Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation

<p/> <p>Background</p> <p>Ongoing technological advances in genome sequencing are allowing bacterial genomes to be sequenced at ever-lower cost. However, nearly all of these new techniques concomitantly decrease genome quality, primarily due to the inability of their relatively short read lengths to bridge certain genomic regions, e.g., those containing repeats. Fragmentation of predicted open reading frames (ORFs) is one possible consequence of this decreased quality. In this study we quantify ORF fragmentation in draft microbial genomes and its effect on annotation efficacy, and we propose a solution to ameliorate this problem.</p> <p>Results</p> <p>A survey of draft-quality genomes in GenBank revealed that fragmented ORFs comprised > 80% of the predicted ORFs in some genomes, and that increased fragmentation correlated with decreased genome assembly quality. In a more thorough analysis of 25 <it>Streptomyces </it>genomes, fragmentation was especially enriched in some protein classes with repeating, multi-modular structures such as polyketide synthases, non-ribosomal peptide synthetases and serine/threonine kinases. Overall, increased genome fragmentation correlated with increased false-negative Pfam and COG annotation rates and increased false-positive KEGG annotation rates. The false-positive KEGG annotation rate could be ameliorated by linking fragmented ORFs using their orthologs in related genomes. Whereas this strategy successfully linked up to 46% of the total ORF fragments in some genomes, its sensitivity appeared to depend heavily on the depth of sampling of a particular taxon's variable genome.</p> <p>Conclusions</p> <p>Draft microbial genomes contain many ORF fragments. Where these correspond to the same gene they have particular potential to confound comparative gene content analyses. Given our findings, and the rapid increase in the number of microbial draft quality genomes, we suggest that accounting for gene fragmentation and its associated biases is important when designing comparative genomic projects.</p

No. 2: The Brain Drain of Health Professionals from Sub-Saharan Africa to Canada

Significant numbers of African-trained health workers migrate every year to developed countries including Canada. They leave severely crippled health systems in a region where life expectancy is only 50 years of age, 16 per cent of children die before their fifth birthday and the HIV/AIDS crisis continues to burgeon. The population of Sub-Saharan Africa (SSA) totals over 660 million, with a ratio of fewer than 13 physicians per 100,000. SSA has seen a resurgence of various diseases that were thought to be receding, while public health systems remain inadequately staffed. According to one report, the region needs approximately 700,000 physicians to meet the Millennium Development Goals. Understaffing results in stress and increased workloads. Many of the remaining health professionals are ill-motivated, not only because of their workload, but also because they are poorly paid, poorly equipped and have limited career opportunities. These, in turn, lead to a downward spiral where workers migrate, crippling the system, placing greater strain on the remaining workers who themselves seek to migrate out of the poor working conditions. The ultimate result is an incontestable crisis in health human resources throughout SSA, the region suffering most from the brain drain of health care professionals. The situation in SSA has become severe enough that the final report of the Joint Learning Initiative on Human Resources for Health – a two-year global initiative sponsored by a number of donors studying various aspects of human resources for health performance – has concluded that the future of global health and development in the 21st century lies in the management of the crisis in human resources for health. There is a considerable body of literature attesting to the fact that the migration of skilled professionals from developing to developed countries is large and increasing dramatically. While different experts espouse different reasons for the increase, all agree that it is happening. Developing countries are hit hardest by the brain drain as they lose sometimes staggering portions of their college-educated workers to wealthy countries which can better weather their relatively smaller losses of skilled workers. Highly skilled professionals account for 65 per cent of migrants moving to industrialized countries. The International Organization for Migration (IOM) estimates that about 20,000 Africans leave Africa every year to take up employment in industrialized countries. We do not know how many of these are health care professionals (largely because of inadequate systems for gathering such statistics in African countries).11 The World Health Organization (WHO), however, found that a quarter to two-thirds of health workers interviewed in a recent study expressed an intention to migrate. Historically, and specific to the SSA context, the brain drain has meant not only the exodus of human capital but financial resources as well, as African health care professionals left countries with their savings and reinvested very little of their foreign earnings back into the region. There is only recent evidence suggesting that, while the numbers of professionals leaving continue to increase, émigrés are slowly reinvesting some of their earnings back into their countries. Other research raises doubts about the value of such reinvestments, however, particularly when they are in the form of remittances that are generally private welfare transfers back to family members and are often used for consumption rather than for savings. In recognition of the enormous challenge posed by the international migration of health personnel to health systems in developing countries, the World Health Organization has proclaimed 2005-2015 the decade on human resources for health (HRH)

Local Health Departments’ Level of Engagement in Population Mental Health Promotion

Background: Mental health conditions are highly prevalent in the U.S. and are associated with physical health problems. Federal initiatives recognize mental health as a public health priority, and local health departments (LHDs) have been identified as partners to promote population mental health. Little is known, however, about the extent to which LHDs address mental health or how LHD officials perceive mental health as a public health concern. Purpose: To describe the cumulative level of LHDs’ engagement in activities to address population mental health and explore how LHD officials perceive their roles in promoting it. Methods: Module 2 of the 2013 National Profile of Local Health Departments Study (N=505) was used to develop a cumulative measure of LHD engagement in mental health activities. Univariate and bivariate analyses were performed to describe LHDs’ level of mental health activity and identify associated LHD characteristics. Semi-structured in-depth interviews were conducted with 30 LHD officials, audio-recorded, transcribed, and analyzed using thematic content analysis. Results: Over half (55.8%) of LHDs performed ≥1 mental health activities, and 21.2% performed ≥4. LHDs that provided primary care services were most engaged in mental health activities, with 30.4% performing ≥4 and 18.2% performing ≥6. LHD officials perceived mental health as a public health issue and felt community pressure to address it, but encountered barriers related to resources and organizational boundaries. Implications: LHDs might benefit from quality improvement and information sharing resources focused on population mental health promotion. Research should examine LHDs relationships with behavioral health departments and roles within broader social service systems

Restricted Quantum Theory of Affine Toda Solitons

We quantise the reduced theory obtained by substituting the soliton solutions of affine Toda theory into its symplectic form. The semi-classical S-matrix is found to involve the classical Euler dilogarithm.Comment: 10pp, LaTe

Deciphering the Microbiome: Integrating Theory, New Technologies, and Inclusive Science

The diversity and functional significance of microbiomes have become increasingly clear through the extensive sampling of Earth\u27s many habitats and the rapid adoption of new sequencing technologies. However, much remains unknown about what makes a “healthy” microbiome, how to restore a disrupted microbiome, and how microbiomes assemble. In December 2019, we convened a workshop that focused on how to identify potential “rules of life” that govern microbiome structure and function. This collection of mSystems Perspective pieces reflects many of the main challenges and opportunities in the field identified by both in-person and virtual workshop participants. By borrowing conceptual and theoretical approaches from other fields, including economics and philosophy, these pieces suggest new ways to dissect microbiome patterns and processes. The application of conceptual advances, including trait-based theory and community coalescence, is providing new insights on how to predict and manage microbiome diversity and function. Technological and analytical advances, including deep transfer learning, metabolic models, and advances in analytical chemistry, are helping us sift through complex systems to pinpoint mechanisms of microbiome assembly and dynamics. Integration of all of these advancements (theory, concepts, technology) across biological and spatial scales is providing dramatically improved temporal and spatial resolution of microbiome dynamics. This integrative microbiome research is happening in a new moment in science where academic institutions, scientific societies, and funding agencies must act collaboratively to support and train a diverse and inclusive community of microbiome scientists

No. 2: The Brain Drain of Health Professionals from Sub-Saharan Africa to Canada

Significant numbers of African-trained health workers migrate every year to developed countries including Canada. They leave severely crippled health systems in a region where life expectancy is only 50 years of age, 16 per cent of children die before their fifth birthday and the HIV/AIDS crisis continues to burgeon. The population of Sub-Saharan Africa (SSA) totals over 660 million, with a ratio of fewer than 13 physicians per 100,000. SSA has seen a resurgence of various diseases that were thought to be receding, while public health systems remain inadequately staffed. According to one report, the region needs approximately 700,000 physicians to meet the Millennium Development Goals. Understaffing results in stress and increased workloads. Many of the remaining health professionals are ill-motivated, not only because of their workload, but also because they are poorly paid, poorly equipped and have limited career opportunities. These, in turn, lead to a downward spiral where workers migrate, crippling the system, placing greater strain on the remaining workers who themselves seek to migrate out of the poor working conditions. The ultimate result is an incontestable crisis in health human resources throughout SSA, the region suffering most from the brain drain of health care professionals. The situation in SSA has become severe enough that the final report of the Joint Learning Initiative on Human Resources for Health – a two-year global initiative sponsored by a number of donors studying various aspects of human resources for health performance – has concluded that the future of global health and development in the 21st century lies in the management of the crisis in human resources for health. There is a considerable body of literature attesting to the fact that the migration of skilled professionals from developing to developed countries is large and increasing dramatically. While different experts espouse different reasons for the increase, all agree that it is happening. Developing countries are hit hardest by the brain drain as they lose sometimes staggering portions of their college-educated workers to wealthy countries which can better weather their relatively smaller losses of skilled workers. Highly skilled professionals account for 65 per cent of migrants moving to industrialized countries. The International Organization for Migration (IOM) estimates that about 20,000 Africans leave Africa every year to take up employment in industrialized countries. We do not know how many of these are health care professionals (largely because of inadequate systems for gathering such statistics in African countries).11 The World Health Organization (WHO), however, found that a quarter to two-thirds of health workers interviewed in a recent study expressed an intention to migrate. Historically, and specific to the SSA context, the brain drain has meant not only the exodus of human capital but financial resources as well, as African health care professionals left countries with their savings and reinvested very little of their foreign earnings back into the region. There is only recent evidence suggesting that, while the numbers of professionals leaving continue to increase, émigrés are slowly reinvesting some of their earnings back into their countries. Other research raises doubts about the value of such reinvestments, however, particularly when they are in the form of remittances that are generally private welfare transfers back to family members and are often used for consumption rather than for savings. In recognition of the enormous challenge posed by the international migration of health personnel to health systems in developing countries, the World Health Organization has proclaimed 2005-2015 the decade on human resources for health (HRH)

Digital Bridges Across Disciplinary, Practical and Pedagogical Divides: An Online Professional Master’s Program in Heritage Resource Management

Growth and diversification in heritage resource management (HRM) archaeology since the 1960s have created new demands for training the next generations of HRM leaders and for addressing persistent and counterproductive divisions between academic and applied archaeologies. The Simon Fraser University Department of Archaeology (SFU) has responded to these demands with an all-new, cohort-based, thesis-focused graduate program created by and for HRM professionals. The program’s target audience is HRM practitioners who hold Bachelor’s credentials, have initiated promising careers in HRM, and desire advanced, research-focused degrees to enable their professional capacity and upward mobility. The SFU program is structured and focused to provide intensive, predominantly online training in the four essential dimensions of HRM: law and policy, ethics and practice, business management, and research design and methods. The program has been successful through initial cohort cycles and in attracting HRM industry interest in collaboration. Industry-academic partnerships in cognate disciplines have proved effective in comparable circumstances but remain underdeveloped as bases for planning and delivering state-of-the-art training in applied archaeology and the broader field of HRM. Critical next steps in program development entail the identification of attributes of HRM futures desired by all or most HRM stakeholders and the collaborative pursuit of those desired futures

Children Are Not Just Small Adults: The Urgent Need for High-Quality Trial Evidence in Children

Terry Klassen and colleagues discuss a new study examining whether children and adults with drug-resistant partial epilepsy respond differently to antiepileptic drugs

Toward a fully implantable ecosystem for adaptive neuromodulation in humans: Preliminary experience with the CorTec BrainInterchange device in a canine model

This article describes initial work toward an ecosystem for adaptive neuromodulation in humans by documenting the experience of implanting CorTec\u27s BrainInterchange (BIC) device in a beagle canine and using the BCI2000 environment to interact with the BIC device. It begins with laying out the substantial opportunity presented by a useful, easy-to-use, and widely available hardware/software ecosystem in the current landscape of the field of adaptive neuromodulation, and then describes experience with implantation, software integration, and post-surgical validation of recording of brain signals and implant parameters. Initial experience suggests that the hardware capabilities of the BIC device are fully supported by BCI2000, and that the BIC/BCI2000 device can record and process brain signals during free behavior. With further development and validation, the BIC/BCI2000 ecosystem could become an important tool for research into new adaptive neuromodulation protocols in humans