Genomic surveillance of SARS-CoV-2 using long-range PCR primers

IntroductionWhole Genome Sequencing (WGS) of the SARS-CoV-2 virus is crucial in the surveillance of the COVID-19 pandemic. Several primer schemes have been developed to sequence nearly all of the ~30,000 nucleotide SARS-CoV-2 genome, using a multiplex PCR approach to amplify cDNA copies of the viral genomic RNA. Midnight primers and ARTIC V4.1 primers are the most popular primer schemes that can amplify segments of SARS-CoV-2 (400 bp and 1200 bp, respectively) tiled across the viral RNA genome. Mutations within primer binding sites and primer-primer interactions can result in amplicon dropouts and coverage bias, yielding low-quality genomes with ‘Ns’ inserted in the missing amplicon regions, causing inaccurate lineage assignments, and making it challenging to monitor lineage-specific mutations in Variants of Concern (VoCs).MethodsIn this study we used a set of seven long-range PCR primer pairs to sequence clinical isolates of SARS-CoV-2 on Oxford Nanopore sequencer. These long-range primers generate seven amplicons approximately 4500 bp that covered whole genome of SARS-CoV-2. One of these regions includes the full-length S-gene by using a set of flanking primers. We also evaluated the performance of these long-range primers with Midnight primers by sequencing 94 clinical isolates in a Nanopore flow cell.Results and discussionUsing a small set of long-range primers to sequence SARS-CoV-2 genomes reduces the possibility of amplicon dropout and coverage bias. The key finding of this study is that long range primers can be used in single-molecule sequencing of RNA viruses in surveillance of emerging variants. We also show that by designing primers flanking the S-gene, we can obtain reliable identification of SARS-CoV-2 variants

Humanism in the Age of COVID-19: Renewing Focus on Communication and Compassion

The global COVID-19 pandemic has become one of the largest clinical and operational challenges faced by emergency medicine, and our EDs continue to see increased volumes of infected patients, many of whom are not only ill, but acutely aware and fearful of their circumstances and potential mortality. Given this, there may be no more important time to focus on staff-patient communication and expression of compassion.However, many of the techniques usually employed by emergency clinicians to provide comfort to patients and their families are made more challenging or impossible by the current circumstances. Geriatric ED patients, who are at increased risk of severe disease, are particularly vulnerable to the effects of isolation.Despite many challenges, emergency clinicians have at their disposal a myriad of tools that can still be used to express compassion and empathy to their patients. Placing emphasis on using these techniques to maximize humanism in the care of COVID-19 patients during this crisis has the potential to bring improvements to ED patient care well after this pandemic has passed

Risk Factors for Major Early Adverse Events Related to Cardiac Catheterization in Children and Young Adults With Pulmonary Hypertension: An Analysis of Data From the IMPACT (Improving Adult and Congenital Treatment) Registry.

BACKGROUND: Cardiac catheterization is the gold standard for assessment and follow-up of patients with pulmonary hypertension (PH). To date, there are limited data about the factors that influence the risk of catastrophic adverse events after catheterization in this population. METHODS AND RESULTS: A retrospective multicenter cohort study was performed to measure risk of catastrophic adverse outcomes after catheterization in children and young adults with PH and identify risk factors for these outcomes. All catheterizations in children and young adults, aged 0 to 21 years, with PH at hospitals submitting data to the IMPACT (Improving Adult and Congenital Treatment) registry between January 1, 2011, and December 31, 2015, were studied. Using mixed-effects multivariable regression, we assessed the association between prespecified subject-, procedure-, and center-level covariates and the risk of death, cardiac arrest, or mechanical circulatory support during or after cardiac catheterization. A total of 8111 procedures performed in 7729 subjects at 77 centers were studied. The observed risk of the composite outcome was 1.4%, and the risk of death before discharge was 5.2%. Catheterization in prematurely born neonates and nonpremature infants was associated with increased risk of catastrophic adverse event, as was precatheterization treatment with inotropes and lower systemic arterial saturation. Secondary analyses demonstrated the following: (1) increasing volumes of catheterization in patients with PH were associated with reduced risk of composite outcome (odds ratio, 0.8 per 10 procedures; CONCLUSIONS: Young patients with PH are a high-risk population for diagnostic and interventional cardiac catheterization. Hospital experience with PH is associated with reduced risk, independent of total catheterization case volume

Severe leptospirosis in tropical Australia: optimising intensive care unit management to reduce mortality

BACKGROUND: Severe leptospirosis can have a case-fatality rate of over 50%, even with intensive care unit (ICU) support. Multiple strategies-including protective ventilation and early renal replacement therapy (RRT)-have been recommended to improve outcomes. However, management guidelines vary widely around the world and there is no consensus on the optimal approach. METHODOLOGY/PRINCIPAL FINDINGS: All cases of leptospirosis admitted to the ICU of Cairns Hospital in tropical Australia between 1998 and 2018 were retrospectively reviewed. The patients' demographics, presentation, management and clinical course were examined. The 55 patients' median (interquartile range (IQR)) age was 47 (32-62) years and their median (IQR) APACHE III score was 67 (48-105). All 55 received appropriate antibiotic therapy, 45 (82%) within the first 6 hours. Acute kidney injury was present in 48/55 (87%), 18/55 (33%) required RRT, although this was usually not administered until traditional criteria for initiation were met. Moderate to severe acute respiratory distress syndrome developed in 37/55 (67%), 32/55 (58%) had pulmonary haemorrhage, and mechanical ventilation was required in 27/55 (49%). Vasopressor support was necessary in 34/55 (62%). Corticosteroids were prescribed in 20/55 (36%). The median (IQR) fluid balance in the initial three days of ICU care was +1493 (175-3567) ml. Only 2/55 (4%) died, both were elderly men with multiple comorbidities. CONCLUSION: In patients with severe leptospirosis in tropical Australia, prompt ICU support that includes early antibiotics, protective ventilation strategies, conservative fluid resuscitation, traditional thresholds for RRT initiation and corticosteroid therapy is associated with a very low case-fatality rate. Prospective studies are required to establish the relative contributions of each of these interventions to optimal patient outcomes

Development and implementation of a mobile device-based pediatric electronic decision support tool as part of a national practice standardization project

OBJECTIVE: Implementing evidence-based practices requires a multi-faceted approach. Electronic clinical decision support (ECDS) tools may encourage evidence-based practice adoption. However, data regarding the role of mobile ECDS tools in pediatrics is scant. Our objective is to describe the development, distribution, and usage patterns of a smartphone-based ECDS tool within a national practice standardization project. MATERIALS AND METHODS: We developed a smartphone-based ECDS tool for use in the American Academy of Pediatrics, Value in Inpatient Pediatrics Network project entitled Reducing Excessive Variation in the Infant Sepsis Evaluation (REVISE). The mobile application (app), PedsGuide, was developed using evidence-based recommendations created by an interdisciplinary panel. App workflow and content were aligned with clinical benchmarks; app interface was adjusted after usability heuristic review. Usage patterns were measured using Google Analytics. RESULTS: Overall, 3805 users across the United States downloaded PedsGuide from December 1, 2016, to July 31, 2017, leading to 14 256 use sessions (average 3.75 sessions per user). Users engaged in 60 442 screen views, including 37 424 (61.8%) screen views that displayed content related to the REVISE clinical practice benchmarks, including hospital admission appropriateness (26.8%), length of hospitalization (14.6%), and diagnostic testing recommendations (17.0%). Median user touch depth was 5 [IQR 5]. DISCUSSION: We observed rapid dissemination and in-depth engagement with PedsGuide, demonstrating feasibility for using smartphone-based ECDS tools within national practice improvement projects. CONCLUSIONS: ECDS tools may prove valuable in future national practice standardization initiatives. Work should next focus on developing robust analytics to determine ECDS tools\u27 impact on medical decision making, clinical practice, and health outcomes

The Effective Lagrangian in the Randall-Sundrum Model and Electroweak Physics

We consider the two-brane Randall-Sundrum (RS) model with bulk gauge fields. We carefully match the bulk theory to a 4D low-energy effective Lagrangian. In addition to the four-fermion operators induced by KK exchange we find that large negative S and T parameters are induced in the effective theory. This is a tree-level effect and is a consequence of the shapes of the W and Z wave functions in the bulk. Such effects are generic in extra dimensional theories where the standard model (SM) gauge bosons have non-uniform wave functions along the extra dimension. The corrections to precision electroweak observables in the RS model are mostly dominated by S. We fit the parameters of the RS model to the experimental data and find somewhat stronger bounds than previously obtained; however, the standard model bound on the Higgs mass from precision measurements can only be slightly relaxed in this theory.Comment: 16 pages, LaTeX, 1 figure included, uses JHEP.cls, extended introduction, added reference

On Machine-Learned Classification of Variable Stars with Sparse and Noisy Time-Series Data

With the coming data deluge from synoptic surveys, there is a growing need for frameworks that can quickly and automatically produce calibrated classification probabilities for newly-observed variables based on a small number of time-series measurements. In this paper, we introduce a methodology for variable-star classification, drawing from modern machine-learning techniques. We describe how to homogenize the information gleaned from light curves by selection and computation of real-numbered metrics ("feature"), detail methods to robustly estimate periodic light-curve features, introduce tree-ensemble methods for accurate variable star classification, and show how to rigorously evaluate the classification results using cross validation. On a 25-class data set of 1542 well-studied variable stars, we achieve a 22.8% overall classification error using the random forest classifier; this represents a 24% improvement over the best previous classifier on these data. This methodology is effective for identifying samples of specific science classes: for pulsational variables used in Milky Way tomography we obtain a discovery efficiency of 98.2% and for eclipsing systems we find an efficiency of 99.1%, both at 95% purity. We show that the random forest (RF) classifier is superior to other machine-learned methods in terms of accuracy, speed, and relative immunity to features with no useful class information; the RF classifier can also be used to estimate the importance of each feature in classification. Additionally, we present the first astronomical use of hierarchical classification methods to incorporate a known class taxonomy in the classifier, which further reduces the catastrophic error rate to 7.8%. Excluding low-amplitude sources, our overall error rate improves to 14%, with a catastrophic error rate of 3.5%.Comment: 23 pages, 9 figure

Effects of Allergen Sensitization on Response to Therapy in Children with Eosinophilic Esophagitis

Background: In children with eosinophilic esophagitis (EoE) foods are the most common disease triggers, but environmental allergens are also suspected culprits. Objective: To determine the effects of environmental allergen sensitization on response to treatment in children with EoE in the southeastern United States. Methods: Patients 2 to 18 years old who were referred to the Arkansas Children’s Hospital Eosinophilic Gastrointestinal Disorders Clinic from January 2012 to January 2016 were enrolled in a prospective, longitudinal cohort study with collection of demographics, clinical symptoms, medical history, allergy sensitization profiles, and response to treatment over time. Comparisons were made between complete responders (peak esophageal eosinophil count \u3c 15 per high-power field [HPF]) and nonresponders (\u3e 25 eosinophils per HPF) after treatment with diet elimination alone, swallowed corticosteroids alone, or diet elimination and swallowed corticosteroids. Sensitization patterns to environmental allergens found in the southeastern United States were analyzed for the effect on treatment response. Results: A total of 223 individuals were enrolled. Of these, 182 had environmental allergy profiling and at least one endoscopy while receiving proton pump inhibitor (PPI) therapy. Twenty-nine individuals had PPI-responsive EoE and were excluded from further analysis, leaving 123 individuals with none-PPI-responsive EoE who were further analyzed; 72 (58.5%) were complete responders and 33 (26.8%) were nonresponders. Seventeen individuals (13.8%) were partial responders (≥ 1 but ≤ 25 eosinophils per HPF) and excluded from further analysis. Nonresponders were more likely to be sensitized to perennial allergens (P = .02). There was no significant difference in response based on seasonal allergen sensitization. Individuals with mold or cockroach sensitization were more likely to fail combination diet and swallowed corticosteroid treatment (P = .02 and P = .002). Conclusion: Perennial allergen and mold sensitization may lead to nonresponse to EoE treatment in some patients. Additional studies are needed to further understand the effect of environmental allergens on EoE

Extreme debris disk variability : exploring the diverse outcomes of large asteroid impacts during the era of terrestrial planet formation

The most dramatic phases of terrestrial planet formation are thought to be oligarchic and chaotic growth, on timescales of up to 100─200 Myr, when violent impacts occur between large planetesimals of sizes up to protoplanets. Such events are marked by the production of large amounts of debris, as has been observed in some exceptionally bright and young debris disks (termed extreme debris disks). Here we report five years of Spitzer measurements of such systems around two young solar-type stars: ID8 and P1121. The short-term (weekly to monthly) and long-term (yearly) disk variability is consistent with the aftermaths of large impacts involving large asteroid-sized bodies. We demonstrate that an impact-produced clump of optically thick dust, under the influence of the dynamical and viewing geometry effects, can produce short-term modulation in the disk light curves. The long-term disk flux variation is related to the collisional evolution within the impact-produced fragments once released into a circumstellar orbit. The time-variable behavior observed in the P1121 system is consistent with a hypervelocity impact prior to 2012 that produced vapor condensates as the dominant impact product. Two distinct short-term modulations in the ID8 system suggest two violent impacts at different times and locations. Its long-term variation is consistent with the collisional evolution of two different populations of impact-produced debris dominated by either vapor condensates or escaping boulders. The bright, variable emission from the dust produced in large impacts from extreme debris disks provides a unique opportunity to study violent events during the era of terrestrial planet formation

Low knowledge of newborn danger signs among pregnant women in Papua New Guinea and implications for health seeking behaviour in early infancy – findings from a longitudinal study

Background: Globally, 2.5 million babies die in the first 28 days of life each year with most of these deaths occurring in low- and middle-income countries. Early recognition of newborn danger signs is important in prompting timely care seeking behaviour. Little is known about women’s knowledge of newborn danger signs in Papua New Guinea. This study aims to assess this knowledge gap among a cohort of women in East New Britain Province. Methods: This study assessed knowledge of newborn danger signs (as defined by the World Health Organization) at three time points from a prospective cohort study of women in East New Britain Province, factors associated with knowledge of danger signs after childbirth were assessed using logistic regression. This study includes quantitative and qualitative interview data from 699 pregnant women enrolled at their first antenatal clinic visit, followed up after childbirth (n = 638) and again at one-month post-partum (n = 599). Results: Knowledge of newborn danger signs was very low. Among the 638 women, only 9.4% knew three newborn danger signs after childbirth and only one knew all four essential danger signs defined by Johns Hopkins University ‘Birth Preparedness and Complication Readiness’ Index. Higher knowledge scores were associated with higher gravidity, income level, partner involvement in antenatal care, and education. Conclusion: Low levels of knowledge of newborn danger signs among pregnant women are a potential obstacle to timely care-seeking in rural Papua New Guinea. Antenatal and postnatal education, and policies that support enhanced education and decision-making powers for women and their families, are urgently needed