Complete genome sequences of two Helicobacter pylori strains from a Canadian Arctic Aboriginal community

We report here the complete genome sequences of two Amerind Helicobacter pylori strains from Aklavik, Northwest Territories, Canada. One strain contains extra iron-cofactored urease genes and ~140 rearrangements in its chromosome relative to other described strains (typically differing from one another by <10 rearrangements), suggesting that it represents a novel lineage of H. pylori

Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life

The field of genomics has benefited greatly from its "openness" approach to data sharing. However, with the increasing volume of sequence information being created and stored and the growing number of international genomics efforts, the equity of openness is under question. The United Nations Convention of Biodiversity aims to develop and adopt a standard policy on access and benefit-sharing for sequence information across signatory parties. This standardization will have profound implications on genomics research, requiring a new definition of open data sharing. The redefinition of openness is not unwarranted, as its limitations have unintentionally introduced barriers of engagement to some, including Indigenous Peoples. This commentary provides an insight into the key challenges of openness faced by the researchers who aspire to protect and conserve global biodiversity, including Indigenous flora and fauna, and presents immediate, practical solutions that, if implemented, will equip the genomics community with both the diversity and inclusivity required to respectfully protect global biodiversity

Fresh takes on five health data sharing domains: Quality, privacy, equity, incentives, and sustainability

As entities around the world invest in repositories and other infrastructure to facilitate health data sharing, scalable solutions to data sharing challenges are needed. We conducted semi-structured interviews with 24 experts to explore views on potential issues and policy options related to health data sharing. In this Perspective, we describe and contextualize unconventional insights shared by our interviewees relevant to issues in five domains: data quality, privacy, equity, incentives, and sustainability. These insights question a focus on granular quality metrics for gatekeeping; challenge enthusiasm for maximalist risk disclosure practices; call attention to power dynamics that potentially compromise the patient's voice; encourage faith in the sharing proclivities of new generations of scientists; and endorse accounting for personal disposition in the selection of long-term partners. We consider the merits of each insight with the broad goal of encouraging creative thinking to address data sharing challenges

Qualitative data sharing and re-use for socio-environmental systems research: A synthesis of opportunities, challenges, resources and approaches

Researchers in many disciplines, both social and natural sciences, have a long history of collecting and analyzing qualitative data to answer questions that have many dimensions, to interpret other research findings, and to characterize processes that are not easily quantified. Qualitative data is increasingly being used in socio-environmental systems research and related interdisciplinary efforts to address complex sustainability challenges. There are many scientific, descriptive and material benefits to be gained from sharing and re-using qualitative data, some of which reflect the broader push toward open science, and some of which are unique to qualitative research traditions. However, although open data availability is increasingly becoming an expectation in many fields and methodological approaches that work on socio-environmental topics, there remain many challenges associated the sharing and re-use of qualitative data in particular. This white paper discusses opportunities, challenges, resources and approaches for qualitative data sharing and re-use for socio-environmental research. The content and findings of the paper are a synthesis and extension of discussions that began during a workshop funded by the National Socio-Environmental Synthesis Center (SESYNC) and held at the Center Feb. 28-March 2, 2017. The structure of the paper reflects the starting point for the workshop, which focused on opportunities, challenges and resources for qualitative data sharing, and presents as well the workshop outputs focused on developing a novel approach to qualitative data sharing considerations and creating recommendations for how a variety of actors can further support and facilitate qualitative data sharing and re-use. The white paper is organized into five sections to address the following objectives: (1) Define qualitative data and discuss the benefits of sharing it along with its role in socio-environmental synthesis; (2) Review the practical, epistemological, and ethical challenges regarding sharing such data; (3) Identify the landscape of resources available for sharing qualitative data including repositories and communities of practice (4) Develop a novel framework for identifying levels of processing and access to qualitative data; and (5) Suggest roles and responsibilities for key actors in the research ecosystem that can improve the longevity and use of qualitative data in the future.This work was supported by the National Socio-Environmental Synthesis Center (SESYNC) under funding received from the National Science Foundation DBI-1052875

The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics

Access and benefits sharing of genetic resources and associated traditional knowledge in northern Canada: understanding the legal environment and creating effective research agreements

Background. Research in northern Canada focused on Aboriginal peoples has historically benefited academia with little consideration for the people being researched or their traditional knowledge (TK). Although this attitude is changing, the complexity of TK makes it difficult to develop mechanisms to preserve and protect it. Protecting TK becomes even more important when outside groups become interested in using TK or materials with associated TK. In the latter category are genetic resources, which may have commercial value and are the focus of this article. Objective. This article addresses access to and use of genetic resources and associated TK in the context of the historical power-imbalances in research relationships in Canadian north. Design. Review. Results. Research involving genetic resources and TK is becoming increasingly relevant in northern Canada. The legal framework related to genetic resources and the cultural shift of universities towards commercial goals in research influence the environment for negotiating research agreements. Current guidelines for research agreements do not offer appropriate guidelines to achieve mutual benefit, reflect unequal bargaining power or take the relationship between parties into account. Conclusions. Relational contract theory may be a useful framework to address the social, cultural and legal hurdles inherent in creating research agreements

Challenges created by data dissemination and access restrictions when attempting to address community concerns: individual privacy versus public wellbeing

Background: Population health data are vital for the identification of public health problems and the development of public health strategies. Challenges arise when attempts are made to disseminate or access anonymised data that are deemed to be potentially identifiable. In these situations, there is debate about whether the protection of an individual&#x0027;s privacy outweighs potentially beneficial public health initiatives developed using potentially identifiable information. While these issues have an impact at planning and policy levels, they pose a particular dilemma when attempting to examine and address community concerns about a specific health problem. Methods: Research currently underway in northern Canadian communities on the frequency of Helicobacter pylori infection and associated diseases, such as stomach cancer, is used in this article to illustrate the challenges that data controls create on the ability of researchers and health officials to address community concerns. Results: Barriers are faced by public health professionals and researchers when endeavouring to address community concerns; specifically, provincial cancer surveillance departments and community-driven participatory research groups face challenges related to data release or access that inhibit their ability to effectively address community enquiries. The resulting consequences include a limited ability to address misinformation or to alleviate concerns when dealing with health problems in small communities. Conclusions: The development of communication tools and building of trusting relationships are essential components of a successful investigation into community health concerns. It may also be important to consider that public wellbeing may outweigh the value of individual privacy in these situations. As such, a re-evaluation of data disclosure policies that are applicable in these circumstances should be considered

The effects of different smoking patterns in pregnancy on perinatal outcomes in the Southampton Women’s Survey

Maternal smoking during pregnancy has established associations with poor perinatal outcomes. Among continuing pregnant smokers, harm-reduction strategies have been suggested, including temporary cessation of smoking during pregnancy, also known as partial quitting. Support for this strategy, however, remains limited. Six hundred and ninety-seven women in the Southampton Women’s Survey who smoked at their last menstrual period were categorised into sustained quitters, partial quitters (quit in either the first or third trimester but not both) or sustained smokers (continued to smoke throughout pregnancy). In regression models, compared with infants born to sustained smokers, infants born to sustained quitters and partial quitters were heavier at birth by β = 0.64 standard deviations (SD) (WHO z-score) (95% CI: 0.47–0.80) and 0.48 SD (WHO z-score) (95% CI: 0.24–0.72) respectively, adjusted for confounders, with similar patterns seen for other anthropometric measures (head circumference and crown–heel length). Sustained quitters had longer gestations by β = 3.5 days (95% CI: 1.8–5.2) compared with sustained smokers, but no difference was seen for partial quitters. While sustained quitting remains the most desired outcome for pregnant smokers, partial quitting should be explored as a strategy to reduce some of the harmful effects of smoking on offspring in those who cannot achieve sustained quitting

A Randomized Controlled Trial Comparing Sequential with Triple Therapy for Helicobacter pylori in an Aboriginal Community in the Canadian North

BACKGROUND: Helicobacter pylori infection occurs more frequently in Arctic Aboriginal settings than elsewhere in North America and Europe. Research aimed at reducing health risks from H pylori infection has been conducted in the Aboriginal community of Aklavik, Northwest Territories