Spatial and temporal variability of disease refuges in an estuary: Implications for the development of resistance

Although the concept of genetic refuge has long been employed in ecological and paleoecological context, it has only rarely been used to identify regions where organisms are protected from diseases that affect the rest of a population. The refuges harbor individuals that have not been exposed to selective mortality and remain susceptible to the disease. They represent a reservoir of susceptibility alleles that can mix with those from resistant survivors of disease and can retard the development of resistance in the population as a whole. Two water-borne protistan parasites affect oysters along the east coast of the United States: Haplosporidium nelsoni (MSX disease) and Perkinsus marinus (dermo disease). Both are sensitive to low salinity and their prevalence is reduced in the upper reaches of estuaries. We investigated the temporal and spatial structure and extent of putative refuges from these diseases in the upper Delaware Bay, USA and their potential to affect the development of resistance in the oyster population. Our results showed that refuges occurred as a continuum of zones, regions where a pathogen (1) was not present; (2) was present, but did not cause observable infections; and (3) caused infection, but neither disease nor mortality. The zones were transient, driven only partly by short-term climatic conditions, and differed according to parasite: H. nelsoni was often not present in the refuges, as inferred by the absence of polymerase chain reaction (PCR) – positive signals on the gills, and when it was present, it did not always cause lethal, or even histologically detectable, infections. In contrast, P. marinus was present in all upper estuary areas sampled, where it caused detectable, although not necessarily lethal-level, infections. Thus, a significant fraction of the oyster population is protected from selective mortality in these refuges even when the parasites are present. An incursion of H. nelsoni into the upper Bay in the 1980s left most of the surviving population highly resistant to MSX disease, although populations in the upper-most reaches are still susceptible. The lack of selection pressure in the refuges likely helps to retard the development of resistance to dermo disease, and theoretically could cause resistance to MSX disease to regress although there is no evidence to date that this has occurred

Guidelines on the diagnosis, clinical assessments, treatment and management for CLN2 disease patients

Background: CLN2 disease (Neuronal Ceroid Lipofuscinosis Type 2) is an ultra-rare, neurodegenerative lysosomal storage disease, caused by an enzyme deficiency of tripeptidyl peptidase 1 (TPP1). Lack of disease awareness and the non-specificity of presenting symptoms often leads to delayed diagnosis. These guidelines provide robust evidence-based, expert-agreed recommendations on the risks/benefits of disease-modifying treatments and the medical interventions used to manage this condition. Methods: An expert mapping tool process was developed ranking multidisciplinary professionals, with knowledge of CLN2 disease, diagnostic or management experience of CLN2 disease, or family support professionals. Individuals were sequentially approached to identify two chairs, ensuring that the process was transparent and unbiased. A systematic literature review of published evidence using Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidance was independently and simultaneously conducted to develop key statements based upon the strength of the publications. Clinical care statements formed the basis of an international modified Delphi consensus determination process using the virtual meeting (Within3) online platform which requested experts to agree or disagree with any changes. Statements reaching the consensus mark became the guiding statements within this manuscript, which were subsequently assessed against the Appraisal of Guidelines for Research and Evaluation (AGREEII) criteria. Results: Twenty-one international experts from 7 different specialities, including a patient advocate, were identified. Fifty-three guideline statements were developed covering 13 domains: General Description and Statements, Diagnostics, Clinical Recommendations and Management, Assessments, Interventions and Treatment, Additional Care Considerations, Social Care Considerations, Pain Management, Epilepsy / Seizures, Nutritional Care Interventions, Respiratory Health, Sleep and Rest, and End of Life Care. Consensus was reached after a single round of voting, with one exception which was revised, and agreed by 100% of the SC and achieved 80% consensus in the second voting round. The overall AGREE II assessment score obtained for the development of the guidelines was 5.7 (where 1 represents the lowest quality, and 7 represents the highest quality). Conclusion: This program provides robust evidence- and consensus-driven guidelines that can be used by all healthcare professionals involved in the management of patients with CLN2 disease and other neurodegenerative disorders. This addresses the clinical need to complement other information available

Three new pancreatic cancer susceptibility signals identified on chromosomes 1q32.1, 5p15.33 and 8q24.21.

Genome-wide association studies (GWAS) have identified common pancreatic cancer susceptibility variants at 13 chromosomal loci in individuals of European descent. To identify new susceptibility variants, we performed imputation based on 1000 Genomes (1000G) Project data and association analysis using 5,107 case and 8,845 control subjects from 27 cohort and case-control studies that participated in the PanScan I-III GWAS. This analysis, in combination with a two-staged replication in an additional 6,076 case and 7,555 control subjects from the PANcreatic Disease ReseArch (PANDoRA) and Pancreatic Cancer Case-Control (PanC4) Consortia uncovered 3 new pancreatic cancer risk signals marked by single nucleotide polymorphisms (SNPs) rs2816938 at chromosome 1q32.1 (per allele odds ratio (OR) = 1.20, P = 4.88x10 -15), rs10094872 at 8q24.21 (OR = 1.15, P = 3.22x10 -9) and rs35226131 at 5p15.33 (OR = 0.71, P = 1.70x10 -8). These SNPs represent independent risk variants at previously identified pancreatic cancer risk loci on chr1q32.1 ( NR5A2), chr8q24.21 ( MYC) and chr5p15.33 ( CLPTM1L- TERT) as per analyses conditioned on previously reported susceptibility variants. We assessed expression of candidate genes at the three risk loci in histologically normal ( n = 10) and tumor ( n = 8) derived pancreatic tissue samples and observed a marked reduction of NR5A2 expression (chr1q32.1) in the tumors (fold change -7.6, P = 5.7x10 -8). This finding was validated in a second set of paired ( n = 20) histologically normal and tumor derived pancreatic tissue samples (average fold change for three NR5A2 isoforms -31.3 to -95.7, P = 7.5x10 -4-2.0x10 -3). Our study has identified new susceptibility variants independently conferring pancreatic cancer risk that merit functional follow-up to identify target genes and explain the underlying biology

Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer

We performed a multistage genome-wide association study including 7,683 individuals with pancreatic cancer and 14,397 controls of European descent. Four new loci reached genome-wide significance: rs6971499 at 7q32.3 (LINC-PINT, per-allele odds ratio (OR) = 0.79, 95% confidence interval (CI) 0.74-0.84, P = 3.0 x 10(-12)), rs7190458 at 16q23.1 (BCAR1/CTRB1/CTRB2, OR = 1.46, 95% CI 1.30-1.65, P = 1.1 x 10(-10)), rs9581943 at 13q12.2 (PDX1, OR = 1.15, 95% CI 1.10-1.20, P = 2.4 x 10(-9)) and rs16986825 at 22q12.1 (ZNRF3, OR = 1.18, 95% CI 1.12-1.25, P = 1.2 x 10(-8)). We identified an independent signal in exon 2 of TERT at the established region 5p15.33 (rs2736098, OR = 0.80, 95% CI 0.76-0.85, P = 9.8 x 10(-14)). We also identified a locus at 8q24.21 (rs1561927, P = 1.3 x 10(-7)) that approached genome-wide significance located 455 kb telomeric of PVT1. Our study identified multiple new susceptibility alleles for pancreatic cancer that are worthy of follow-up studies

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes

Discrete Choice Experiments: A Guide to Model Specification, Estimation and Software

We provide a user guide on the analysis of data (including best–worst and best–best data) generated from discrete-choice experiments (DCEs), comprising a theoretical review of the main choice models followed by practical advice on estimation and post-estimation. We also provide a review of standard software. In providing this guide, we endeavour to not only provide guidance on choice modelling but to do so in a way that provides a ‘way in’ for researchers to the practicalities of data analysis. We argue that choice of modelling approach depends on the research questions, study design and constraints in terms of quality/quantity of data and that decisions made in relation to analysis of choice data are often interdependent rather than sequential. Given the core theory and estimation of choice models is common across settings, we expect the theoretical and practical content of this paper to be useful to researchers not only within but also beyond health economics

Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer

We performed a multistage genome-wide association study (GWAS) including 7,683 individuals with pancreatic cancer and 14,397 controls of European descent. Four new loci reached genome-wide significance: rs6971499 at 7q32.3 (LINC-PINT; per-allele odds ratio [OR] = 0.79; 95% confidence interval [CI] = 0.74–0.84; P = 3.0×10−12), rs7190458 at 16q23.1 (BCAR1/CTRB1/CTRB2; OR = 1.46; 95% CI = 1.30–1.65; P = 1.1×10−10), rs9581943 at 13q12.2 (PDX1; OR = 1.15; 95% CI = 1.10–1.20; P = 2.4×10−9), and rs16986825 at 22q12.1 (ZNRF3; OR = 1.18; 95% CI = 1.12–1.25; P = 1.2×10−8). An independent signal was identified in exon 2 of TERT at the established region 5p15.33 (rs2736098; OR = 0.80; 95% CI = 0.76–0.85; P = 9.8×10−14). We also identified a locus at 8q24.21 (rs1561927; P = 1.3×10−7) that approached genome-wide significance located 455 kb telomeric of PVT1. Our study has identified multiple new susceptibility alleles for pancreatic cancer worthy of follow-up studies

Ciliate xenomas in Crassostrea virginica from Great Bay, New Hampshire

During routine histological examination of oysters (Crassostrea virginica) from Great Bay, New Hampshire, a high prevalence and intensity of ciliate xenomas has been noted since 1997. Xenomas are hypertrophic lesions on the gills of bivalve molluscs caused by ciliates. Although not known to cause mortality in oysters, xenomas have not previously been reported at this high level of abundance. The objectives of this study were to characterize the xenomas, classify the ciliates, and gather baseline epizootiological data with correlations to environmental and biological parameters. Upon gross examination, xenomas appeared as white nodules located in the gill tissue, up to 3 mm in diameter, occasionally fusing into large masses along the gill filaments. Light microscopy of histological sections revealed xenomas located in the gill water tubes that often occupied the entire cross sectional area. Higher magnification revealed dual nuclei, eight kineties, and conjugation. Transmission electron microscopy revealed dual nuclei that vary in density, a maximum of twenty cilia in each kinety radiating from the oral apparatus to the posterior, and a 9+2 axoneme structure within the cilia. Sequencing of the 18S rRNA gene produced a unique sequence not present in GenBank. These oyster gill ciliates are generally listed as Sphenophrya dosiniae (Order Rhynchodida) and although there are no representatives of Rhynchodida in GenBank’s database, all similar matches were within the class Phyllopharyngea. Since 1997, xenoma prevalence has fluctuated with peaks in 2000, 2004, and 2011. Infected oysters generally contained 100, sharply contrasting the rare prevalence and low intensity reported elsewhere. Prevalence increased with oyster size, leveling off near 50% in oysters >60mm. Infection intensity peaked in 70-90mm oysters. Individually, oyster condition was not associated with xenoma intensity, but sites with oysters in higher condition generally had a greater prevalence and intensity of xenoma infections. Seasonal data indicated an infection cycle increasing from summer to fall, peaking at 55-65% in November and dropping to <10% by spring. The oyster population at Great Bay, NH warrants further examination to understand the mechanisms and conditions controlling xenoma formation, as well as the possible effects of a changing climate.M.S.Includes bibliographical referencesby Emily Scarpa McGur

Spatial and temporal variability of disease refuges in an estuary: Implications for the development of resistance

Although the concept of genetic refuge has long been employed in ecological and paleoecological context, it has only rarely been used to identify regions where organisms are protected from diseases that affect the rest of a population. The refuges harbor individuals that have not been exposed to selective mortality and remain susceptible to the disease. They represent a reservoir of susceptibility alleles that can mix with those from resistant survivors of disease and can retard the development of resistance in the population as a whole. Two water-borne protistan parasites affect oysters along the east coast of the United States: Haplosporidium nelsoni (MSX disease) and Perkinsus marinus (dermo disease). Both are sensitive to low salinity and their prevalence is reduced in the upper reaches of estuaries. We investigated the temporal and spatial structure and extent of putative refuges from these diseases in the upper Delaware Bay, USA and their potential to affect the development of resistance in the oyster population. Our results showed that refuges occurred as a continuum of zones, regions where a pathogen (1) was not present; (2) was present, but did not cause observable infections; and (3) caused infection, but neither disease nor mortality. The zones were transient, driven only partly by short-term climatic conditions, and differed according to parasite: H. nelsoni was often not present in the refuges, as inferred by the absence of polymerase chain reaction (PCR) – positive signals on the gills, and when it was present, it did not always cause lethal, or even histologically detectable, infections. In contrast, P. marinus was present in all upper estuary areas sampled, where it caused detectable, although not necessarily lethal-level, infections. Thus, a significant fraction of the oyster population is protected from selective mortality in these refuges even when the parasites are present. An incursion of H. nelsoni into the upper Bay in the 1980s left most of the surviving population highly resistant to MSX disease, although populations in the upper-most reaches are still susceptible. The lack of selection pressure in the refuges likely helps to retard the development of resistance to dermo disease, and theoretically could cause resistance to MSX disease to regress although there is no evidence to date that this has occurred