The epidemiology of invasive pneumococcal disease in the Canadian North from 1999 to 2010

Introduction . The International Circumpolar Surveillance network is a population-based surveillance system that collects data on invasive pneumococcal disease (IPD) in Northern Canada. A 7-valent pneumococcal conjugate vaccine was first introduced in some regions of Northern Canada in 2002, followed by 10-valent (2009) and 13-valent (PCV-13) vaccines (2010). A 23-valent polysaccharide (PPV-23) vaccine was first introduced in 1988 for special populations and adults aged 65 years and older. To describe the epidemiology in the context of pneumococcal vaccination programs, we analysed surveillance data from Northern Canada from 1999 to 2010. Methods . A standardized case report form capturing demographic and clinical information was completed for all IPD cases in Northern Canada meeting the national case definition. Isolates were sent to a reference laboratory for confirmation, serotyping and antimicrobial resistance testing. Both laboratory and epidemiological data were sent to the Public Health Agency of Canada for analysis. Population denominators were obtained from Statistics Canada. Results . From 1999 to 2010, 433 IPD cases were reported (average 36 cases per year). Incidence was greatest among infants aged <2 years and among those aged 65 years and older, with an average annual incidence of 133 and 67 cases per 100,000 population, respectively. After a peak in incidence in 2008, rates among infants have declined. Incidence rates varied from 2 to 16 times greater, depending on the year, among Aboriginals compared to non-Aboriginals. Hospitalization was reported in 89% of all cases and the case fatality ratio was 6.0%. Clinical manifestations varied, with some patients reporting >1 manifestation. Pneumonia was the most common (70%), followed by bacteremia/septicaemia (30%) and meningitis (8%). Approximately, 42% of cases aged <2 years in 2009 and 2010 had serotypes covered by the PCV-13. In addition, the majority (89%) of serotypes isolated in cases aged 65 years and older were included in the PPV-23 vaccine. Conclusion . IPD continues to be a major cause of disease in Northern Canadian populations, with particularly high rates among infants and Aboriginals. Continued surveillance is needed to determine the impact of conjugate pneumococcal vaccine programs. Additional studies investigating factors that predispose infants and Aboriginal peoples would also be beneficial

Families of Canonical Transformations by Hamilton-Jacobi-Poincar\'e equation. Application to Rotational and Orbital Motion

The Hamilton-Jacobi equation in the sense of Poincar\'e, i.e. formulated in the extended phase space and including regularization, is revisited building canonical transformations with the purpose of Hamiltonian reduction. We illustrate our approach dealing with orbital and attitude dynamics. Based on the use of Whittaker and Andoyer symplectic charts, for which all but one coordinates are cyclic in the Hamilton-Jacobi equation, we provide whole families of canonical transformations, among which one recognizes the familiar ones used in orbital and attitude dynamics. In addition, new canonical transformations are demonstrated.Comment: 21 page

Ambient habitat noise and vibration at the Georgia Aquarium

Underwater and in-air noise evaluations were completed in performance pool systems at Georgia Aquarium under normal operating conditions and with performance sound tracks playing. Ambient sound pressure levels at in-pool locations, with corresponding vibration measures from life support system (LSS) pumps, were measured in operating configurations, from shut down to full operation. Results indicate noise levels in the low frequency ranges below 100 Hz were the highest produced by the LSS relative to species hearing thresholds. The LSS had an acoustic impact of about 10 dB at frequencies up to 700 Hz, with a 20 dB re 1 μPa impact above 1000 Hz

CloneQC: lightweight sequence verification for synthetic biology

Synthetic biology projects aim to produce physical DNA that matches a designed target sequence. Chemically synthesized oligomers are generally used as the starting point for building larger and larger sequences. Due to the error rate of chemical synthesis, these oligomers can have many differences from the target sequence. As oligomers are joined together to make larger and larger synthetic intermediates, it becomes essential to perform quality control to eliminate intermediates with errors and retain only those DNA molecules that are error free with respect to the target. This step is often performed by transforming bacteria with synthetic DNA and sequencing colonies until a clone with a perfect sequence is identified. Here we present CloneQC, a lightweight software pipeline available as a free web server and as source code that performs quality control on sequenced clones. Input to the server is a list of desired sequences and forward and reverse reads for each clone. The server generates summary statistics (error rates and success rates target-by-target) and a detailed report of perfect clones. This software will be useful to laboratories conducting in-house DNA synthesis and is available at http://cloneqc.thruhere.net/ and as Berkeley Software Distribution (BSD) licensed source

Exciting new advances in oral cancer diagnosis: avenues to early detection

The prognosis for patients with oral squamous cell carcinoma remains poor in spite of advances in therapy of many other malignancies. Early diagnosis and treatment remains the key to improved patient survival. Because the scalpel biopsy for diagnosis is invasive and has potential morbidity, it is reserved for evaluating highly suspicious lesions and not for the majority of oral lesions which are clinically not suspicious. Furthermore, scalpel biopsy has significant interobserver and intraobserver variability in the histologic diagnosis of dysplasia. There is an urgent need to devise critical diagnostic tools for early detection of oral dysplasia and malignancy that are practical, noninvasive and can be easily performed in an out-patient set-up. Diagnostic tests for early detection include brush biopsy, toluidine blue staining, autofluorescence, salivary proteomics, DNA analysis, biomarkers and spectroscopy. This state of the art review critically examines these tests and assesses their value in identifying oral squamous cell carcinoma and its precursor lesions

Diagnostic aids in the screening of oral cancer

The World Health Organization has clearly indentified prevention and early detection as major objectives in the control of the oral cancer burden worldwide. At the present time, screening of oral cancer and its pre-invasive intra-epithelial stages, as well as its early detection, is still largely based on visual examination of the mouth. There is strong available evidence to suggest that visual inspection of the oral mucosa is effective in reducing mortality from oral cancer in individuals exposed to risk factors. Simple visual examination, however, is well known to be limited by subjective interpretation and by the potential, albeit rare, occurrence of dysplasia and early OSCC within areas of normal-looking oral mucosa. As a consequence, adjunctive techniques have been suggested to increase our ability to differentiate between benign abnormalities and dysplastic/malignant changes as well as to identify areas of dysplasia/early OSCC that are not visible to naked eye. These include the use of toluidine blue, brush biopsy, chemiluminescence and tissue autofluorescence. The present paper reviews the evidence supporting the efficacy of the aforementioned techniques in improving the identification of dysplastic/malignant changes of the oral mucosa. We conclude that available studies have shown promising results, but strong evidence to support the use of oral cancer diagnostic aids is still lacking. Further research with clear objectives, well-defined population cohorts, and sound methodology is strongly required

The benefits and risks of bacille Calmette-Guérin vaccination among infants at high risk for both tuberculosis and severe combined immunodeficiency: assessment by Markov model

BACKGROUND: Bacille Calmette-Guérin (BCG) vaccine is given to Canadian Aboriginal neonates in selected communities. Severe reactions and deaths associated with BCG have been reported among infants born with immunodeficiency syndromes. The main objective of this study was to estimate threshold values for severe combined immunodeficiency (SCID) incidence, above which BCG is associated with greater risk than benefit. METHODS: A Markov model was developed to simulate the natural histories of tuberculosis (TB) and SCID in children from birth to 14 years. The annual risk of tuberculous infection (ARI) and SCID incidence were varied in analyses. The model compared a scenario of no vaccination to intervention with BCG. Appropriate variability and uncertainty analyses were conducted. Outcomes included TB incidence and quality-adjusted life years (QALYs). RESULTS: In sensitivity analyses, QALYs were lower among vaccinated infants if the ARI was 0.1% and the rate of SCID was higher than 4.2 per 100,000. Assuming an ARI of 1%, this threshold increased to 41 per 100,000. In uncertainty analyses (Monte Carlo simulations) which assumed an ARI of 0.1%, QALYs were not significantly increased by BCG unless SCID incidence is 0. With this ARI, QALYs were significantly decreased among vaccinated children if SCID incidence exceeds 23 per 100,000. BCG is associated with a significant increase in QALYs if the ARI is 1%, and SCID incidence is below 5 per 100,000. CONCLUSION: The possibility that Canadian Aboriginal children are at increased risk for SCID has serious implications for continued BCG use in this population. In this context, enhanced TB Control – including early detection and treatment of infection – may be a safer, more effective alternative

Oral squamous cell cancer: early detection and the role of alcohol and smoking

Objective: Oral squamous cell carcinoma has a remarkable incidence worldwide and a fairly onerous prognosis, encouraging further research on factors that might modify disease outcome. Data sources: A web-based search for all types of articles published was initiated using Medline/Pub Med, with the key words such as oral cancer, alcohol consumption, genetic polymorphisms, tobacco smoking and prevention. The search was restricted to articles published in English, with no publication date restriction (last update 2010). Review Methods: In this review article, we approach the factors for a cytologic diagnosis during OSCC development and the markers used in modern diagnostic technologies as well. We also reviewed available studies of the combined effects of alcohol drinking and genetic polymorphisms on alcohol-related cancer risk. Results: The interaction of smoking and alcohol significantly increases the risk for aero-digestive cancers. The interaction between smoking and alcohol consumption seems to be responsible for a significant amount of disease. Conclusion: Published scientific data show promising pathways for the future development of more effective prognosis. There is a clear need for new prognostic indicators, which could be used in diagnostics and, therefore a better selection of the most effective treatment can be achieved

Diagnostic accuracy of oral cancer cytology in a pilot study

BACKGROUND: Recently, cytology has been applied to the diagnosis of oral lesions. We aimed to explore the diagnostic accuracy of oral cytology based on the histological diagnosis. METHODS: Histological diagnoses of 327 cases were classified as Negative, Borderline lesion –, Borderline lesion +, oral intraepithelial neoplasia/carcinoma in situ (OIN/CIS), or Positive. Cytological diagnoses were classified as NILM (negative for intraepithelial lesion or malignancy), LSIL (low-grade squamous intraepithelial lesion), HSIL (high-grade squamous intraepithelial lesion), or SCC (squamous cell carcinoma). The cytology slides were evaluated by 10 raters and the results were compared with the histology results. RESULTS: In 142 cases that were histologically negative, the number of NILM, LSIL, HSIL, and SCC and other malignancy was 77 (54.2%), 47 (34.3%), 8 (5.6%), and 10 (7.0%), respectively. Among 32 cases of Borderline lesion –, the number of NILM, LSIL, HSIL, and SCC and other malignancy was 11 (34.3%), 11 (34.3%), 9 (28.1%), and 1 (3.1%), respectively. Also, in 4 cases of Borderline lesion +, the number of NILM, LSIL, HSIL, and SCC and other malignancy was 2 (50.0%), 0 (0.0%), 0 (0.0%), 2 (50.0%), respectively. Among 12 cases of OIN/CIS, the number of NILM, LSIL, HSIL, and SCC and other malignancy was 1 (8.3%), 2 (16.7%), 4 (33.3%), and 5 cases (41.7%), respectively. Among 137 cases with a histological diagnosis of Positive, the number of NILM, LSIL, HSIL, and SCC and other malignancy was 7 (5.1%), 22 (16.1%), 19 (13.9%), and 89 (65.0%), respectively. Sensitivity, specificity, and positive predictive and negative predictive values were 93.5, 50.6, 62.4, and 89.8%, respectively, when the cytological diagnosis of Negative was assumed to be NILM; they were 77.8, 83.9, 81.0 and 81.1%, respectively, if the cytological diagnosis of Negative was assumed to be NILM and LSIL. The number of false-positive and false-negative diagnosis affected cases with LSIL and HSIL may indicate the difficulty in the cytological diagnosis of borderline lesions. While the negative predictive value was relatively high (89.8%) when cytological Negative was assumed to be NILM only. CONCLUSION: Histopathological examination should be recommended in cases with cytological diagnoses of LSIL, HSIL, and SCC