Communication, trust and dental anxiety:a person-centred approach for dental attendance behaviours

Effective communication forges the dentist-patient treatment alliance and is thus essential for providing person-centred care. Social rank theory suggests that shame, trust, communication and anxiety are linked together, they are moderated by socio-economic position. The study is aimed to propose and test an explanatory model to predict dental attendance behaviours using person-centred and socio-economic position factors. A secondary data analysis was conducted on a cross-sectional representative survey of a two-stage cluster sample of adults including England, Wales and Northern Ireland. Data were drawn from structured interview. Path analysis of proposed model was calculated following measurement development and confirmation of reliable constructs. The findings show model fit was good. Dental anxiety was predicted negatively by patient’s trust and positively by reported dentist communication. Patient’s shame was positively associated with dental anxiety, whereas self-reported dental attendance was negatively associated with dental anxiety. Both patient’s trust and dentist’s communication effects were moderated by social class. Manual classes were most sensitive to the reported dentist’s communications. Some evidence for the proposed model was found. The relationships reflected in the model were illuminated further when social class was introduced as moderator and indicated dentists should attend to communication processes carefully across different categories of patients.Publisher PDFPeer reviewe

Mandrake : visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation

In less than a decade, population genomics of microbes has progressed from the effort of sequencing dozens of strains to thousands, or even tens of thousands of strains in a single study. There are now hundreds of thousands of genomes available even for a single bacterial species, and the number of genomes is expected to continue to increase at an accelerated pace given the advances in sequencing technology and widespread genomic surveillance initiatives. This explosion of data calls for innovative methods to enable rapid exploration of the structure of a population based on different data modalities, such as multiple sequence alignments, assemblies and estimates of gene content across different genomes. Here, we present Mandrake, an efficient implementation of a dimensional reduction method tailored for the needs of large-scale population genomics. Mandrake is capable of visualizing population structure from millions of whole genomes, and we illustrate its usefulness with several datasets representing major pathogens. Our method is freely available both as an analysis pipeline (https://github.com/johnlees/mandrake) and as a browser-based interactive application (https://gtonkinhill.github.io/mandrake-web/).This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.Peer reviewe

Putting uncertainty under the cultural lens of Traditional Owners from the Great Barrier Reef Catchments

Indigenous peoples in Australia, and globally, are situated in an unusual context of both significant vulnerability and unique resilience to climate change which influence their perceptions of climate risk and uncertainty. Their vulnerability to climate change arises in part from their contexts of living in many of the harshest and isolated environments. Their resilience originates from their accumulated knowledge of specific environments over millennia, mediated through sui generis cultural institutions. Our results illustrate that indigenous groups primarily perceive uncertainties related to volition of actors and institutions. When they are involved in climate adaptation planning in ways that mobilise their cultural institutions and knowledge, they can safely manage these uncertainties through their agency to determine and control key risks. We demonstrate that climate justice approaches can be strengthened for indigenous peoples by applying a linked vulnerability-resilience analytical framework. This enables stronger consideration of how unique cultural institutions and knowledge, which are not available to all vulnerable groups, affect indigenous perceptions of uncertainty in climate adaptation planning. We use this analytical approach in a case study with Yuibera and Koinmerburra Traditional Owner groups within the Great Barrier Reef Catchment. We conclude that a specific focus on sui generis indigenous knowledge and cultural institutions as a source of resilience can strengthen climate justice approaches and work more effectively with indigenous peoples in climate change contexts

Using NMR Techniques to Find Partition Coefficients Across Biphasic Systems

A model biphasic system was studied using acetone on 1-octanol and water. The partition coefficient was found using z-axis single pulse slice-selective spatially resolved excitation (SPS3RE) nuclear magnetic resonance (NMR) spectroscopy. This SPS3RE NMR experiment allows for the collection of a one-dimensional look at 1H spectra at defined spatial intervals along the z-axis, providing analyte quantitation through the entire sample. With this in mind, the concentration of acetone was characterized as a function of spatial location from the two-phase interface leading to the determination of partition coefficients by signal integration. This system was then expanded to analyze the hydrolysis of parathion in a biphasic system of parathion and deuterated sodium hydroxide with varying amounts of tert-butylammonium chloride. From this, the utility of a simplified, slice-selective pulse for analyzing heterogeneous samples is observed

A comprehensive and high-quality collection of Escherichia coli genomes and their genes

Escherichia coli is a highly diverse organism that includes a range of commensal and pathogenic variants found across a range of niches and worldwide. In addition to causing severe intestinal and extraintestinal disease, E. coli is considered a priority pathogen due to high levels of observed drug resistance. The diversity in the E. coli population is driven by high genome plasticity and a very large gene pool. All these have made E. coli one of the most well- studied organisms, as well as a commonly used laboratory strain. Today, there are thousands of sequenced E. coli genomes stored in public databases. While data is widely available, accessing the information in order to perform analyses can still be a challenge. Collecting relevant available data requires accessing different sources, where data may be stored in a range of formats, and often requires further manipulation and processing to apply various analyses and extract useful information. In this study, we collated and intensely curated a collection of over 10 000 E. coli and Shigella genomes to provide a single, uniform, high- quality dataset. Shigella were included as they are considered specialized pathovars of E. coli. We provide these data in a number of easily accessible formats that can be used as the foundation for future studies addressing the biological differences between E. coli lineages and the distribution and flow of genes in the E. coli population at a high resolution. The analysis we present emphasizes our lack of understanding of the true diversity of the E. coli species, and the biased nature of our current understanding of the genetic diversity of such a key pathogen.Peer reviewe

Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae

Whole-genome sequencing has facilitated genome-wide analyses of association, prediction and heritability in many organisms. However, such analyses in bacteria are still in their infancy, being limited by difficulties including genome plasticity and strong population structure. Here we propose a suite of methods including linear mixed models, elastic net and LD-score regression, adapted to bacterial traits using innovations such as frequency-based allele coding, both insertion/deletion and nucleotide testing and heritability partitioning. We compare and validate our methods against the current state-of-art using simulations, and analyse three phenotypes of the major human pathogen Streptococcus pneumoniae, including the first analyses of minimum inhibitory concentrations (MIC) for penicillin and ceftriaxone. We show that the MIC traits are highly heritable with high prediction accuracy, explained by many genetic associations under good population structure control. In ceftriaxone MIC, this is surprising because none of the isolates are resistant as per the inhibition zone criteria. We estimate that half of the heritability of penicillin MIC is explained by a known drug-resistance region, which also contributes a quarter of the ceftriaxone MIC heritability. For the within-host carriage duration phenotype, no associations were observed, but the moderate heritability and prediction accuracy indicate a moderately polygenic trait.Peer reviewe

Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe

Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.Peer reviewe

rPinecone : Define sub-lineages of a clonal expansion via a phylogenetic tree

The ability to distinguish different circulating pathogen clones from each other is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low-variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this software was demonstrated using both simulated outbreaks and real genomic data of two LV populations: a hospital outbreak of methicillin-resistant Staphylococcus aureus and endemic Salmonella Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.Peer reviewe

RCandy: an R package for visualizing homologous recombinations in bacterial genomes

SUMMARY: Homologous recombination is an important evolutionary process in bacteria and other prokaryotes, which increases genomic sequence diversity and can facilitate adaptation. Several methods and tools have been developed to detect genomic regions recently affected by recombination. Exploration and visualization of such recombination events can reveal valuable biological insights, but it remains challenging. Here, we present RCandy, a platform-independent R package for rapid, simple and flexible visualization of recombination events in bacterial genomes. AVAILABILITY AND IMPLEMENTATION: RCandy is an R package freely available for use under the MIT license. It is platform-independent and has been tested on Windows, Linux and MacOSX. The source code comes together with a detailed vignette available on GitHub at https://github.com/ChrispinChaguza/RCandy. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Primordial germ cell DNA demethylation and development require DNA translesion synthesis

Mutations in DNA damage response (DDR) factors are associated with human infertility, which affects up to 15% of the population. The DDR is required during germ cell development and meiosis. One pathway implicated in human fertility is DNA translesion synthesis (TLS), which allows replication impediments to be bypassed. We find that TLS is essential for premeiotic germ cell development in the embryo. Loss of the central TLS component, REV1,significantly inhibits the induction of human PGC-like cells (hPGCLCs). This is recapitulated in mice, where deficiencies in TLS initiation (Rev1-/- or PcnaK164R/K164R) or extension (Rev7-/-) result in a &gt;150-fold reduction in the number of primordial germ cells (PGCs) and complete sterility. In contrast, the absence of TLS does not impact the growth, function, or homeostasis of somatic tissues. Surprisingly, we find a complete failure in both activation of the germ cell transcriptional program and in DNA demethylation, a critical step in germline epigenetic reprogramming. Our findings show that for normal fertility, DNA repair is required not only for meiotic recombination but for progression through the earliest stages of germ cell development in mammals.<br/