Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel

Albiglutide and cardiovascular outcomes in patients with type 2 diabetes and cardiovascular disease (Harmony Outcomes): a double-blind, randomised placebo-controlled trial

Background: Glucagon-like peptide 1 receptor agonists differ in chemical structure, duration of action, and in their effects on clinical outcomes. The cardiovascular effects of once-weekly albiglutide in type 2 diabetes are unknown. We aimed to determine the safety and efficacy of albiglutide in preventing cardiovascular death, myocardial infarction, or stroke. Methods: We did a double-blind, randomised, placebo-controlled trial in 610 sites across 28 countries. We randomly assigned patients aged 40 years and older with type 2 diabetes and cardiovascular disease (at a 1:1 ratio) to groups that either received a subcutaneous injection of albiglutide (30–50 mg, based on glycaemic response and tolerability) or of a matched volume of placebo once a week, in addition to their standard care. Investigators used an interactive voice or web response system to obtain treatment assignment, and patients and all study investigators were masked to their treatment allocation. We hypothesised that albiglutide would be non-inferior to placebo for the primary outcome of the first occurrence of cardiovascular death, myocardial infarction, or stroke, which was assessed in the intention-to-treat population. If non-inferiority was confirmed by an upper limit of the 95% CI for a hazard ratio of less than 1·30, closed testing for superiority was prespecified. This study is registered with ClinicalTrials.gov, number NCT02465515. Findings: Patients were screened between July 1, 2015, and Nov 24, 2016. 10 793 patients were screened and 9463 participants were enrolled and randomly assigned to groups: 4731 patients were assigned to receive albiglutide and 4732 patients to receive placebo. On Nov 8, 2017, it was determined that 611 primary endpoints and a median follow-up of at least 1·5 years had accrued, and participants returned for a final visit and discontinuation from study treatment; the last patient visit was on March 12, 2018. These 9463 patients, the intention-to-treat population, were evaluated for a median duration of 1·6 years and were assessed for the primary outcome. The primary composite outcome occurred in 338 (7%) of 4731 patients at an incidence rate of 4·6 events per 100 person-years in the albiglutide group and in 428 (9%) of 4732 patients at an incidence rate of 5·9 events per 100 person-years in the placebo group (hazard ratio 0·78, 95% CI 0·68–0·90), which indicated that albiglutide was superior to placebo (p<0·0001 for non-inferiority; p=0·0006 for superiority). The incidence of acute pancreatitis (ten patients in the albiglutide group and seven patients in the placebo group), pancreatic cancer (six patients in the albiglutide group and five patients in the placebo group), medullary thyroid carcinoma (zero patients in both groups), and other serious adverse events did not differ between the two groups. There were three (<1%) deaths in the placebo group that were assessed by investigators, who were masked to study drug assignment, to be treatment-related and two (<1%) deaths in the albiglutide group. Interpretation: In patients with type 2 diabetes and cardiovascular disease, albiglutide was superior to placebo with respect to major adverse cardiovascular events. Evidence-based glucagon-like peptide 1 receptor agonists should therefore be considered as part of a comprehensive strategy to reduce the risk of cardiovascular events in patients with type 2 diabetes. Funding: GlaxoSmithKline

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

South Park Blocks Area Development Strategy: Priorities and Actions to Strengthen Neighborhood Identity

Past and current planning efforts by the City of Portland, such as the South Park Blocks Urban Renewal Area and the West End plan, have sought to promote new mixed-use development through increasing the residential density and investment in the area. The West End plan focused primarily on the area north of SW Salmon Street and the urban renewal area currently does not have a standing advisory committee to represent the Downtown neighborhood’s interests. This project consists of a neighborhood analysis to distill the identity of the area, an identification of the opportunities and challenges to development, and a strategy for DNA to be an active participant in the development of the South Park Blocks Area (SPBA). This project was conducted under the supervision of Deborah Howe, Barry Messer, and Ethan Seltzer

Treatment of Post-Traumatic Stress Disorder Nightmares at a Veterans Affairs Medical Center

The effectiveness of medications for PTSD in general has been well studied, but the effectiveness of medicatio.ns prescribed specifically for post-traumatic stress disorder (PTSD) nightmares is less well known. This retrospective chart review examined the efficacy of various medications used in actual treatment of PTSD nightmares at one Veteran Affairs Hospital. Records at the Salem, VA Veterans Affairs Medical Center (VAMC) were examined from 2009 to 2013 to check for the efficacy of actual treatments used in comparis.on with treatments suggested in three main review articles. The final sample consisted of 327 patients and 478 separate medication trials involving 21 individual medications plus 13 different medication combinations. The three most frequently utilized medications were prazosin (107 trials), risperidone (81 trials), and quetiapine (72 trials). Five medications had 20 or more trials with successful results (partial to full nightmare cessation) in >50% of trials: risperidone (77%, 1.0–6.0 mg), clonidine (63%, 0.1–2.0 mg), quetiapine (50%, 12.5–800.0 mg), mirtazapine (50%; 7.5–30.0 mg), and terazosin (64%, 50.0–300.0 mg). Notably, olanzapine (2.5–10.0) was successful (full remission) in all five prescription trials in five separate patients. Based on the clinical results, the use of risperidone, clonidine, terazosin, and olanzapine warrants additional investigation in clinically controlled trials as medications prescribed specifically for PTSD nightmares

UAV Recharging Opportunities and Policies for Sensor Networks

Recharging sensor networks using Unmanned Aerial Vehicles (UAVs) provides a possible method for increasing network lifetime. In this paper, we evaluate that approach, determining how much of a benefit it provides and under what conditions. We base our simulations and field experiments on data collected from charging with our UAV-based wireless power transfer system, which has similar transfer ranges and efficiencies as other such systems. We determine that a UAV can increase the network lifetime up to 290% compared to no recharging, that the UAV should recharge 30% of the sensor node battery capacity at one time for the maximum benefit, and that the UAV should recharge the lowest powered node until the network reaches a size of approximately 306 nodes at which point it should recharge the sink.We also examine how the sensor network can aid this through sink selection. The policy varies as network size increases, with a static approach working well until 200 nodes, and then either a perimeter or heuristic approach works best.These results inform future use of UAVs in recharging and working with sensor networks

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat.

Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes

Crucial role for pathology residents in laboratory self-inspection, a single Institute's experience.

BackgroundTraining in patient safety, quality, and management is a key component of Graduate Medical Education (GME) training in all specialties. However, residency programs, especially Pathology programs, often find it challenging to create strong learning opportunities in these areas.ObjectivesFocused quality assurance (QA) projects are one approach to teach and engage trainees in these key areas. Residents have been historically involved in different QA projects in our department but mainly in small secondary roles. Leading a large QA project that can enhance residents' management skills and improve clinical operations in our laboratory was the main objective of our project.DescriptionA new process for laboratory self-inspection led by residents was implemented that simulates the exact process of a formal outside College of American Pathologists (CAP) inspection. We aim to prove that resident-led QA activities not only have profound educational benefit but can also result in significant performance and operational improvement.ResultsFor this paper, we focus on the Histology laboratory since the ramifications from the self-inspection process during a three year period were profound leading to change in management, workflow changes, and notable improvement in staff morale.ConclusionThe self-inspection process exposed the residents to operational issues and corrective actions that provided them the opportunity to take a more active role in laboratory management and helped prepare them for post-graduation challenges. It also helped the department identify and rectify many operational issues, confirmed by the enumeration of CAP deficiencies and significant improvement of staff morale

Crucial role for pathology residents in laboratory self-inspection, a single Institute's experience.

BackgroundTraining in patient safety, quality, and management is a key component of Graduate Medical Education (GME) training in all specialties. However, residency programs, especially Pathology programs, often find it challenging to create strong learning opportunities in these areas.ObjectivesFocused quality assurance (QA) projects are one approach to teach and engage trainees in these key areas. Residents have been historically involved in different QA projects in our department but mainly in small secondary roles. Leading a large QA project that can enhance residents' management skills and improve clinical operations in our laboratory was the main objective of our project.DescriptionA new process for laboratory self-inspection led by residents was implemented that simulates the exact process of a formal outside College of American Pathologists (CAP) inspection. We aim to prove that resident-led QA activities not only have profound educational benefit but can also result in significant performance and operational improvement.ResultsFor this paper, we focus on the Histology laboratory since the ramifications from the self-inspection process during a three year period were profound leading to change in management, workflow changes, and notable improvement in staff morale.ConclusionThe self-inspection process exposed the residents to operational issues and corrective actions that provided them the opportunity to take a more active role in laboratory management and helped prepare them for post-graduation challenges. It also helped the department identify and rectify many operational issues, confirmed by the enumeration of CAP deficiencies and significant improvement of staff morale