The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Prospective Cohort Study

Osteoclasts are specialized cells derived from the monocyte/macrophage haematopoietic lineage that develop and adhere to bone matrix, then secrete acid and lytic enzymes that degrade it in a specialized, extracellular compartment. Discovery of the RANK signalling pathway in the osteoclast has provided insight into the mechanisms of osteoclastogenesis and activation of bone resorption, and how hormonal signals impact bone structure and mass. Further study of this pathway is providing the molecular basis for developing therapeutics to treat osteoporosis and other diseases of bone loss.

Osteoclast differentiation and activation

The TNF and TNF receptor superfamilies: integrating mammalian biology.

Osteoporosis, a disease endemic in Western society, typically reflects an imbalance in skeletal turnover so that bone resorption exceeds bone formation. Bone resorption is the unique function of the osteoclast, and anti-osteoporosis therapy to date has targeted this cell. The osteoclast is a specialized macrophage polykaryon whose differentiation is principally regulated by macrophage colony-stimulating factor, RANK ligand, and osteoprotegerin. Reflecting integrin-mediated signals, the osteoclast develops a specialized cytoskeleton that permits it to establish an isolated microenvironment between itself and bone, wherein matrix degradation occurs by a process involving proton transport. Osteopetrotic mutants have provided a wealth of information about the genes that regulate the differentiation of osteoclasts and their capacity to resorb bone.

https://science.sciencemag.org/content/sci/289/5484/1504.full.pdf

Bone Resorption by Osteoclasts

Certain types of the Human Papillomavirus (HPV) are sexually transmitted and highly associated with development of cervical dysplasia and cervical cancer but the distribution of HPV infection in the North, particularly amongst First Nations, Metis, and Inuit peoples, is little known. The purposes of the study are to identify the prevalence of type-specific HPV infections and the association of different HPV types with cervical dysplasia among women in Northern Canada. This was a cross-sectional study with attendants of the routine or scheduled Pap testing program in the Northwest Territories (NWT), Nunavut, Labrador and Yukon, Canada. Approximately half of each sample was used for Pap test and the remaining was used for HPV genotyping using a Luminex-based method. Pap test results, HPV types, and demographic information were linked for analyses. Results from 14,598 specimens showed that HPV infection was approximately 50% higher among the Aboriginal than the non-Aboriginal population (27.6% vs. 18.5%). Although the most common HPV type detected was HPV 16 across region, the prevalence of other high risk HPV types was different. The age-specific HPV prevalence among Aboriginal showed a ‘U’ shape which contrasted to non-Aboriginal. The association of HPV infection with cervical dysplasia was similar in both Aboriginal and non-Aboriginal populations. The HPV prevalence was higher in Northern Canada than in other Areas in Canada. The prevalence showed a higher rate of other high risk HPV infections but no difference of HPV 16/18 infections among Aboriginal in comparison with non-Aboriginal women. This study provides baseline information on HPV prevalence that may assist in surveillance and evaluation systems to track and assess HPV vaccine programs.

/pdf/the-prevalence-of-human-papillomavirus-and-its-impact-on-1vmtwn32u9.pdf

The prevalence of human papillomavirus and its impact on cervical dysplasia in Northern Canada

BACKGROUND The Public Health Agency of Canada (PHAC) estimates that, in 2011, 25% of people living with HIV in Canada were undiagnosed Hesitation to seek testing may arise from fear, stigma and discrimination associated with the HIV diagnosis and related risk behaviours This guide is designed to complement existing efforts to support care providers involved in HIV testing, in order to reduce the number of undiagnosed HIV infections in Canada APPROACH PHAC commissioned a literature review and consulted with provinces and territories, and key stakeholders, including people living with HIV/AIDS, academics, nurses, physicians, professional associations, non-governmental organizations, policy-makers, community workers, and legal and ethical experts As a result, the recommendations outlined in the guide are based on the most up-to-date evidence and expert opinion SCREENING AND TESTING GUIDE The consideration and discussion of HIV testing should be made a component of routine periodic medical care Offering HIV testing routinely can help normalize testing, and address the multiple barriers to reducing the number of undiagnosed cases in Canada Begin with a brief explanation to the client on how HIV is transmitted: through unprotected sex, the sharing of drug-use equipment, and from a pregnant mother to her child Clients can then consider their own situation and indicate whether they would like to have an HIV test Upon request, a risk assessment may be conducted As with other tests, testing is voluntary and verbal consent is sufficient Negative test results provide an opportunity to remind clients of those practices that can help them maintain an HIV-negative status There are a range of referrals and resources available to assist clients in reducing at-risk activities and maintaining a negative status Those who are part of a couple should be encouraged to discuss HIV testing with their partners so they're not unknowingly involved in a serodiscordant relationship Positive test results should always be provided in person and ideally by the initial care provider who has information resources and support referrals at the ready An HIV positive diagnosis can be difficult news; it is important to take the time to discuss the results and answer any questions the client might have Focus on positive messages by highlighting advances in HIV care, treatment and support Note that HIV is now considered a chronic illness, and people living with HIV can live long, active and healthy lives Advise the client about strategies for managing HIV and link them to care Provide risk reduction information to prevent transmission Make the client aware that positive test results will be shared confidentially with the local public health department, which can assist in notifying previous and current partners of the need to be tested while protecting the client's anonymity and privacy Strategies for informing past, current and future partners can be reviewed If not already completed with the HIV test, clients should be tested for other STIs, hepatitis B and C, and tuberculosis

https://www.canada.ca/content/dam/phac-aspc/migration/phac-aspc/publicat/ccdr-rmtc/13vol39/briefs-resumes/assets/pdf/ccdrv39i01a01-eng.pdf

Brief - synopsis of the human immunodeficiency virus (hiv) screening and testing guide.

After several years of decline, reported gonorrhoea rates in Canada have recently increased substantially. National goals for gonorrhoea control were developed in 1997, but it appears that reliance on secular trends is insufficient to attain the goal of eliminating locally transmitted infection by Neisseria gonorrhoeae by 2010. We have examined disease surveillance reports from 1994 to 2001 inclusive to assess demographic and epidemiologic trends in reported cases of gonococcal infection. Since 1997, reported cases have increased by 53% among men and 33% among women. The largest proportion of cases in women is in those aged 15-24; the most dramatic increase in males has been among those aged 30-39. Reasons for the resurgence remain unclear, but disease reports indicate that renewed attention to enhanced surveillance and targeted prevention are essential for gonorrhoea control in Canada.

Gonorrhoea resurgence in Canada

Readers of CMAJ were first alerted to the rising incidence of ciprofloxacin-resistant Neisseria gonorrhoeae infection in Canada last year.[1][1] On the basis of this trend, the recommended treatment for gonorrhea in some areas of Canada and for some infected patients has changed.

The reported rate

/pdf/gonorrhea-treatment-guidelines-in-canada-2004-update-3zto7bixpr.pdf

Gonorrhea treatment guidelines in Canada: 2004 update

Syphilis is a sexually transmitted disease (STD) caused by the spirochete Treponema pallidum which is restricted to humans. Transmission occurs primarily during the infectious phase which consists of primary, secondary, and early latent syphilis. Primary syphilis is characterized by a painless ulcer approximately 3 weeks after exposure. Secondary syphilis is characterized by a generalized eruption 4 to 6 weeks after the primary stage in untreated patients. After weeks or several months, secondary manifestations resolve and about one-third of untreated cases become clinically latent sometimes leading to late manifestations involving the cardiovascular system, the central nervous system, skin, bones, and viscera. A diagnosis of early latent syphilis is made when the clinical situation and nontreponemal antibody titres reflect recent infection for which aggressive follow-up is necessary. Perinatal transmission can occur, especially during the infectious phase. The diagnosis of syphilis relies on clinical examination, darkfield demonstration of spirochetes in lesion exudate, nonspecific treponemal antibody tests (rapid plasma reagin test and Venereal Disease Research Laboratory test), and specific treponemal antibody tests (microhemagglutination for Treponema pallidum and fluorescent treponemal antibody absorption test). The current treatment of choice is intramuscular benzathine penicillin G.

Tom Wong

Papers

The prevalence of human papillomavirus and its impact on cervical dysplasia in Northern Canada

Brief - synopsis of the human immunodeficiency virus (hiv) screening and testing guide.

Gonorrhoea resurgence in Canada

Gonorrhea treatment guidelines in Canada: 2004 update

Mass treatment/prophylaxis during an outbreak of infectious syphilis in Vancouver, British Columbia.