Understanding how Characteristics of the Nest Site Affect Nest Success of Wild Turkeys

Wild turkeys (Meleagris gallapavo) are a highly-desirable game species throughout the United States, but harvest records in the northern Black Hills, South Dakota suggest that this population is declining.  We wondered whether vegetation characteristics at the nest site would affect nest fate (success/failure).  We monitored 40 nests during summer 2016 to determine nest fate and 27 were successful (?1 egg hatched).  At the actual or expected hatch date, we quantified characteristics of the understory vegetation at the nest bowl, namely total cover, shrub cover, woody debris, and the degree of visual obstruction.  We compared these characteristics between successful and unsuccessful nests. Successful nests had slightly less woody debris and total cover than unsuccessful nests.  We did not detect differences in shrub cover or the degree of visual obstruction.  Our results suggest that there may be some optimal amount of total cover and woody debris at the nest bowl that contributes to a higher chance of nest success.  We recommend additional research that focuses on how vegetation characteristics found at nest sites compares to what is available.  This information in conjunction with our findings could provide guidance for managers regarding vegetation characteristics that may be optimal for nest success.  Although these data may help manage turkey populations, nesting represents only one part of the life cycle of a wild turkey.  We recommend that managers strive for a mosaic of vegetation characteristics to accommodate the needs of turkey populations throughout their life history

Children\u27s Folklore

A collection of original essays by scholars from a variety of fields—including American studies, folklore, anthropology, psychology, sociology, and education—Children\u27s Folklore: A Source Book moves beyond traditional social-science views of child development. It reveals the complexity and artistry of interactions among children, challenging stereotypes of simple childhood innocence and conventional explanations of development that privilege sober and sensible adult outcomes. Instead, the play and lore of children is shown to be often disruptive, wayward, and irrational. The contributors variably con-sider and demonstrate contextual and textual ways of studying the folklore of children. Avoiding a narrow definition of the subject, they examine a variety of resources and approaches for studying, researching, and teaching it. These range from surveys of the history and literature of children\u27s folklore to methods of field research, studies of genres of lore, and attempts to capture children\u27s play and games.https://digitalcommons.usu.edu/usupress_pubs/1059/thumbnail.jp

Choice of assembly software has a critical impact on virome characterisation

peer-reviewedBackground The viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets. Design This study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in human virome studies. Assemblers were assessed using four independent virome datasets, namely, simulated reads, two mock communities, viromes spiked with a known phage and human gut viromes. Results Assembly performance varied significantly across all test datasets, with SPAdes (meta) performing consistently well. Performance of MIRA and VICUNA varied, highlighting the importance of using a range of datasets when comparing assembly programs. It was also found that while some assemblers addressed the challenges of virome data better than others, all assemblers had limitations. Low read coverage and genomic repeats resulted in assemblies with poor genome recovery, high degrees of fragmentation and low-accuracy contigs across all assemblers. These limitations must be considered when setting thresholds for downstream analysis and when drawing conclusions from virome data

Evaluation of a library of FDA-approved drugs for their ability to potentiate antibiotics against multidrug resistant Gram-negative pathogens

The Prestwick library was screened for antibacterial activity or 'antibiotic-resistance breaking' (ARB) potential against four species of Gram-negative pathogens. Discounting known antibacterials, the screen identified very few ARB hits, which were strain/drug specific. These ARB hits included antimetabolites (zidovudine, floxuridine, didanosine, gemcitabine), anthracyclines (daunorubicin, mitoxantrone, epirubicin) and psychoactive drugs (gabapentin, fluspirilene, oxethazaine). This suggests that there are few approved drugs which could be directly repositioned as adjunct-antibacterials and these will need robust testing to validate efficacy. [Abstract copyright: © Crown copyright 2019.

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

peer-reviewedBackground Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood. Results In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms. Conclusions Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2–165T = DSM 17677T = JCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768T = NCIMB 13872T).This research was conducted with the financial support of Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2273, a Science Foundation Ireland’s Spokes Programme which is co-funded under the European Regional Development Fund under Grant Number SFI/14/SP APC/B3032, and a research grant from Janssen Biotech, Inc

Self-help materials for the prevention of smoking relapse: study protocol for a randomized controlled trial.

BACKGROUND: Most people who stop smoking successfully for a few weeks will return to smoking again in the medium term. There are few effective interventions to prevent this relapse and none used routinely in clinical practice. A previous exploratory meta-analysis suggested that self-help booklets may be effective but requires confirmation. This trial aims to evaluate the effectiveness and cost-effectiveness of a set of self-help educational materials to prevent smoking relapse in the National Health Service (NHS) Stop Smoking Service. METHODS/DESIGN: This is an open, randomized controlled trial. The target population is carbon monoxide (CO) verified quitters at four weeks in the NHS stop smoking clinic (total sample size N = 1,400). The experimental intervention tested is a set of eight revised Forever Free booklets, including an introduction booklet and more extensive information on all important issues for relapse prevention. The control intervention is a leaflet that has no evidence to suggest it is effective but is currently given to some patients using NHS stop smoking services. Two follow-up telephone interviews will be conducted at three and 12 months after the quit date. The primary outcome will be prolonged abstinence from months four to 12 with no more than five lapses, confirmed by a CO test at the 12-month assessment. The secondary outcomes will be seven-day self-report point prevalence abstinence at three months and seven-day biochemically confirmed point prevalence abstinence at 12 months. To assess cost-effectiveness, costs will be estimated from a health service perspective and the EQ-5D will be used to estimate the QALY (Quality Adjusted Life Year) gain associated with each intervention. The comparison of smoking abstinence rates (and any other binary outcomes) between the two trial arms will be carried out using odds ratio as the outcome statistic and other related statistical tests. Exploratory subgroup analyses, including logistic regression analyses with interaction terms, will be conducted to investigate possible effect-modifying variables. DISCUSSION: The possible effect of self-help educational materials for the prevention of smoking relapse has important public health implications. TRIAL REGISTRATION: Current Controlled Trials ISRCTN36980856.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Heartland Virus in Lone Star Ticks, Alabama, USA

We detected Heartland virus (HRTV) in lone star nymphs collected in 2018 in northern Alabama, USA. Real-time reverse transcription PCR selective for the small segment of the HRTV genome and confirmatory sequencing of positive samples showed high identity with HRTV strains sequenced from Tennessee and Missouri

Dynamics of Light Antiquarks in the Proton

We present a comprehensive analysis of the recent data from the E866 experiment at Fermilab on Drell-Yan production in pD and pp collisions, which indicates a non-trivial x-dependence for the asymmetry between u-bar and d-bar quark distributions in the proton. The relatively fast decrease of the asymmetry at large x suggests the important role played by the chiral structure of the nucleon, in particular the pi-N and pi-Delta components of the nucleon wave function. At small x the data require an additional non-chiral component, which may be attributed to the Pauli exclusion principle as first suggested by Field and Feynman.Comment: version to appear in Phys. Rev.

Self-help educational booklets for the prevention of smoking relapse following smoking cessation treatment: a randomized controlled trial.

AIMS: Most people who quit smoking for a short term will return to smoking again in 12 months. We tested whether self-help booklets can reduce relapse in short-term quitters after receiving behavioural and pharmacological cessation treatment. DESIGN: A parallel-arm, pragmatic individually randomized controlled trial. SETTING: Smoking cessation clinics in England. Participants People who stopped smoking for 4 weeks after receiving cessation treatment in stop smoking clinics. INTERVENTION: Participants in the experimental group (n=703) were mailed eight booklets, each of which taught readers how to resist urges to smoke. Participants in the control group (n=704) received a leaflet currently used in practice. MEASUREMENTS: The primary outcome was prolonged, carbon monoxide-verified abstinence from months 4 to 12. The secondary outcomes included 7-day self-reported abstinence at 3 and 12 months. Mixed-effects logistic regression was used to estimate treatment effects and to investigate possible effect modifying variables. FINDINGS: There were no statistically significant differences between the groups in prolonged abstinence from months 4 to 12 (36.9% versus 38.6%; odds ratio 0.93, 95% confidence interval 0.75-1.16; P=0.524). In addition, there were no significant differences between the groups in any secondary outcomes. However, people who reported knowing risky situations for relapse and using strategies to handle urges to smoke were less likely to relapse. CONCLUSIONS: In people who stop smoking successfully with behavioural support, a comprehensive self-help educational programme to teach people skills to identify and respond to high-risk situations for return to smoking did not reduce relapse

Reproducible protocols for metagenomic analysis of human faecal phageomes

peer-reviewedAll sequence data used in the analyses were deposited in the Sequence read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under BioProject PRJNA407341. Sample IDs, meta data and corresponding accession numbers are summarised in Additional file 2: Table S2. All raw count tables, 16S taxonomic assignments, BLAST top hits for viral contigs and R code used for the analysis are available at (https://figshare.com/s/71163558b4f78e3e7ed6).Background Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing. The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing. Results Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at + 4 °C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples. Conclusions The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results