range. Some attributes of sea lamprey population ecology are particularly useful for both control programs in the Great Lakes and restoration programs in the native range. First, traps within fish ladders are beneficial for removing sea lampreys in Great Lakes streams and passing sea lampreys in the native range. Second, attractants and repellants are suitable for luring sea lampreys into traps for control in the Great Lakes and guiding sea lamprey passage for conservation in the native range. Third, assessment methods used for targeting sea lamprey control in the Great Lakes are useful for targeting habitat protection in the native range. Last, assessment methods used to quantify numbers of all life stages of sea lampreys would be appropriate for measuring success of control in the Great Lakes and success of conservation in the native range

A Research Agenda for Helminth Diseases of Humans: Intervention for Control and Elimination

Recognising the burden helminth infections impose on human populations, and particularly the poor, major intervention programmes have been launched to control onchocerciasis, lymphatic filariasis, soil-transmitted helminthiases, schistosomiasis, and cysticercosis. The Disease Reference Group on Helminth Infections (DRG4), established in 2009 by the Special Programme for Research and Training in Tropical Diseases (TDR), was given the mandate to review helminthiases research and identify research priorities and gaps. A summary of current helminth control initiatives is presented and available tools are described. Most of these programmes are highly dependent on mass drug administration (MDA) of anthelmintic drugs (donated or available at low cost) and require annual or biannual treatment of large numbers of at-risk populations, over prolonged periods of time. The continuation of prolonged MDA with a limited number of anthelmintics greatly increases the probability that drug resistance will develop, which would raise serious problems for continuation of control and the achievement of elimination. Most initiatives have focussed on a single type of helminth infection, but recognition of co-endemicity and polyparasitism is leading to more integration of control. An understanding of the implications of control integration for implementation, treatment coverage, combination of pharmaceuticals, and monitoring is needed. To achieve the goals of morbidity reduction or elimination of infection, novel tools need to be developed, including more efficacious drugs, vaccines, and/or antivectorial agents, new diagnostics for infection and assessment of drug efficacy, and markers for possible anthelmintic resistance. In addition, there is a need for the development of new formulations of some existing anthelmintics (e.g., paediatric formulations). To achieve ultimate elimination of helminth parasites, treatments for the above mentioned helminthiases, and for taeniasis and food-borne trematodiases, will need to be integrated with monitoring, education, sanitation, access to health services, and where appropriate, vector control or reduction of the parasite reservoir in alternative hosts. Based on an analysis of current knowledge gaps and identification of priorities, a research and development agenda for intervention tools considered necessary for control and elimination of human helminthiases is presented, and the challenges to be confronted are discussed

Preferred color gamut boundaries for wide-gamut and multiprimary displays

\u3cp\u3ePreferred chroma enhancement and its dependence on hue are studied in a two-part experiment using a wide-gamut multiprimary display. Earlier research showed a clear dependence on hue but was limited by the gamut of the display it employed; the present work builds on this while easing the gamut constraints. In the first part of the present experiment, a tuning task was used to refine the preference for chroma boost starting with standard-gamut (Rec. 709) images. The overall median preferred boost is roughly 20%, but it is not uniform over hues: the preferred boost for orange, yellow, green, and cyan colors is greater than that for blue, magenta, and red colors. Dependence on image content and observer is noted, though a content-independent chroma boost created by aggregating preference over many images performs well. An adjustment parameter for overall chroma, which incorporates the hue dependence averaged over image content, should be sufficient to handle the vast majority of interobserver variance in preference. In the second part of the experiment, various chroma boost algorithms were evaluated through a paired comparison task. The prescribed hue-dependent chroma boost is preferred over all other variations, and all hue-preserving chroma boost variations are preferred over both colorimetrically accurate and nabox drawings light down and lefẗve same-drive-signal renderings. The results may be applied in display design to select gamut boundaries that maximize satisfaction over the observer population. © 2012 Wiley Periodicals, Inc. Col Res Appl, 39, 169-178, 2014\u3c/p\u3

Visualizing lighting with images : converging between the predictive value of renderings and photographs

Performing psychophysical experiments to investigate lighting perception can be expensive and time consuming if complex lighting systems need to be implemented. In this paper, display-based experiments are explored as a cost effective and less time consuming alternative to real-world experiments. The aim of this work is to better understand the upper limit of prediction accuracy that can be achieved when presenting an image on a display rather than the real-world scene. We compare the predictive value of photographs and physically-based renderings on a number of perceptual lighting attributes. It is shown that the photographs convey statistically the same lighting perception as in a real-world scenario. Initial renderings have an inferior performance, but are shown to converge towards the performance of the photographs through iterative improvements. © (2013) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

Perceived speed of changing color in chroma and hue directions in CIELAB

\u3cp\u3eIn dynamic LED lighting, the perceived speed of changing color is an important concept; however, there exists no suitable temporal color space. In a psychophysical experiment, we compared the perceived speed of periodic temporal transitions in CIELAB chroma and hue directions around five base colors [the five Munsell hues: 5R (red), 5Y (yellow), 5G (green), 5B (blue), and 5P (purple)]. The experiment was conducted in a light laboratory, with the main illumination stimulus subtending a visual angle of 101 × 77 deg. In sequential paired presentations, observers were asked to identify which transition appeared faster, and points of subjective equality between transitions were computed. The speed of transitions was defined in CIELAB ΔE \u3csub\u3eab\u3c/sub\u3e∕s, which was shown to be temporally non-uniform; uniformity was improved using a modified color space based on speeds in the DKL space of Derrington et al. \u3c/p\u3

Assessing the temporal uniformity of CIELAB hue angle

In recent work [J. Opt. Soc. Am. A 36, 1022 (2019)], we found that ΔE∗ab/s in CIELAB is not suitable for describing the perceived speed of temporal color changes in full-room illumination. Two hue transitions with the same physical speed of change, in terms of ΔE∗ab/s, were not perceived to change at the same speed. This is not really surprising, since CIELAB was not designed to characterize the perception of temporal color transitions in illumination. In this study, we further investigate the temporal uniformity of CIELAB. The stimuli were presented in a square of 4.3° visual angle surrounded by a 4000 K adapting field, similar to the viewing condition for which CIELAB was designed (i.e., where color stimuli are presented on-axis surrounded by a static adaptation field). The human observers viewed pairs of temporal color transitions which were presented sequentially, and were asked to select the one that appeared to change faster. The results confirmed that under these conditions CIELAB was also not temporally uniform. We present preliminary attempts to improve the temporal uniformity for both CIELAB and cone-excitation spaces (i.e., LMS and DKL (Derrington–Krauskopf–Lennie [J. Physiol. 357, 241 (1984)])