CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU

Bacteria protect themselves from infection by bacteriophages (phages) using different defence systems, such as CRISPR-Cas. Although CRISPR-Cas provides phage resistance, fitness costs are incurred, such as through autoimmunity. CRISPR-Cas regulation can optimise defence and minimise these costs. We recently developed a genome-wide functional genomics approach (SorTn-seq) for high-throughput discovery of regulators of bacterial gene expression. Here, we applied SorTn-seq to identify loci influencing expression of the two type III-A Serratia CRISPR arrays. Multiple genes affected CRISPR expression, including those involved in outer membrane and lipopolysaccharide synthesis. By comparing loci affecting type III CRISPR arrays and cas operon expression, we identified PigU (LrhA) as a repressor that co-ordinately controls both arrays and cas genes. By repressing type III-A CRISPR-Cas expression, PigU shuts off CRISPR-Cas interference against plasmids and phages. PigU also represses interference and CRISPR adaptation by the type I-F system, which is also present in Serratia. RNA sequencing demonstrated that PigU is a global regulator that controls secondary metabolite production and motility, in addition to CRISPR-Cas immunity. Increased PigU also resulted in elevated expression of three Serratia prophages, indicating their likely induction upon sensing PigU-induced cellular changes. In summary, PigU is a major regulator of CRISPR-Cas immunity in Serratia.

Identification of Streptococcus pneumoniae genes associated with hypothiocyanous acid tolerance through genome-wide screening

Streptococcus pneumoniae is a commensal bacterium and invasive pathogen that causes millions of deaths worldwide. The pneumococcal vaccine offers limited protection, and the rise of antimicrobial resistance will make treatment increasingly challenging, emphasizing the need for new antipneumococcal strategies. One possibility is to target antioxidant defenses to render S. pneumoniae more susceptible to oxidants produced by the immune system. Human peroxidase enzymes will convert bacterial-derived hydrogen peroxide to hypothiocyanous acid (HOSCN) at sites of colonization and infection. Here, we used saturation transposon mutagenesis and deep sequencing to identify genes that enable S. pneumoniae to tolerate HOSCN. We identified 37 genes associated with S. pneumoniae HOSCN tolerance, including genes involved in metabolism, membrane transport, DNA repair, and oxidant detoxification. Single-gene deletion mutants of the identified antioxidant defense genes sodA, spxB, trxA, and ahpD were generated and their ability to survive HOSCN was assessed. With the exception of ΔahpD, all deletion mutants showed significantly greater sensitivity to HOSCN, validating the result of the genome-wide screen. The activity of hypothiocyanous acid reductase or glutathione reductase, known to be important for S. pneumoniae tolerance of HOSCN, was increased in three of the mutants, highlighting the compensatory potential of antioxidant systems. Double deletion of the gene encoding glutathione reductase and sodA sensitized the bacteria significantly more than single deletion. The HOSCN defense systems identified in this study may be viable targets for novel therapeutics against this deadly pathogen. IMPORTANCE Streptococcus pneumoniae is a human pathogen that causes pneumonia, bacteremia, and meningitis. Vaccination provides protection only against a quarter of the known S. pneumoniae serotypes, and the bacterium is rapidly becoming resistant to antibiotics. As such, new treatments are required. One strategy is to sensitize the bacteria to killing by the immune system. In this study, we performed a genome-wide screen to identify genes that help this bacterium resist oxidative stress exerted by the host at sites of colonization and infection. By identifying a number of critical pneumococcal defense mechanisms, our work provides novel targets for antimicrobial therapy.

Dosimetric Implications of Prostate Bed Deformability: An Analysis of the SCIMITAR Clinical Trial

PURPOSE/OBJECTIVE(S)

The post-operative prostate bed is a dynamic target volume due to the deformable nature of the bladder and rectum. These changes can lead to incorrect dosing of the prostate bed and organs at risk (OARs). Our objective was to quantify the dosimetric impact of prostate bed and OAR deformation.

MATERIALS/METHODS

SCIMITAR (NCT03541850) is a prospective phase II clinical trial evaluating stereotactic body radiotherapy (SBRT) in the post-prostatectomy setting. This analysis included a subset of patients who received 5 fractions of 6-6.8 Gy to the prostate bed under CT-based image guidance. The clinical target volume (CTV) and OARs were contoured on fractional CBCT images. Changes in volume, shape (via the dice similarity coefficient [DSC]), and dosimetry were quantified. Student's t-test was used to analyze the differences between planning and daily treatment outcomes.

RESULTS

A total of 29 patients (145 fractional images) were analyzed. We found the CTV volume remained stable (median change 1.1%; IQR: -15.1% - 16.1%), whereas the CTV shape was deformable (DSC of 0.76 [IQR: 0.71 - 0.79]). The bladder and rectum exhibited changes with median volume change of 5.7% (IQR: -24.3% - 51.0%) and 5.5% (IQR: -8.7% - 21.9%), respectively and median DSC of 0.77 (IQR: 0.68 - 0.84) and 0.74 (IQR: 0.69 - 0.80) respectively. The CTV received less radiation dose than planned (volume receiving 95%: 93.2% actual vs 99.6% planned, p < 0.01). 39% (56/145) of total fractions and 52% (15/29) of patients met criteria for CTV under-coverage (volume receiving 95% of the prescription dose < 93%). The rectum received higher dose than planned on several parameters (e.g., V27.5 Gy increased from 15.4% to 21.0% [p = 0.009] and V32.5 Gy increased from 6.0% to 10.9% [p = 0.006]) (Table 1).

CONCLUSION

We found underdosing of the prostate CTV and overdosing of the rectum in patients receiving CT-guided postoperative SBRT. While future work will correlate these dosimetric consequences with toxicity, these data suggest that approaches such as adaptive radiotherapy may be beneficial.

Fixed-Field IMRT for Cervix Carcinoma Patients on an MR-LINAC Platform: Dosimetric Feasibility and Challenges

PURPOSE/OBJECTIVE(S)

To investigate the impact of MR-LINAC performance characteristics and inverse planning implementation on the feasibility of fixed-field IMRT for cervix carcinoma patients by benchmarking MR-LINAC plans against clinically used VMAT plans in a single institution study and multi-institutional treatment planning challenge.

MATERIALS/METHODS

For 10 cervix cancer patients who had previously received Linac-based VMAT, new treatment plans were optimized for MR-LINAC IMRT using 6X FFF fixed fields with maximum available field size of 27.4 x 24.1 cm2. Dose optimization was performed on the clinically used planning CT and structure set. Prescribed dose was 48.6 Gy in 27 fractions for all patients with 6 patients receiving an additional integrated boost for a total of 58.05 Gy to involved nodes. Constraints were based on our institutional protocol as per Table 1. IMRT delivery time was limited to 20 min. Original clinically used VMAT plans were generated on Eclipse (Varian Medical System) using 3 to 4 arcs. For the multi-institutional planning challenge, the data set from a single patient was anonymized and shared to participants. Participants used a single MR-based Linac planning platform to generate a plan based on our institutional constraints, with maximum treatment time limited to 20 min. For all analyses, a paired samples t-test was used to compare the significance defined at p < 0.05.

RESULTS

For MR-LINAC plans, the mean number of fields used was 23, mean number of segments 229, and the average estimated treatment delivery time was 17.3 minutes. MR-LINAC plans showed a significantly higher heterogeneity and dose to organs at risk compared to VMAT plans (Table 1). For the planning challenge, a total of 30 participants registered interest. Of this, seven plans were submitted to the challenge. On average, participants generated a plan that would be acceptable based on our institutional constraints (Table 1). However, the volumetric dose to bowel and pelvic bones were higher on MR-LINAC plans compared to the reference VMAT plan.

CONCLUSION

MR-LINAC fixed-field IMRT for cervix cancer patients is feasible but system constraints and optimization implementation result in greater dose heterogeneity and worse organ-at-risk sparing compared to Linac based VMAT. Further research is needed to determine if potential reduction of treatment margins, allowed by better MRI soft-tissue visualization, will result in MR-LINAC IMRT superior to Linac VMAT.

An evolutionary epigenetic clock in plants

Molecular clocks are the basis for dating the divergence between lineages over macroevolutionary timescales (~105 to 108 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes display a clocklike behavior. This "epimutation clock" is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation clocks recapitulate known topologies and branching times of intraspecies phylogenetic trees in the self-fertilizing plant Arabidopsis thaliana and the clonal seagrass Zostera marina, which represent two major modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.

An evolutionary epigenetic clock in plants

Molecular clocks are the basis for dating the divergence between lineages over macro-evolutionary timescales (~10 5 -10 8 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes possess a clock-like behavior. This 'epimutation-clock' is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation-clocks recapitulate known topologies and branching times of intra-species phylogenetic trees in the selfing plant A. thaliana and the clonal seagrass Z. marina , which represent two major modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.

An OmpW-dependent T4-like phage infects Serratia sp. ATCC 39006

Serratia sp. ATCC 39006 is a Gram-negative bacterium that has been used to study the function of phage defences, such as CRISPR-Cas, and phage counter-defence mechanisms. To expand our phage collection to study the phage-host interaction with Serratia sp. ATCC 39006, we isolated the T4-like myovirus LC53 in Ōtepoti Dunedin, Aotearoa New Zealand. Morphological, phenotypic and genomic characterization revealed that LC53 is virulent and similar to other Serratia, Erwinia and Kosakonia phages belonging to the genus Winklervirus. Using a transposon mutant library, we identified the host ompW gene as essential for phage infection, suggesting that it encodes the phage receptor. The genome of LC53 encodes all the characteristic T4-like core proteins involved in phage DNA replication and generation of viral particles. Furthermore, our bioinformatic analysis suggests that the transcriptional organization of LC53 is similar to that of Escherichia coli phage T4. Importantly, LC53 encodes 18 tRNAs, which likely compensate for differences in GC content between phage and host genomes. Overall, this study describes a newly isolated phage infecting Serratia sp. ATCC 39006 that expands the diversity of phages available to study phage-host interactions.

Review: Smart agri-systems for the pig industry

The projected rise in the global human population and the anticipated increase in demand for meat and animal products, albeit with a greatly reduced environmental footprint, offers a difficult set of challenges to the livestock sector. Primarily, how do we produce more, but in a way that is healthier for the animals, public, and the environment? Implementing a smart agri-systems approach, utilising multiplatform precision technologies, internet of things, data analytics, machine learning, digital twinning and other emerging technologies can support a more informed decision-making and forecasting position that will allow us to move towards greater sustainability in future. If we look to precision agronomy, there are a wide range of technologies available and examples of how digitalisation and integration of platform outputs can lead to advances in understanding the agricultural system and forecasting upcoming events and performance that have hitherto been impossible to achieve. There is much for the livestock sector and animal scientists to learn from the developments of precision technologies and smart agri-system approaches in the arable and horticultural contexts. However, there are several barriers the livestock sector must overcome: (i) the development and implementation of precision livestock farming technologies that can be easily integrated and analysed without the support of a dedicated data analyst in house; (ii) the lack of extensive validation of many developed and available precision livestock farming technologies means that reliability and accuracy are likely to be compromised when applied in commercial practice; (iii) the best smart agri-systems approaches are reliant on large quantities of data from across a wide variety of conditions, but at present the complications of data sharing, commercial sensitivities, data ownership, and permissions make it challenging to obtain or knit together data from different parts of the system into a comprehensive picture; and (iv) the high level of investment needed to develop and scale these technologies is substantial and represents significant risk for companies when a technology is emerging. Using a case study of the National Pig Centre (a flagship pig research facility in the UK) we discuss how a smart agri-systems approach can be applied in practice to investigate alternative future systems for production, and enable monitoring of these systems as a commercial demonstrator site for future pork production.

The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems

CRISPR-Cas systems provide bacteria with adaptive immunity against phages and plasmids; however, pathways regulating their activity are not well defined. We recently developed a high-throughput genome-wide method (SorTn-seq) and used this to uncover CRISPR-Cas regulators. Here, we demonstrate that the widespread Rsm/Csr pathway regulates the expression of multiple CRISPR-Cas systems in Serratia (type I-E, I-F and III-A). The main pathway component, RsmA (CsrA), is an RNA-binding post-transcriptional regulator of carbon utilisation, virulence and motility. RsmA binds cas mRNAs and suppresses type I and III CRISPR-Cas interference in addition to adaptation by type I systems. Coregulation of CRISPR-Cas and flagella by the Rsm pathway allows modulation of adaptive immunity when changes in receptor availability would alter susceptibility to flagella-tropic phages. Furthermore, we show that Rsm controls CRISPR-Cas in other genera, suggesting conservation of this regulatory strategy. Finally, we identify genes encoding RsmA homologues in phages, which have the potential to manipulate the physiology of host bacteria and might provide an anti-CRISPR activity.

Reference range for 24-h urine calcium, calcium/creatinine ratio, and correlations with calcium absorption and serum vitamin D metabolites in normal women

A study of 959 black and white women shows that the normal range for 24-h urine calcium excretion in white women is 30-300 mg and 10-285 mg in black women. Clinical laboratories use a normal range for 24-h urine calcium excretion of 100-300 mg; there is a need for them to update their age- and race-specific ranges.

INTRODUCTION

Recommendations for a normal range for 24-h urine calcium vary from a low of 50 mg to a high of 400 mg; most "laboratory normal ranges" based on older literature are incorrect. The objective of this analysis is to define a normal range for young women age 25-45 years and older women age 55-90 years, white and black, for 24-h urine calcium and calcium/creatinine ratio, and to examine the relationship between 24-h urine calcium, calcium absorption, and vitamin D metabolites.

METHODS

Data from 3 studies was collected on 959 normal black and white women, ages 25-87 years, for 24-h urine calcium, creatinine, calcium intake, serum 25-hydroxyvitamin D (25OHD),1,25 dihydroxyvitamin D (1,25(OH)₂D), and calcium absorption. Urine calcium and creatinine were measured on an auto-analyzer. Calcium absorption was measured by a single isotope method. Serum 25OHD and 1,25(OH)₂D were measured by competitive protein binding assay or radioimmunoassay. Because 24-h urine calcium did not fit a normal distribution, non-parametric methods were used to determine the 95% reference interval (RI) and 90% non-parametric confidence intervals (CI) calculated for groups.

RESULTS

The 95% reference intervals for 24-h urine calcium for women were as follows: black older 7-225 mg, black younger 8-285 mg; white older 37-275 mg, and white younger 23-287 mg. In older white women, 24-h urine calcium was significantly correlated with serum 1,25(OH)₂ D, r = 0.23, p < 0.001, calcium intake r = 0.12, p = 0.001, and calcium absorption r = 0.18, p = 0.003, but not serum 25OHD r = 0.07, p = 0.06.

CONCLUSIONS

The normal reference interval for 24-h urine calcium for black women is lower than white women. Twenty-four-hour urine calcium was correlated with serum 1,25(OH)₂ D calcium intake and calcium absorption, but not serum 25OHD. This range will be useful clinically for defining hypercalciuria and for following patients on vitamin D and calcium treatment.

The Rcs stress response inversely controls surface and CRISPR-Cas adaptive immunity to discriminate plasmids and phages

Bacteria harbour multiple innate defences and adaptive CRISPR-Cas systems that provide immunity against bacteriophages and mobile genetic elements. Although some bacteria modulate defences in response to population density, stress and metabolic state, a lack of high-throughput methods to systematically reveal regulators has hampered efforts to understand when and how immune strategies are deployed. We developed a robust approach called SorTn-seq, which combines saturation transposon mutagenesis, fluorescence-activated cell sorting and deep sequencing to characterize regulatory networks controlling CRISPR-Cas immunity in Serratia sp. ATCC 39006. We applied our technology to assess csm gene expression for ~300,000 mutants and uncovered multiple pathways regulating type III-A CRISPR-Cas expression. Mutation of igaA or mdoG activated the Rcs outer-membrane stress response, eliciting cell-surface-based innate immunity against diverse phages via the transcriptional regulators RcsB and RcsA. Activation of this Rcs phosphorelay concomitantly attenuated adaptive immunity by three distinct type I and III CRISPR-Cas systems. Rcs-mediated repression of CRISPR-Cas defence enabled increased acquisition and retention of plasmids. Dual downregulation of cell-surface receptors and adaptive immunity in response to stress by the Rcs pathway enables protection from phage infection without preventing the uptake of plasmids that may harbour beneficial traits.

Projecting effects of land use change on human well-being through changes in ecosystem services

Changing patterns of land use, temperature, and precipitation are expected to impact ecosystem services, including water quality and quantity, buffering of extreme events, soil quality, and biodiversity. Scenario analyses that link such impacts on ecosystem services to human well-being may be valuable in anticipating potential consequences of change that are meaningful to people living in a community. Ecosystem services provide numerous benefits to community well-being, including living standards, health, cultural fulfillment, education, and connection to nature. Yet assessments of impacts of ecosystem services on human well-being have largely focused on human health or monetary benefits (e.g. market values). This study applies a human well-being modelling framework to demonstrate the potential impacts of alternative land use scenarios on multi-faceted components of human well-being through changes in ecosystem services (i.e., ecological benefits functions). The modelling framework quantitatively defines these relationships in a way that can be used to project the influence of ecosystem service flows on indicators of human well-being, alongside social service flows and economic service flows. Land use changes are linked to changing indicators of ecosystem services through the application of ecological production functions. The approach is demonstrated for two future land use scenarios in a Florida watershed, representing different degrees of population growth and environmental resource protection. Increasing rates of land development were almost universally associated with declines in ecosystem services indicators and associated indicators of well-being, as natural ecosystems were replaced by impervious surfaces that depleted the ability of ecosystems to buffer air pollutants, provide habitat for biodiversity, and retain rainwater. Scenarios with increases in indicators of ecosystem services, however, did not necessarily translate into increases in indicators of well-being, due to covarying changes in social and economic services indicators. The approach is broadly transferable to other communities or decision scenarios and serves to illustrate the potential impacts of changing land use on ecosystem services and human well-being.

Functional genomics reveals the toxin-antitoxin repertoire and AbiE activity in Serratia

Bacteriophage defences are divided into innate and adaptive systems. Serratia sp. ATCC 39006 has three CRISPR-Cas adaptive immune systems, but its innate immune repertoire is unknown. Here, we re-sequenced and annotated the Serratia genome and predicted its toxin-antitoxin (TA) systems. TA systems can provide innate phage defence through abortive infection by causing infected cells to 'shut down', limiting phage propagation. To assess TA system function on a genome-wide scale, we utilized transposon insertion and RNA sequencing. Of the 32 TA systems predicted bioinformatically, 4 resembled pseudogenes and 11 were demonstrated to be functional based on transposon mutagenesis. Three functional systems belonged to the poorly characterized but widespread, AbiE, abortive infection/TA family. AbiE is a type IV TA system with a predicted nucleotidyltransferase toxin. To investigate the mode of action of this toxin, we measured the transcriptional response to AbiEii expression. We observed dysregulated levels of tRNAs and propose that the toxin targets tRNAs resulting in bacteriostasis. A recent report on a related toxin shows this occurs through addition of nucleotides to tRNA(s). This study has demonstrated the utility of functional genomics for probing TA function in a high-throughput manner, defined the TA repertoire in Serratia and shown the consequences of AbiE induction.

Projected estimates of cancer in Canada in 2020

BACKGROUND

Cancer projections to the current year help in policy development, planning of programs and allocation of resources. We sought to provide an overview of the expected incidence and mortality of cancer in Canada in 2020 in follow-up to the Canadian Cancer Statistics 2019 report.

METHODS

We obtained incidence data from the National Cancer Incidence Reporting System (1984-1991) and Canadian Cancer Registry (1992-2015). Mortality data (1984-2015) were obtained from the Canadian Vital Statistics - Death Database. All databases are maintained by Statistics Canada. Cancer incidence and mortality counts and age-standardized rates were projected to 2020 for 23 cancer types by sex and geographic region (provinces and territories) for all ages combined.

RESULTS

An estimated 225 800 new cancer cases and 83 300 cancer deaths are expected in Canada in 2020. The most commonly diagnosed cancers are expected to be lung overall (29 800), breast in females (27 400) and prostate in males (23 300). Lung cancer is also expected to be the leading cause of cancer death, accounting for 25.5% of all cancer deaths, followed by colorectal (11.6%), pancreatic (6.4%) and breast (6.1%) cancers. Incidence and mortality rates will be generally higher in the eastern provinces than in the western provinces.

INTERPRETATION

The number of cancer cases and deaths remains high in Canada and, owing to the growing and aging population, is expected to continue to increase. Although progress has been made in reducing deaths for most major cancers (breast, prostate and lung), there has been limited progress for pancreatic cancer, which is expected to be the third leading cause of cancer death in Canada in 2020. Additional efforts to improve uptake of existing programs, as well as to advance research, prevention, screening and treatment, are needed to address the cancer burden in Canada.

The autoregulator Aca2 mediates anti-CRISPR repression

CRISPR-Cas systems are widespread bacterial adaptive defence mechanisms that provide protection against bacteriophages. In response, phages have evolved anti-CRISPR proteins that inactivate CRISPR-Cas systems of their hosts, enabling successful infection. Anti-CRISPR genes are frequently found in operons with genes encoding putative transcriptional regulators. The role, if any, of these anti-CRISPR-associated (aca) genes in anti-CRISPR regulation is unclear. Here, we show that Aca2, encoded by the Pectobacterium carotovorum temperate phage ZF40, is an autoregulator that represses the anti-CRISPR–aca2 operon. Aca2 is a helix-turn-helix domain protein that forms a homodimer and interacts with two inverted repeats in the anti-CRISPR promoter. The inverted repeats are similar in sequence but differ in their Aca2 affinity, and we propose that they have evolved to fine-tune, and downregulate, anti-CRISPR production at different stages of the phage life cycle. Specific, high-affinity binding of Aca2 to the first inverted repeat blocks the promoter and induces DNA bending. The second inverted repeat only contributes to repression at high Aca2 concentrations in vivo, and no DNA binding was detectable in vitro. Our investigation reveals the mechanism by which an Aca protein regulates expression of its associated anti-CRISPR.

Effect of vitamin D supplementation on total and free 25 hydroxyvitamin D and parathyroid hormone. An analysis of two randomized controlled trials

BACKGROUND

It is questionable as to whether total serum 25 hydroxyvitamin D (T25D) levels are lower in African Americans. We measured serum T25D, free 25hydroxyvitamin D (F25D) and serum parathyroid hormone (PTH) in African American and Caucasian women and studied the effect of vitamin D dosing to determine if differences by race or age occur.

METHODS

Healthy young and older Caucasian and African American women who were vitamin D insufficient were randomized in two clinical trials to escalating daily doses of vitamin D from 400 to 4800 IU and placebo for 12 months.

RESULTS

Baseline F25D and T25D were significantly lower in young but not older African American compared to Caucasian women. At baseline, the rate of change, or slope, in F25D with T25D was significantly greater in younger women than in older women, but difference in the rate of change in F25D with T25D is similar in African American and Caucasian women. After vitamin D supplementation, there was an increase in F25D, and the dose response was not significantly different by age or race. The ratio of F25D/T25D decreased in all groups once T25D exceeded ~60 nmol L^-1 . There was a progressive decrease in serum PTH with increasing vitamin D doses and the per cent change was similar for F25D and T25D.

CONCLUSION

Serum F25D and T25D are lower in younger African American women, and since dietary vitamin D is similar in the groups, it is likely that the cause of low serum 25OHD in African American women is due to reduced UV exposure and reduced skin production of vitamin D.

The burden of cancer attributable to modifiable risk factors in Canada: Methods overview

Up-to-date estimates of current and projected future cancer burden attributable to various exposures are essential for planning and implementing cancer prevention initiatives. The Canadian Population Attributable Risk of Cancer (ComPARe) study was conducted to: i) estimate the number and proportion of cancers diagnosed among adults in Canada in 2015 that are attributable to modifiable risk factors and ii) project the future avoidable cancers by 2042 under various intervention targets. We estimated the population attributable risk (with 95% confidence intervals) and the potential impact fraction of cancers associated with selected lifestyle, environmental, and infectious factors. Exposure-specific sensitivity analyses were also completed where appropriate. Several exposures of interest included active and passive smoking, obesity and abdominal adiposity, leisure-time physical inactivity, sedentary behaviour, alcohol consumption, insufficient fruit and vegetable intake, red and processed meat consumption, air pollution (PM2.5, NO₂), indoor radon gas, ultraviolet radiation (UVR), hepatitis B and C virus, Helicobacter pylori, Epstein-Barr virus, human papillomavirus, human herpesvirus type 8 and human T-cell lymphotropic virus type 1. We used the 2015 cancer incidence data for 35 cancer sites from the Canadian Cancer Registry and projected cancer incidence to 2042 using historical data from 1983 to 2012. Here, we provide an overview of the data sources and methods used in estimating the current and future cancer burden in Canada. Specific methodologic details for each exposure are included in the individual articles included as part of this special issue.

SHH pathway inhibition is protumourigenic in adamantinomatous craniopharyngioma

Pharmacological inhibition of the sonic hedgehog (SHH) pathway can be beneficial against certain cancers but detrimental in others. Adamantinomatous craniopharyngioma (ACP) is a relevant pituitary tumour, affecting children and adults, that is associated with high morbidity and increased mortality in long-term follow-up. We have previously demonstrated overactivation of the SHH pathway in both human and mouse ACP. Here, we show that this activation is ligand dependent and induced by the expression of SHH protein in a small proportion of tumour cells. We investigate the functional relevance of SHH signalling in ACP through MRI-guided preclinical studies using an ACP mouse model. Treatment with vismodegib, a clinically approved SHH pathway inhibitor, results in a significant reduction in median survival due to premature development of highly proliferative and vascularised undifferentiated tumours. Reinforcing the mouse data, SHH pathway inhibition in human ACP leads to a significant increase in tumour cell proliferation both ex vivo, in explant cultures, and in vivo, in a patient-derived xenograft model. Together, our results demonstrate a protumourigenic effect of vismodegib-mediated SHH pathway inhibition in ACP.

Effect of increasing doses of vitamin D on bone mineral density and serum N-terminal telopeptide in elderly women: a randomized controlled trial

BACKGROUND

There are few controlled studies of the effect of different doses of vitamin D3 on bone mineral density (BMD).

OBJECTIVES

We conducted a randomized placebo-controlled trial of increasing doses of vitamin D3 in 163 Caucasian and 31 African American women with serum 25-hydroxyvitamin D (25OHD) ≤50 nmol/L. This is an analysis of secondary outcome BMD to see if there is an association between percent change in BMD and dose of vitamin D3.

METHODS

Participants were randomly assigned to placebo, vitamin D3 400, 800, 1600, 2400, 3200, 4000, or 4800 IU/day; calcium supplements, average 600mg, were given to provide a total calcium intake of 1200 mg/d. The primary outcome was 12-month serum 25OHD level. Analysis methods include ANOVA and Pearson correlations.

RESULTS

The mean percent increase (±SD) in BMD at 12 months for all women was small; total body, 0.62% (± 2.72), femoral neck 0.59% (±3.58) and spine 0.43% (±2.80). There was no difference in BMD or serum N-telopeptide in response to vitamin D by dose or race. The increase in total body, spine and hip BMD in elderly women given vitamin D doses between 400 and 4800 IU daily and calcium supplementation is small, unrelated to dose or 12-month serum 25OHD, free 25OHD or 1,25(OH)2D. There was no evidence of a threshold change in BMD with increasing serum 25OHD or free 25OHD in this population.

CONCLUSIONS

We found no significant effect of daily vitamin D dose ranging from 400 to 4800 IU/day on BMD or serum N-terminal telopeptides in elderly women with initially low serum 25OHD.

An Approach to Assigning In Vitro Potency to Unfractionated and Low Molecular Weight Heparins Based on the Inhibition of Prothrombin Activation and Catalysis of Thrombin Inhibition

Unfractionated and low molecular weight (LMW) heparins with good antithrombotic activity invariably catalyze thrombin inhibition and inhibit the appearance of thrombin activity in contact-activated plasma. Conversely, the antithrombotic efficacy of LMW heparins decreases as their ability to catalyze thrombin inhibition and to inhibit the appearance of thrombin activity in plasma decrease. The activated partial thromboplastin time (APTT) has proven a reliable test for assaying unfractionated heparin. We therefore compared 2 unfractionated and 3 LMW heparins on the basis of the minimum concentrations required to double the APTT of normal plasma and by then determined how this anticoagulant effect was achieved. The amount of unfractionated and LMW heparin which doubled the APTT was found to be equivalent to —0.25 antithrombin units. This concentration of each glycosaminoglycan completely inhibited prothrombin activation for 45 s after CaCl2 was added to contact-activated plasma; accelerated thrombin inhibition by purified antithrombin III by approximately 50-fold; and accelerated thrombin inhibition equally by anti thrombin III in undiluted plasma. This concentration of the three LMW heparins increased, by approximately 70fold, the rate of factor Xa inhibition by purified antithrombin III compared to the 50-fold increase seen with the two unfractionated heparins. These results thus suggest that tests based on the inhibition of prothrombin activation and/or on the catalysis of thrombin inhibition provide a useful basis for assigning in vitro potency to both unfractionated and LMW heparins.

Quadrivalent human papillomavirus vaccination in girls and the risk of autoimmune disorders: the Ontario Grade 8 HPV Vaccine Cohort Study

BACKGROUND

Despite demonstrated effectiveness in real-world settings, concerns persist regarding the safety of the quadrivalent human papillomavirus (HPV4) vaccine. We sought to assess the risk of autoimmune disorders following HPV4 vaccination among grade 8 girls eligible for Ontario's school-based HPV vaccination program.

METHODS

We undertook a population-based retrospective cohort study using Ontario's administrative health and vaccination databases from 2007 to 2013. The self-controlled case series method was used to compare the rate of a composite end point of autoimmune disorders diagnosed during days 7-60 post-vaccination ("exposed" follow-up) to that at any other time ("unexposed"). The analysis was repeated to assess the effect of a history of immune-mediated diseases and time since vaccination. We also conducted an exploratory analysis of individual autoimmune disorders. Rate ratios and 95% confidence intervals (CIs) were estimated using conditional Poisson regression, adjusted for age, seasonality, concomitant vaccinations and infections.

RESULTS

The study cohort consisted of 290 939 girls aged 12-17 years who were eligible for vaccination between 2007 and 2013. There was no significant risk for developing an autoimmune disorder following HPV4 vaccination (n = 681; rate ratio 1.12, 95% CI 0.85-1.47), and the association was unchanged by a history of immune-mediated disorders and time since vaccination. Exploratory analyses of individual autoimmune disorders found no significant risks, including for Bell palsy (n = 65; rate ratio 1.73, 95% CI 0.77-3.89), optic neuritis (n = 67; rate ratio 1.57, 95% CI 0.74-3.33) and Graves disease (n = 47; rate ratio 1.55, 95% CI 0.92-2.63).

INTERPRETATION

We did not observe an increased risk of autoimmune disorders following HPV4 vaccination among teenaged girls. These findings should reassure parents and health care providers.

Tear Histamine and Histaminase during the Early (Epr) and Late (Lpr) Phases of the Allergic Reaction and the Effects of Lodoxamide

The objectives of this study were two-fold: to identify tear histamine content and its relationship to changes in tear histaminase activity during the early (EPR) and late phases (LPR) of the allergic reaction induced by a conjunctival provocation test (CPT) and to evaluate the effects of lodoxamide on histamine release and allergic signs and symptoms during EPR and LPR. A baseline CPT was administered to 20 allergic patients with no baseline signs or symptoms of allergy. Clinical signs and symptoms were evaluated after 20 minutes and 6 hours. Tear samples were taken after 5-10 minutes and after 6 hours for subsequent analyses of cytology and histamine content (ELISA). Patients were then randomly assigned to receive lodoxamide or placebo four times daily for one week in a double-masked fashion. A second CPT was done after this therapy and the same parameters were re-evaluated. During EPR, tear histamine increased significantly with respect to baseline values (p < 0.05). During LPR, tear histamine increased significantly (p < 0.05) only in histamine inactivated samples. Histaminase enzymes were also significantly less active during the EPR (5.5 +/- 0.7) than the LPR (9.9 +/- 2.3) and at baseline. Histamine levels significantly correlated with allergic signs and symptoms (p < 0.05) only during the EPR. Lodoxamide significantly reduced histamine release during EPR (p < 0.05), allergic signs and symptoms during both EPR (p < 0.001) and LPR (p < 0.005), and tear cytology counts during LPR. In conclusion, greater histaminase activity may account for the smaller amount of tear histamine generally found during LPR, while these enzymes seem to play less of a role during the surge of histamine release and activity in the EPR. Lodoxamide was shown to ideally inhibit various aspects of the allergic reaction: clinical signs and symptoms in both the early and late phases, the primarily EPR-related peak of histamine release, and the primarily LPR-related changes in tear cytology.

Characterizing the experience of auditory verbal hallucinations and accompanying delusions in individuals with a diagnosis of bipolar disorder: A systematic review

OBJECTIVES

The aim of the current study was to inform ongoing attempts to identify clinically meaningful subcategories of auditory verbal hallucination (AVH), and to evaluate evidence that might pertain to the suitability of current psychological interventions for people with bipolar disorder (BD) who experience psychotic symptoms.

METHODS

A comprehensive synthesis of findings on the phenomenology of AVH and delusions in BD is included, alongside a critical review of clinical and cognitive correlates. Studies published in the previous 20 years, until December 2016, were retrieved from the following databases: Embase, CINAHL, MEDLINE, PsycINFO and Web of Science. Thirty-two articles were reviewed after applying a set of predetermined inclusion criteria.

RESULTS

Psychotic symptoms were common in both manic and depressive phases, although higher frequencies were indicated in mania. Few detailed characterizations of AVH phenomenology were identified. Delusions with persecutory, grandiose and referential themes were the most common in BD. AVHs were associated with delusions and there was evidence to suggest that delusion subtype may vary according to mood state and type of AVH. Data on clinical correlates of AVH in BD were sparse. However, the results indicated that cognitive appraisals or interpretations of voices might be different in BD from those established to be predictive of clinical outcomes in schizophrenia spectrum disorders.

CONCLUSIONS

Clear gaps exist in our current understanding of the first-person experience of AVH in BD and the potential relationship to co-occurring symptoms, including delusions. Further research into cognitive interpretations of AVH in BD might inform adapted psychological interventions for psychotic symptoms in this population.

Population structure of an orchid mycorrhizal fungus with genus-wide specificity

Fundamental life history processes of mycorrhizal fungi with inconspicuous fruiting bodies can be difficult to elucidate. In this study we investigated the species identities and life history of the orchid mycorrhizal Tulasnella fungi, which associate with the south eastern Australia orchid genus Chiloglottis. Tulasnella prima was the primary partner and was found to be associated with all 17 Chiloglottis species across a range of >1000 km, and to occur in the two edaphic conditions investigated (soil and sphagnum hammocks). Another Tulasnella species (T. sphagneti) appears to be restricted to moist conditions of alpine sphagnum hammocks. The population genetic structure of the widespread species T. prima, was investigated at 10 simple sequence repeat (SSR) markers and at four cross-amplified SSR loci for T. sphagneti. For both taxa, no sharing of multilocus genotypes was found between sites, but clones were found within sites. Evidence for inbreeding within T. prima was found at 3 of 5 sites. Significant genetic differentiation was found within and between taxa. Significant local positive spatial genetic autocorrelation was detected among non-clonal isolates at the scale of two metres. Overall, the population genetic patterns indicated that in Tulasnella mating occurs by inbreeding and dispersal is typically restricted to short-distances.

Strategies for evaluating the assumptions of the regression discontinuity design: a case study using a human papillomavirus vaccination programme

Background

The regression discontinuity design (RDD) is a quasi-experimental approach used to avoid confounding bias in the assessment of new policies and interventions. It is applied specifically in situations where individuals are assigned to a policy/intervention based on whether they are above or below a pre-specified cut-off on a continuously measured variable, such as birth date, income or weight. The strength of the design is that, provided individuals do not manipulate the value of this variable, assignment to the policy/intervention is considered as good as random for individuals close to the cut-off. Despite its popularity in fields like economics, the RDD remains relatively unknown in epidemiology where its application could be tremendously useful.

Methods

In this paper, we provide a practical introduction to the RDD for health researchers, describe four empirically testable assumptions of the design and offer strategies that can be used to assess whether these assumptions are met in a given study. For illustrative purposes, we implement these strategies to assess whether the RDD is appropriate for a study of the impact of human papillomavirus vaccination on cervical dysplasia.

Results

We found that, whereas the assumptions of the RDD were generally satisfied in our study context, birth timing had the potential to confound our effect estimate in an unexpected way and therefore needed to be taken into account in the analysis.

Conclusions

Our findings underscore the importance of assessing the validity of the assumptions of this design, testing them when possible and making adjustments as necessary to support valid causal inference.

Striatal mRNA expression patterns underlying peak dose L-DOPA-induced dyskinesia in the 6-OHDA hemiparkinsonian rat

L-DOPA is the primary pharmacological treatment for relief of the motor symptoms of Parkinson's disease (PD). With prolonged treatment (⩾5 years) the majority of patients will develop abnormal involuntary movements as a result of L-DOPA treatment, known as L-DOPA-induced dyskinesia. Understanding the underlying mechanisms of dyskinesia is a crucial step toward developing treatments for this debilitating side effect. We used the 6-hydroxydopamine (6-OHDA) rat model of PD treated with a three-week dosing regimen of L-DOPA plus the dopa decarboxylase inhibitor benserazide (4 mg/kg and 7.5 mg/kgs.c., respectively) to induce dyskinesia in 50% of individuals. We then used RNA-seq to investigate the differences in mRNA expression in the striatum of dyskinetic animals, non-dyskinetic animals, and untreated parkinsonian controls at the peak of dyskinesia expression, 60 min after L-DOPA administration. Overall, 255 genes were differentially expressed; with significant differences in mRNA expression observed between all three groups. In dyskinetic animals 129 genes were more highly expressed and 14 less highly expressed when compared with non-dyskinetic and untreated parkinsonian controls. In L-DOPA treated animals 42 genes were more highly expressed and 95 less highly expressed when compared with untreated parkinsonian controls. Gene set cluster analysis revealed an increase in expression of genes associated with the cytoskeleton and phosphoproteins in dyskinetic animals compared with non-dyskinetic animals, which is consistent with recent studies documenting an increase in synapses in dyskinetic animals. These genes may be potential targets for drugs to ameliorate L-DOPA-induced dyskinesia or as an adjunct treatment to prevent their occurrence.

Tropism of subgroup J avian leukosis virus as detected by in situ hybridization

The HPRS-103 strain of avian retrovirus is the prototype of subgroup J avian leukosis virus (ALV-J) and causes myeloid leukosis in meat-type chickens. Using immunohistochemical detection of the viral groupspecific antigen (Gag) we have previously demonstrated that the induction of myeloid leukosis by ALV-J is associated with viral tropism for myelomonocytic cells. In this paper we describe an in situ hybridization (ISH) technique using digoxigenin (DIG)-labelled probes for detecting RNA transcripts in tissues from chickens infected with avian leukosis viruses (ALV) of subgroups J (HPRS-103 strain) and A (RAV-1 strain). Virus-specific RNA was detected mainly in the heart, kidney, proventriculus and adrenal in locations similar to those of the Gag protein. Viral gene expression could not be detected in the bone marrow or tumour tissues using this test. Higher levels of viral gene expression in the bursa of Fabricius infected with RAV-1, but not with HPRS-103, might help explain the inability of the latter virus to induce lymphoid leukosis.

Mice deficient in Muc4 are resistant to experimental colitis and colitis-associated colorectal cancer

MUC4, a large transmembrane mucin normally expressed in the small and large intestine, is differentially expressed during inflammatory and malignant conditions of the colon. However, the expression pattern and the role of MUC4 in colitis and colorectal cancer (CRC) are inconclusive. Therefore, the aim of this study was to understand the role of Muc4 during inflammatory and malignant conditions of the colon. Here, we generated Muc4(-/-) mice and addressed its role in colitis and colitis-associated CRC using dextran sodium sulfate (DSS) and azoxymethane (AOM)-DSS experimental models, respectively. Muc4(-/-) mice were viable, fertile with no apparent defects. Muc4(-/-) mice displayed increased resistance to DSS-induced colitis compared with wild-type (WT) littermates that was evaluated by survival rate, body weight loss, diarrhea and fecal blood score, and histological score. Reduced infiltration of inflammatory cells, that is, CD3(+) lymphocytes and F4/80(+) macrophages was observed in the inflamed mucosa along with reduction in the mRNA levels of inflammatory cytokines interleukin (IL)-1β and tumor necrosis factor (TNF)-α and anti-microbial genes Lysozyme M and SLPI in the colon of Muc4(-/-) mice compared with WT littermates. Compensatory upregulation of Muc2 and Muc3 mucins under basal and DSS treatment conditions partly explains the resistance observed in Muc4(-/-) mice. Accordingly, Muc4(-/-) mice exhibited significantly reduced tumor burden compared with WT mice assessed in a colitis-induced tumor model using AOM/DSS. An increased percentage of Ki67(+) nuclei was observed in the tumors from WT compared with Muc4(-/-) mice suggesting Muc4 to be critical in intestinal cell proliferation during tumorigenesis. Taken together, we conclusively demonstrate for the first time the role of Muc4 in driving intestinal inflammation and inflammation-associated tumorigenesis using a novel Muc4(-/-) mouse model.

The early benefits of human papillomavirus vaccination on cervical dysplasia and anogenital warts

BACKGROUND

Despite widespread promotion of quadrivalent human papillomavirus (qHPV) vaccination for young girls, there is limited information on the vaccine's real-world effectiveness and none on the effectiveness of qHPV vaccination programs. We assessed the impact of the qHPV vaccine and Ontario's grade 8 qHPV vaccination program on cervical dysplasia and anogenital warts (AGW).

METHODS

By using administrative health databases of Ontario, Canada, we identified a population-based retrospective cohort of girls in grade 8 before (2005/2006-2006/2007) and after (2007/2008-2008/2009) program implementation. Vaccine exposure was ascertained in grades 8 to 9 and outcomes in grades 10 to 12. A quasi-experimental approach known as regression discontinuity was used to estimate absolute risk differences (RDs), relative risks (RRs), and 95% confidence intervals (CIs) attributable to vaccination and program eligibility (intention-to-treat analysis).

RESULTS

The cohort comprised 131,781 ineligible and 128,712 eligible girls (n = 260,493). We identified 2436 cases of dysplasia and 400 cases of AGW. Vaccination significantly reduced the incidence of dysplasia by 5.70 per 1000 girls (95% CI -9.91 to -1.50), corresponding to a relative reduction of 44% (RR 0.56; 95% CI 0.36 to 0.87). Program eligibility also had a significant protective effect on dysplasia: RD -2.32/1000 (95% CI -4.02 to -0.61); RR 0.79 (95% CI 0.66 to 0.94). Results suggested decreases in AGW attributable to vaccination (RD -0.83/1000, 95% CI -2.54 to 0.88; RR 0.57, 95% CI 0.20 to 1.58) and program eligibility (RD -0.34/1000, 95% CI -1.03 to 0.36; RR 0.81, 95% CI 0.52 to 1.25).

CONCLUSIONS

This study provides strong evidence of the early benefits of qHPV vaccination among girls aged 14 to 17 years, offering additional justification for not delaying vaccination.

Effect of human papillomavirus (HPV) vaccination on clinical indicators of sexual behaviour among adolescent girls: the Ontario Grade 8 HPV Vaccine Cohort Study

BACKGROUND

Suboptimal human papillomavirus (HPV) vaccine coverage in some jurisdictions is partly attributed to fears that vaccination may increase risky sexual behaviour. We assessed the effect of HPV vaccination on clinical indicators of sexual behaviour among adolescent girls in Ontario.

METHODS

Using Ontario's administrative health databases, we identified a population-based cohort of girls in grade 8 in the 2 years before (2005/06 and 2006/07) and after (2007/08 and 2008/09) implementation of Ontario's grade 8 HPV vaccination program. For each girl, we then obtained data on vaccine receipt in grades 8 and 9 and data on indicators of sexual behaviour (pregnancy and non-HPV-related sexually transmitted infections) in grades 10-12. Using a quasi-experimental method known as regression discontinuity, we estimated, for each outcome, the risk difference (RD) and relative risk (RR) attributable to vaccination and to program eligibility.

RESULTS

The cohort comprised 260 493 girls, of whom 131 781 were ineligible for the program and 128 712 were eligible. We identified 15 441 (5.9%) cases of pregnancy and sexually transmitted infection and found no evidence that vaccination increased the risk of this composite outcome: RD per 1000 girls -0.61 (95% confidence interval [CI] -10.71 to 9.49) and RR 0.96 (95% CI 0.81 to 1.14). Similarly, we found no discernible effect of program eligibility: RD per 1000 girls -0.25 (95% CI -4.35 to 3.85) and RR 0.99 (95% CI 0.93 to 1.06). The findings were similar when outcomes were assessed separately.

INTERPRETATION

We present strong evidence that HPV vaccination does not have any significant effect on clinical indicators of sexual behaviour among adolescent girls. These results suggest that concerns over increased promiscuity following HPV vaccination are unwarranted and should not deter from vaccinating at a young age.

Individual- and regional-level determinants of human papillomavirus (HPV) vaccine refusal: the Ontario Grade 8 HPV vaccine cohort study

Background

Studies on the determinants of human papillomavirus (HPV) vaccine use have generally focused on individual-level characteristics, despite the potentially important influence of regional-level characteristics. Therefore, we undertook a population-based, retrospective cohort study to identify individual- and regional-level determinants of HPV vaccine refusal (non-receipt) in Ontario’s (Canada) Grade 8 HPV Immunization Program.

Methods

Ontario’s administrative health and immunization databases were used to identify girls eligible for free HPV vaccination in 2007–2011 and to ascertain individual-level characteristics of cohort members (socio-demographics, vaccination history, health care utilization, medical history). The social and material characteristics of the girl’s region (health unit) were derived from the 2006 Canadian Census. Generalized estimating equations (binomial distribution, logit link) were used to estimate the population-average effects of individual- and regional-level characteristics on HPV vaccine refusal.

Results

Our cohort consisted of 144,047 girls, 49.3% of whom refused HPV vaccination. Factors associated with refusal included a previous diagnosis of Down’s syndrome (OR = 1.37, 95% CI 1.16-1.63) or autism (OR = 1.60, 95% CI 1.34-1.90), few physician visits (OR = 1.45, 95% CI 1.35-1.55), and previous refusal of mandatory (OR = 2.23, 95% CI 2.07-2.40) and optional (OR = 3.96, 95% CI 3.87-4.05) vaccines. Refusal was highest among the lowest and highest income levels. Finally, a previous diagnosis of obesity and living in an area of high deprivation were associated with lower refusal (OR = 0.87, 95% CI 0.83-0.92 and OR = 0.82 95%, CI 0.79-0.86, respectively).

Conclusions

Studies on HPV vaccine determinants should consider regional-level factors. Efforts to increase HPV vaccine acceptance should include vulnerable populations (such as girls of low income) and girls with limited contact with the healthcare system.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2458-14-1047) contains supplementary material, which is available to authorized users.

Evidence of effective delivery of the human papillomavirus (HPV) vaccine through a publicly funded, school-based program: the Ontario Grade 8 HPV Vaccine Cohort Study

BACKGROUND

Proper administration of the human papillomavirus (HPV) vaccine (three doses at 0, 2, and 6 months) will likely influence the vaccine's effectiveness and the impact of vaccination programs on health outcomes. Therefore, we assessed HPV vaccine series completion and on-time dosing in Canada's largest publicly funded, school-based HPV vaccination program.

METHODS

Using administrative health and immunization databases, we identified a population-based cohort of girls eligible for Ontario's Grade 8 HPV vaccination program in the 2007/08-2009/10 program years who received at least one dose of the vaccine. We determined the number of doses received and calculated the percentage of girls that completed the three-dose series in Grade 8 and Grades 8-9. To assess on-time dosing, the number of days between doses 1-2, 2-3, and 1-3 was calculated and categorized (e.g., too short, on schedule, too long) based on the manufacturer's recommendations. Analyses were also stratified by program year.

RESULTS

We identified a cohort of 55,798 girls who initiated the vaccination series. Series completion was high in the Grade 8 window (81.8%) and increased by approximately 6% in Grade 9. Series completion was similar across the three program years. 70.8%, 98.5%, and 86.1% of girls were classified as 'on schedule' for dosing intervals 1-2, 2-3, and 1-3, respectively; 70.0% of girls received all three doses in perfect accordance with dosing recommendations. Stratification revealed that on-time dosing was highest in the first two years of the program (85.6% and 80.6%), but dropped to 42.1% in the 2009/10 year when H1N1 vaccination programs were prioritized.

CONCLUSIONS

Our study demonstrates that delivery of the HPV vaccine through a free, school-based program is an effective method of ensuring high completion and on-time dosing, but may not be sufficient to guarantee high coverage.

The role of social and intergenerational equity in making changes in human well-being sustainable

A sustainable world is one in which human needs are met equitably and without sacrificing the ability of future generations to meet their needs. Human well-being is described by four primary elements-basic human needs, economic needs, environmental needs, and subjective well-being. These elements can interact in a myriad of ways to influence overall well-being. What makes changes in human well-being sustainable for a population or a nation? Two major interactional concepts can push changes in human well-being toward a sustainable state in space and time-social equity and intergenerational equity. The concept of social equity distributes well-being over space, ensuring the fair treatment of all members of society promoting spatial sustainability of a well-being decision. The concept of intergenerational equity distributes well-being through time, ensuring the well-being of present and future generations of a population or nation, promoting temporal sustainability of a well-being decision. The roles of social and intergenerational equity in terms of their influence on human well-being are examined with a focus on more sustainable decision-making.

Multicentre, randomized, open-label study of on-demand treatment with two prophylaxis regimens of recombinant coagulation factor IX in haemophilia B subjects

Few randomized studies have reported on the use of factor IX (FIX) for secondary prophylaxis in haemophilia B patients. This study aimed to evaluate the efficacy and safety of two secondary prophylaxis regimens of recombinant coagulation FIX, nonacog alfa, compared with on-demand therapy. Male subjects aged 6-65 years with severe or moderately severe haemophilia B (FIX:C ≤ 2, n = 50) and ≥12 bleeding episodes (including ≥6 haemarthroses episodes) within 12 months of study participation were enrolled in this multicentre, randomized, open-label, four-period crossover trial. The primary measure was the annualized bleeding rate (ABR) of two prophylactic regimens vs. on-demand therapy. In the intent-to-treat group, mean ABR values were 35.1, 2.6 and 4.6 for the first on-demand period, the 50 IU kg(-1) twice-weekly period, and the 100 IU kg(-1) once-weekly period respectively. Differences in ABR between the first on-demand period and both prophylaxis regimens were significant (P < 0.0001); no significant differences were observed between prophylaxis regimens (P = 0.22). Seven serious adverse events occurred in five subjects, none related to study drug. Results demonstrated that secondary prophylaxis therapy with nonacog alfa 50 IU kg(-1) twice weekly or 100 IU kg(-1) once weekly reduced ABR by 89.4% relative to on-demand treatment. Both prophylaxis regimens demonstrated favourable safety profiles in subjects with haemophilia B.

Cenozoic climate change and diversification on the continental shelf and slope: evolution of gastropod diversity in the family Solariellidae (Trochoidea)

Recent expeditions have revealed high levels of biodiversity in the tropical deep-sea, yet little is known about the age or origin of this biodiversity, and large-scale molecular studies are still few in number. In this study, we had access to the largest number of solariellid gastropods ever collected for molecular studies, including many rare and unusual taxa. We used a Bayesian chronogram of these deep-sea gastropods (1) to test the hypothesis that deep-water communities arose onshore, (2) to determine whether Antarctica acted as a source of diversity for deep-water communities elsewhere and (3) to determine how factors like global climate change have affected evolution on the continental slope. We show that although fossil data suggest that solariellid gastropods likely arose in a shallow, tropical environment, interpretation of the molecular data is equivocal with respect to the origin of the group. On the other hand, the molecular data clearly show that Antarctic species sampled represent a recent invasion, rather than a relictual ancestral lineage. We also show that an abrupt period of global warming during the Palaeocene Eocene Thermal Maximum (PETM) leaves no molecular record of change in diversification rate in solariellids and that the group radiated before the PETM. Conversely, there is a substantial, although not significant increase in the rate of diversification of a major clade approximately 33.7 Mya, coinciding with a period of global cooling at the Eocene-Oligocene transition. Increased nutrients made available by contemporaneous changes to erosion, ocean circulation, tectonic events and upwelling may explain increased diversification, suggesting that food availability may have been a factor limiting exploitation of deep-sea habitats. Tectonic events that shaped diversification in reef-associated taxa and deep-water squat lobsters in central Indo-West Pacific were also probably important in the evolution of solariellids during the Oligo-Miocene.

The genome of murine cytomegalovirus is shaped by purifying selection and extensive recombination

The herpesvirus lifestyle results in a long-term interaction between host and invading pathogen, resulting in exquisite adaptation of virus to host. We have sequenced the genomes of nine strains of murine cytomegalovirus (a betaherpesvirus), isolated from free-living mice trapped at locations separated geographically and temporally. Despite this separation these genomes were found to have low levels of nucleotide variation. Of the more than 160 open reading frames, almost 90% had a dN/dS ratio of amino acid substitutions of less than 0.6, indicating the level of purifying selection on the coding potential of MCMV. Examination of selection acting on individual genes at the codon level however indicates some level of positive selection, with 0.03% of codons showing strong evidence for positive selection. Conversely, 1.3% of codons show strong evidence of purifying selection. Alignments of both genome sequences and coding regions suggested that high levels of recombination have shaped the MCMV genome.

Controlling DNA Fragmentation in MALDI-MS by Chemical Modification

Fragmentation has proven to be a major factor limiting accessible mass range, sensitivity, and mass resolution in the analysis of DNA by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Previous work has shown that this DNA fragmentation is strongly dependent on both the MALDI matrix and the nucleic acid sequence employed. Fragmentation is initiated by nucleobase protonation, leading to cleavage of the N-glycosidic bond with base loss, followed by cleavage of the phosphodiester backbone. In this study, asymmetric oligonucleotides incorporating cytidine and cytidine analogs such as 5-methyl-2'-deoxycytidine, 5-bromo-2'-deoxycytidine, aracytidine, and 2'-fluorodeoxycytidine nucleosides were used to systematically investigate the influence of the structural changes on the stability of the N-glycosidic bond. Modifications of the deoxyribose sugar ring by replacing the 2'-hydrogen with more electron-withdrawing groups such as the hydroxyl or fluoro group stabilize the N-glycosidic bond to a greater extent than the C5 nucleobase modifications. 2'-Hydroxyl and 2'-fluoro groups respectively are shown to partially or completely block fragmentation at the modified nucleosides. Mixtures of oligonucleotides incorporating such modifications demonstrate remarkably extended accessible mass range, as well as increased sensitivity and mass resolution. The stabilization provided by these chemical modifications also expands the range of matrices useful for nucleic acid analysis, yielding in some cases greatly improved performance.

A review of the elements of human well-being with an emphasis on the contribution of ecosystem services

Natural ecosystems perform fundamental life-support services upon which human civilization depends. However, many people believe that nature provides these services for free and therefore, they are of little or no value. While we do not pay for them, we pay significantly for their loss in terms of wastewater treatment facilities, moratoriums on greenhouse gases, increased illnesses, reduced soil fertility and losses in those images of nature that contribute to our basic happiness. Little is understood about the well-being benefits of the natural environment and its ecosystem services. The interwoven relationship of ecosystems and human well-being is insufficiently acknowledged in the wider philosophical, social, and economic well-being literature. In this article, we discuss an approach to examine human well-being and the interactions of its four primary elements-basic human needs, economic needs, environmental needs, and subjective well-being-and ecosystem services.

Factors associated with initiation and completion of the quadrivalent human papillomavirus vaccine series in an Ontario cohort of grade 8 girls

Background

Although over a hundred million dollars have been invested in offering free quadrivalent human papillomavirus (HPV) vaccination to young girls in Ontario, there continues to be very little information about its usage. In order to successfully guide future HPV vaccine programming, it is important to monitor HPV vaccine use and determine factors associated with use in this population.

Methods

Linking administrative health and immunization databases, we conducted a population-based, retrospective cohort study of girls eligible for Ontario's Grade 8 HPV vaccination program in Kingston, Frontenac, Lennox, and Addington. We determined the proportion of girls who initiated (at least one dose) and completed (all three doses) the vaccination series overall and according to socio-demographics, vaccination history, health services utilization, medical history, and program year. Multivariable logistic regression was used to estimate the strength of association between individual factors and initiation and completion, adjusted for all other factors.

Results

We identified a cohort of 2519 girls, 56.6% of whom received at least one dose of the HPV vaccine. Among vaccinated girls, 85.3% received all three doses. Vaccination history was the strongest predictor of initiation in that girls who received the measles-mumps-rubella, meningococcal C, and hepatitis B vaccines were considerably more likely to also receive the HPV vaccine (odds ratio 4.89; 95% confidence interval 4.04-5.92). Nevertheless, HPV vaccine uptake was more than 20% lower than that of these other vaccines. In addition, while series initiation was not influenced by income, series completion was. In particular, girls of low income were the least likely to receive all three indicated doses of the HPV vaccine (odds ratio 0.45; 95% confidence interval 0.28-0.72).

Conclusions

The current low level of HPV vaccine acceptance in Kingston, Frontenac, Lennox, and Addington will likely have important implications in terms of the health benefits and cost-effectiveness of its publicly funded program. We identified important factors associated with series initiation and completion that should be considered in efforts to improve HPV vaccine use in this population.

The morphology and evolution of bipyramidal gold nanoparticles

We examine the growth and evolution with time of bipyramidal gold nanoparticles grown by a seed-mediated process. The nanoparticles are characterized both by their physical dimensions determined by transmission electron microscopy and by the wavelength position of their localized surface plasmon resonance. Each growth's physical dimensions correspond to particular initial conditions, and we observe two distinct modes of temporal evolution during growth. The effects of varying silver nitrate concentration and growth time are also explored. We observe a linear relationship between the tip radius of curvature and the wavelength of the longitudinal localized surface plasmon resonance (LSPR) peak. Critical parameters for synthesizing bipyramidal nanoparticles with sharp tips and correct length to width ratio are determined.

Activated KrasG¹²D is associated with invasion and metastasis of pancreatic cancer cells through inhibition of E-cadherin

Background:

Pancreatic cancer (PC) harbours an activated point mutation (Kras^G12D) in the Kras proto-oncogene that has been demonstrated to promote the development of PC.

Methods:

This study was designed to investigate the effect of the oncogenic Kras^G12D allele on aggressiveness and metastatic potential of PC cells. We silenced the oncogenic Kras^G12D allele expression in CD18/HPAF and ASPC1 cell lines by stable expression of shRNA specific to the Kras^G12Dallele.

Results:

The Kras^G12D knockdown cells exhibited a significant decrease in motility (P<0.0001), invasion (P<0.0001), anchorage-dependent (P<0.0001) and anchorage-independent growth (P<0.0001), proliferation (P<0.005) and an increase in cell doubling time (P<0.005) in vitro and a decrease in the incidence of metastases upon orthotopic implantation into nude mice. The knockdown of the Kras^G12D allele led to a significant increase in the expression of E-cadherin (mRNA and protein) both in vitro and in vivo. This was associated with a decrease in the expression of phoshpo-ERK-1/2, NF-κB and MMP-9, and transcription factors such as δEF1, Snail and ETV4. Furthermore, the expression of several proteins involved in cell survival, invasion and metastasis was decreased in the Kras^G12D knockdown cells.

Conclusions:

The results of this study suggest that the Kras^G12D allele promotes metastasis in PC cells partly through the downregulation of E-cadherin.

Prevalence of overweight, obesity and underweight among 5-year-old children in Saint Lucia by three methods of classification and a comparison with historical rates

BACKGROUND

The study aimed to determine if child obesity rates have risen in the Caribbean nation of Saint Lucia, as found globally, and whether under-nutrition coexists, as in other developing nations. The average adult in Saint Lucia is overweight, thus considerable child obesity might be expected, but there are no current data.

METHODS

Heights and weights were obtained from a sample (n= 425) of the 2001 birth cohort of Saint Lucian children measured during the nation-wide 2006/2007 Prior to School Entry Five-Year Assessment. Prevalence of overweight, obesity and underweight were estimated by Centers for Disease Control (CDC), Cole et al. and new World Health Organization (WHO) methods. Previously reported 1976 estimates, including children ≤60 months of age only, based on National Centre for Health Statistics curves, were adjusted to new WHO equivalents using an algorithm developed by Yang and de Onis, and compared with rates in our subsample of children ≤60 months of age (n= 99).

RESULTS

Regardless of classification method, overweight and obesity rates were high: 14.4% and 9.2% (WHO); 11.3% and 12.0% (CDC); and 9.9% and 7.1% (Cole et al.), respectively. Underweight estimates also varied: 4.7% (WHO); 11.3% (CDC) and 6.6% (Cole et al.). Obesity in our young subsample (15.2%; WHO) was more than 3 times the adjusted 1976 rate (4.3%).

CONCLUSIONS

Obesity among Saint Lucian pre-schoolers has tripled in 30 years. Our findings also suggest that this country, like many undergoing a 'nutrition transition', faces the dual challenge of over-nutrition and under-nutrition. Routine monitoring of overweight and underweight is needed in Saint Lucia, as is the implementation and evaluation of programmes to address these problems.

Fall predictors in the community dwelling elderly: a cross sectional and prospective cohort study

OBJECTIVES

To ascertain the risk factors for falls, stumbles and recurrent falls in a cohort of elderly people with mean age of 76.7-/+6.1 years.

METHODS

137 community dwelling elderly living independently or in assisted living institutions participated in the study. Each subject was assessed by history, physical examination and physical performance tests at the beginning and end of study. Falls and stumbles were recorded in a falls dairy for 1 year.

RESULTS

Significant predictors of being a faller were a history of falls at baseline (Odds Ratio (OR) = 3.85, 95% Confidence Interval (CI) = 1.56 - 9.50), depression (OR = 1.19, 95% CI = 1.02 - 1.38) and timed rise (Incident Rate Ratio (IRR) = 1.24, 95% CI = 1.03 - 1.50). For predicting recurrent fallers Receiver Operator Characteristic (ROC) curves were as follows: 0.71 (95%CI 0.61-0.81) for timed up and go, 0.67 (95%CI 0.56-0.78) for timed rise and 0.70 (95%CI 0.60-0.80) for timed walk fast pace.

CONCLUSIONS

Timed rise was the single most important test that was able to predict both a first time faller and recurrent faller. Timed up and go was the most significant test to predict recurrent fallers.

Novel growth and properties of GaAs nanowires on Si substrates

Straight, vertically aligned GaAs nanowires were grown on Si(111) substrates coated with thin GaAs buffer layers. We find that the V/III precursor ratio and growth temperature are crucial factors influencing the morphology and quality of buffer layers. A double layer structure, consisting of a thin initial layer grown at low V/III ratio and low temperature followed by a layer grown at high V/III ratio and high temperature, is crucial for achieving straight, vertically aligned GaAs nanowires on Si(111) substrates. An in situ annealing step at high temperature after buffer layer growth improves the surface and structural properties of the buffer layer, which further improves the morphology of the GaAs nanowire growth. Through such optimizations we show that vertically aligned GaAs nanowires can be fabricated on Si(111) substrates and achieve the same structural and optical properties as GaAs nanowires grown directly on GaAs(111)B substrates.

Altered neurometabolites and motor integration in children exposed to methamphetamine in utero

Methamphetamine (METH) is a neurotoxic drug. This study aimed to evaluate brain metabolite levels and cognitive function in young children with prenatal METH exposure. 101 children ages 3-4 years were evaluated with neuropsychological tests and underwent proton magnetic resonance spectroscopy ((1)H-MRS) without sedation. Complete datasets from 49 METH-exposed and 49 controls who completed the neuropsychological test battery, and 38 METH-exposed and 37 controls with high-quality MR spectra are reported here. Despite similar physical characteristics (including head circumference), global cognitive function (on Stanford-Binet), parental education, intelligence, mood, and socioeconomic status, METH-exposed children had higher total creatine (tCr: +7%, p=0.003), N-acetyl compounds (NA: +4.3%, p=0.004) and glutamate+glutamine (GLX: +9.6%, p=0.02) concentrations in the frontal white matter, but lower myoinositol (MI: -7%, p=0.01) and MI/tCr (-7.5%, p=0.03) in the thalamus, than control children. The higher frontal white matter NA in the METH-exposed children was due to the higher NA in the METH-exposed girls (+10.2%, p=0.003), but not the boys (+0.8%) compared to sex-matched controls. Furthermore, the METH-exposed children had poorer performance on a visual motor integration (VMI) task, which correlated with lower MI in the thalamus (r=0.26, p=0.03). The higher NA, tCr and GLX concentrations suggest higher neuronal density or cellular compactness in the white matter, especially in the girls, whereas the lower MI suggests lower glial content in the thalamus of these METH-expose children. These findings combined with their poorer performance on VMI also suggest accelerated but aberrant neuronal and glial development in these brain regions.

The effect of V/III ratio and catalyst particle size on the crystal structure and optical properties of InP nanowires

InP nanowires were grown on 111B InP substrates by metal-organic chemical vapour deposition in the presence of colloidal gold particles as catalysts. Transmission electron microscopy and photoluminescence measurements were carried out to investigate the effects of V/III ratio and nanowire diameter on structural and optical properties. Results show that InP nanowires grow preferably in the wurtzite crystal structure than the zinc blende crystal structure with increasing V/III ratio or decreasing diameter. Additionally, time-resolved photoluminescence (TRPL) studies have revealed that wurtzite nanowires show longer recombination lifetimes of approximately 2500 ps with notably higher quantum efficiencies.

Tuning spin properties of excitons in single CdTe quantum dots by annealing

Using polarization-resolved photoluminescence imaging in external magnetic fields we measure statistically significant distributions of exchange splitting, diamagnetic shift and effective g-factor of excitons in tens of single CdTe quantum dots. Comparison between the as-grown and annealed structures shows strong suppression of ensemble inhomogeneities, with the average exchange splitting reduced by half and significant narrowing of the g-factor distribution. Remarkably, the average value of the excitonic g-factor remains unchanged. This unique ability to yield highly uniform quantum dot ensembles without hampering the exciton Zeeman splitting makes annealing a highly attractive means for tuning the spin properties of quantum dot excitons.

Comparison of several traps for catching German cockroaches (Dictyoptera: Blattellidae) under laboratory conditions

German cockroach, Blattella germanica (L.) (Dictyoptera: Blattellidae), catch by five types of traps and modifications of each, were tested under controlled laboratory conditions. Cockroach catch differed significantly among traps. Lo-line trap caught the greatest number of cockroaches in the test arena for each size class (23% small nymphs, 39% of gravid females, and 60% of other size classes in the experimental arena). Jar traps caught the least number of cockroaches in the test arena for each size class (range, 7-23% of each size class trapped). Modifications of traps also altered catch of cockroaches. Food bait tablets increased catch significantly; however, increases were small (<10%). Size of traps did not affect catch; whole traps or half traps caught the same number of cockroaches. Jar traps were much less effective than sticky traps, catching only half the number of cockroaches as sticky traps. A thin layer of petrolatum was a more effective barrier in jar traps to cockroach escape than powdered Olancha clay. Traps with petrolatum caught about twice as many cockroaches as traps with clay. Trapping of any of six life stages was not significantly affected by catch of any of the other stages. Rather, trap catch of each life stage was dependent on the number of that life stage available in the experimental arenas. In conclusion, of the traps tested, the Lo-line trap was the most sensitive for measuring cockroach catch, whereas the Detector trap (one third of trap) was the most economical trap (greatest sensitivity for lowest cost).