Greater Sage-Grouse Survival, Breeding Ecology, Resource Selection, and West Nile Virus Prevalence on the Eastern Fringe of their Range

The greater sage-grouse (Centrocercus urophasianus) is a sagebrush (Artemisia spp.) obligate species that has experienced population declines over the past several decades. Sage-grouse are a species of conservation concern throughout the Intermountain West and are considered a species of greatest conservation need in South Dakota. Numerous studies have documented drivers of demographic performance at the core of their distribution; however, relatively few studies have examined sage-grouse inhabiting the eastern extent of their range, in South Dakota. We sought to examine sage-grouse space use in multiple seasons, estimate survival, and determine factors affecting nest success in South Dakota during 2016 and 2017. Additionally, we quantified resource selection during spring/summer, winter, at nest-sites, and at brood-sites. Lastly, sagegrouse are highly susceptible to West Nile virus (WNV); thus, we evaluated the impact of WNV to this population of sage-grouse while simultaneously estimating infection rates in the primary arthropod vector, Culex tarsalis. We found that at a landscape scale, sagegrouse consistently exhibit positive selection responses to sagebrush and leks, and negative responses to forest, roads, and rugged terrain. At a local scale, when selecting nest-sites and brood-sites, sage-grouse consistently select for shrub cover and taller grass, while avoiding areas with greater percent grass cover. Estimated nest success was 29% (95% CI=20−42%). Distance to forest, distance to lek, road density, and percent undisturbed (unplowed) land had the greatest influenced on nest survival. Using remotely triggered cameras, we identified the American badger (Taxidea taxus) as the primary nest predator of sage-grouse. Adult female sage-grouse survival during the reproductive season (1 April−15 September) was estimated to be 68% (95% CI=56–78%). Survival varied temporally with lower survival during the nesting season compared to other periods during the reproductive season. We observed limited resistance to WNV (Culex tarsalis (minimum infection rate=1.6−3.3/1,000 mosquitoes tested). We did not observe a severe WNV outbreak during our study, but these data do serve as a baseline for enzootic levels of the virus in this landscape. Lastly, with our data we were able to develop a priority sage-grouse area in South Dakota, which encompasses known utilization as well as predicted use. Overall, this research has provided data from a population with limited prior information, as well as provided information that can enhance landscape management for the species

A Qualitative Study of Perceived Barriers to Fruit and Vegetable Consumption Among Low-Income Populations, North Carolina, 2011

IntroductionObesity is the leading preventable cause of illness and a major contributor to chronic disease. Eating fresh fruits and vegetables can help manage and prevent weight gain and reduce the risk of chronic diseases. Low-income communities often lack stores that sell fresh fruit and vegetables and have instead stores that sell foods low in nutritional value. The objective of this study was to understand perceived community-level barriers to fruit and vegetable consumption among low-income people.MethodsWe conducted 8 focus groups involving 68 low-income participants in 2 North Carolina counties, from May 2011 through August 2011. The socioecological model of health guided data analysis, and 2 trained researchers coded transcripts and summarized findings. Four focus groups were conducted in each county; 1 was all male, 5 all female, and 2 mixed sexes. Most participants were black (68%), most were women (69.1%), and most had a high school education or less (61.8%). Almost half received support from either the Supplemental Nutrition Assistance Program or another government assistance program.ResultsWe identified 6 major community-level barriers to access to fruits and vegetables: cost, transportation, quality, variety, changing food environment, and changing societal norms on food.ConclusionPolicymakers should consider supporting programs that decrease the cost and increase the supply of high-quality fruits and vegetables in low-income communities

A Multi-Proxy Assessment of the Impact of Environmental Instability on Late Holocene (4500-3800 BP) Native American Villages of the Georgia Coast

Circular shell rings along the South Atlantic Coast of North America are the remnants of some of the earliest villages that emerged during the Late Archaic (5000-3000 BP). Many of these villages, however, were abandoned during the Terminal Late Archaic (ca 3800-3000 BP). We combine Bayesian chronological modeling with mollusk shell geochemistry and oyster paleobiology to understand the nature and timing of environmental change associated with the emergence and abandonment of circular shell ring villages on Sapelo Island, Georgia. Our Bayesian models indicate that Native Americans occupied the three Sapelo shell rings at varying times with some generational overlap. By the end of the complex\u27s occupation, only Ring III was occupied before abandonment ca. 3845 BP. Ring III also consists of statistically smaller oysters harvested from less saline estuaries compared to earlier occupations. Integrating shell biochemical and paleobiological data with recent tree ring analyses shows a clear pattern of environmental fluctuations throughout the period in which the rings were occupied. We argue that as the environment became unstable around 4300 BP, aggregation at villages provided a way to effectively manage fisheries that are highly sensitive to environmental change. However, with the eventual collapse of oyster fisheries and subsequent rebound in environmental conditions ca. post-3800 BP, people dispersed from shell rings, and shifted to non-marine subsistence economies and other types of settlements. This study provides the most comprehensive evidence for correlations between large-scale environmental change and societal transformations on the Georgia coast during the Late Archaic period

Community Engagement newsletter, Faculty of Veterinary Science, Autumn, May 2018

Locuming in paradise / Luke Arnot -- Real about rabies at Ribane-Laka / Sylvia-Anne Farmer, Daniel Parsons, Matthew Woods and Hendre van Zyl -- Lending a helping paw / Kgopotso Mabote -- One Health efforts in Gauteng put to the test / Lindsey Burgess, Devon Seaton and John Burgess -- Community engagement project goes viral / Andrè Els and Nydia-Lee BritsNews articles with colour photos about the various community engagement projects of the Faculty of Veterinary Science, University of Pretoria.ab201

Severe Facial Herpes Vegetans and Viremia in NFKB2-Deficient Common Variable Immunodeficiency

With the accessibility of next-generation sequencing modalities, an increasing number of primary immunodeficiency disorders (PIDDs) such as common variable immunodeficiency (CVID) have gained improved understanding of molecular pathogenesis and disease phenotype with the identification of a genetic etiology. We report a patient with early-onset CVID due to an autosomal dominant loss-of-function mutation in NFKB2 who developed a severe herpes vegetans cutaneous infection as well as concurrent herpes simplex virus viremia. The case highlights features of CVID, unique aspects of NF-κB2 deficiency including susceptibility to herpesvirus infections, the detection of neutralizing anticytokine antibodies, and the complexity of medical management of patients with a PIDD that can be aided by a known genetic diagnosis

Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th July 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onward transmission, earlier identification of nosocomial cases will be required to break hospital transmission chains

periscope: sub-genomic RNA identification in SARS-CoV-2 genomic sequencing data

We have developed periscope, a tool for the detection and quantification of sub-genomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed “sub-genomic RNAs”. sgRNAs are produced through discontinuous transcription which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L which is located in the 5’ UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5’ end of all sgRNA. We applied periscope to 1,155 SARS-CoV-2 genomes from Sheffield, UK and validated our findings using orthogonal datasets and in vitro cell systems. Using a simple local alignment to detect reads which contain the leader sequence we were able to identify and quantify reads arising from canonical and non-canonical sgRNA. We were able to detect all canonical sgRNAs at expected abundances, with the exception of ORF10. A number of recurrent non-canonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6 ACE2+/− cell lines, periscope can detect the changes in the kinetics of sgRNA in orthogonal sequencing datasets. Finally, variants found in genomic RNA are transmitted to sgRNAs with high fidelity in most cases. This tool can be applied to all sequenced COVID-19 samples worldwide to provide comprehensive analysis of SARS-CoV-2 sgRNA

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research