PTF11kx: A Type Ia Supernova with Hydrogen Emission Persisting After 3.5 Years

The optical transient PTF11kx exhibited both the characteristic spectral features of Type Ia supernovae (SNe Ia) and the signature of ejecta interacting with circumstellar material (CSM) containing hydrogen, indicating the presence of a nondegenerate companion. We present an optical spectrum at $1342$ days after peak from Keck Observatory, in which the broad component of H$\alpha$ emission persists with a similar profile as in early-time observations. We also present $Spitzer$ IRAC detections obtained $1237$ and $1818$ days after peak, and an upper limit from $HST$ ultraviolet imaging at $2133$ days. We interpret our late-time observations in context with published results - and reinterpret the early-time observations - in order to constrain the CSM's physical parameters and compare to theoretical predictions for recurrent nova systems. We find that the CSM's radial extent may be several times the distance between the star and the CSM's inner edge, and that the CSM column density may be two orders of magnitude lower than previous estimates. We show that the H$\alpha$ luminosity decline is similar to other SNe with CSM interaction, and demonstrate how our infrared photometry is evidence for newly formed, collisionally heated dust. We create a model for PTF11kx's late-time CSM interaction and find that X-ray reprocessing by photoionization and recombination cannot reproduce the observed H$\alpha$ luminosity, suggesting that the X-rays are thermalized and that H$\alpha$ radiates from collisional excitation. Finally, we discuss the implications of our results regarding the progenitor scenario and the geometric properties of the CSM for the PTF11kx system.Comment: 15 pages, 8 figures, 3 tables; submitted to Ap

End of life hospitalisations differ for older Australian women according to death trajectory: a longitudinal data linkage study

BACKGROUND: Hospitalisations are the prime contributor to healthcare expenditure, with older adults often identified as high hospital users. Despite the apparent high use of hospitals at the end of life, limited evidence currently exists regarding reasons for hospitalisation. Understanding complex end of life care needs is required for future health care planning as the global population ages. This study aimed to investigate patterns of hospitalisation in the last year of life by cause of death (COD) as well as reasons for admission and short-term predictors of hospital use. METHODS: Survey data from 1,205 decedents from the 1921-1926 cohort of the Australian Longitudinal Study on Women's Health were matched with the state-based hospital records and the National Death Index. Hospital patterns based on COD were graphically summarised and multivariate logistic regression models examined the impact of short-term predictors of length of stay (LOS). RESULTS: 85 % of women had at least one admission in the last year of life; and 8 % had their first observed admission during this time. Reasons for hospitalisation, timing of admissions and LOS differed by COD. Women who died of cancer, diabetes and 'other' causes were admitted earlier than women who died of organ failure, dementia and influenza. Women who died of organ failure overall spent the longest time in hospital, and women with cancer had the highest median LOS. Longer LOS was associated with previous short- and medium-term- hospitalisations and type of hospital separation. CONCLUSIONS: Reducing acute care admissions and LOS at the end of life is complex and requires a shift in perceptions and treatment regarding end of life care and chronic disease management

A population-level data linkage study to explore the association between health facility level factors and unintended pregnancy in Bangladesh

The objective of this study was to investigate the effects of health facility-level factors, including the availability of long-acting modern contraceptives (LAMC) at the nearest health facility and its distance from women’s homes, on the occurrence of unintended pregnancy that resulted in a live birth. We analysed the 2017/18 Bangladesh Demographic and Health Survey data linked with the 2017 Bangladesh Health Facility Survey. The weighted sample comprised 5051 women of reproductive age, who had at least one live birth within 3 years of the survey. The outcome variable was women’s intention to conceive at their most recent pregnancy that ended with a live birth. The major explanatory variables were the health facility level factors. A multi-level multinomial logistic regression model was used to assess the association of the outcome variable with explanatory variables adjusting for individual, household, and community-level factors. Nearly 21% of the total respondents reported that their most recent live birth was unintended at conception. Better health facility management systems and health facility infrastructure were found to be 14–30% protective of unintended pregnancy that resulted in a live birth. LAMC availability at the nearest health facility was associated with a 31% reduction (95% CI 0.50–0.92) in the likelihood of an unwanted pregnancy that resulted in a live birth. Health facility readiness to provide LAMC was also associated with a 14–16% reduction in unintended pregnancies that ended with a birth. The likelihood of unintended pregnancy that resulted in a live birth increased around 20–22% with the increased distance of the nearest health facility providing LAMC from the women’s homes.The availability of health facilities near women’s homes and access to LAMC can significantly reduce unintended pregnancy. Policies and programs to ensure access and affordability of LAMC across current health facilities and to increase the number of health facilities are recommended

Evaluating the use of high-fidelity simulators during mock neonatal resuscitation scenarios in trying to improve confidence in residents

Objective: The purpose of this study was to investigate the effect of the use of high-fidelity simulators with multidisciplinary teaching on self-reported confidence in residents. Methods: A total of 26 residents participated in a session led by a pediatric faculty member and a Neonatal Intensive Care Unit transport nurse using a high-fidelity pediatric simulator. Multiple scenarios were presented and each resident took turns in various roles. Pre-intervention surveys based on a 5-point Likert-type scale were given before the scenarios and were compared to the results of identical post-intervention surveys. Results: Statistically significant (p \u3c 0.05) pre to post gains for self-confidence were observed. Improvements in confidence were analyzed using the mean difference. The largest improvement in confidence was seen in the ability to treat neonatal respiratory arrest. This was followed by the ability to supervise/run a code, and the ability to place an umbilical venous catheter. Conclusion: These results revealed that high-fidelity simulation-based training has significant positive gains in residents’ self-reported confidence

VarSight: prioritizing clinically reported variants with binary classification algorithms.

BackgroundWhen applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient's phenotypes. Typically, this is done through annotation, filtering, and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance.MethodsWe tested the application of classification algorithms that ingest variant annotations along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network.ResultsWe treated the classifiers as variant prioritization systems and compared them to four variant prioritization algorithms and two single-measure controls. We showed that the trained classifiers outperformed all other tested methods with the best classifiers ranking 72% of all reported variants and 94% of reported pathogenic variants in the top 20.ConclusionsWe demonstrated how freely available binary classification algorithms can be used to prioritize variants even in the presence of real-world variability. Furthermore, these classifiers outperformed all other tested methods, suggesting that they may be well suited for working with real rare disease patient datasets

A novel biologically-based approach to evaluating soil phosphorus availability across complex landscapes

Plants employ a range of strategies to increase phosphorus (P) availability in soil. Current soil P extraction methods (e.g. Olsen P), however, often fail to capture the potential importance of rhizosphere processes in supplying P to the plant. This has led to criticism of these standard approaches, especially in non-agricultural soils of low P status and when comparing soil types across diverse landscapes. Similarly, more complex soil P extraction protocols (e.g. Hedley sequential fractionation) lack functional significance from a plant ecology perspective. In response to this, we present a novel procedure using a suite of established extraction protocols to explore the concept of a protocol that characterizes P pools available via plant and microbial P acquisition mechanisms. The biologically based P (BBP) extraction was conducted by using four extractions in parallel: (1) 10 mM CaCl2 (soluble P); (2) 10 mM citric acid (chelate extractable P); (3) phytase and phosphatase solution (enzyme extractable organic P); (4) 1 M HCl (mineral occluded P). To test the protocol, we conducted the analyses on a total of 204 soil samples collected as part of a UK national ecosystem survey (Countryside Survey) in 1998 and repeated again in 2007. In the survey, Olsen P showed a net decline in national soil P levels during this 10 year period. In agreement with these results, soluble P, citrate extractable P and mineral occluded P were all found to decrease over the 10 year study period. In contrast, enzyme extractable organic P increased over the same period likely due to the accumulation of organic P in the mineral soil. The method illustrates a noted shift in P pools over the 10 year period, but no net loss of P from the system. This new method is simple and inexpensive and therefore has the potential to greatly improve our ability to characterise and understand changes in soil P status across complex landscapes

Forces associated with launch into space do not impact bone fracture healing

Segmental bone defects (SBDs) secondary to trauma invariably result in a prolonged recovery with an extended period of limited weight bearing on the affected limb. Soldiers sustaining blast injuries and civilians sustaining high energy trauma typify such a clinical scenario. These patients frequently sustain composite injuries with SBDs in concert with extensive soft tissue damage. For soft tissue injury resolution and skeletal reconstruction a patient may experience limited weight bearing for upwards of 6 months. Many small animal investigations have evaluated interventions for SBDs. While providing foundational information regarding the treatment of bone defects, these models do not simulate limited weight bearing conditions after injury. For example, mice ambulate immediately following anesthetic recovery, and in most cases are normally ambulating within 1-3 days post-surgery. Thus, investigations that combine disuse with bone healing may better test novel bone healing strategies. To remove weight bearing, we have designed a SBD rodent healing study in microgravity (µG) on the International Space Station (ISS) for the Rodent Research-4 (RR-4) Mission, which launched February 19, 2017 on SpaceX CRS-10 (Commercial Resupply Services). In preparation for this mission, we conducted an end-to-end mission simulation consisting of surgical infliction of SBD followed by launch simulation and hindlimb unloading (HLU) studies. In brief, a 2 mm defect was created in the femur of 10 week-old C57BL6/J male mice (n = 9-10/group). Three days after surgery, 6 groups of mice were treated as follows: 1) Vivarium Control (maintained continuously in standard cages); 2) Launch Negative Control (placed in the same spaceflight-like hardware as the Launch Positive Control group but were not subjected to launch simulation conditions); 3) Launch Positive Control (placed in spaceflight-like hardware and also subjected to vibration followed by centrifugation); 4) Launch Positive Experimental (identical to Launch Positive Control group, but placed in qualified spaceflight hardware); 5) Hindlimb Unloaded (HLU, were subjected to HLU immediately after launch simulation tests to simulate unloading in spaceflight); and 6) HLU Control (single housed in identical HLU cages but not suspended). Mice were euthanized 28 days after launch simulation and bone healing was examined via micro-Computed Tomography (µCT). These studies demonstrated that the mice post-surgery can tolerate launch conditions. Additionally, forces and vibrations associated with launch did not impact bone healing (p = .3). However, HLU resulted in a 52.5% reduction in total callus volume compared to HLU Controls (p = .0003). Taken together, these findings suggest that mice having a femoral SBD surgery tolerated the vibration and hypergravity associated with launch, and that launch simulation itself did not impact bone healing, but that the prolonged lack of weight bearing associated with HLU did impair bone healing. Based on these findings, we proceeded with testing the efficacy of FDA approved and novel SBD therapies using the unique spaceflight environment as a novel unloading model on SpaceX CRS-10

The complete costs of genome sequencing: a microcosting study in cancer and rare diseases from a single center in the United Kingdom

Abstract: Purpose: The translation of genome sequencing into routine health care has been slow, partly because of concerns about affordability. The aspirational cost of sequencing a genome is $1000, but there is little evidence to support this estimate. We estimate the cost of using genome sequencing in routine clinical care in patients with cancer or rare diseases. Methods: We performed a microcosting study of Illumina-based genome sequencing in a UK National Health Service laboratory processing 399 samples/year. Cost data were collected for all steps in the sequencing pathway, including bioinformatics analysis and reporting of results. Sensitivity analysis identified key cost drivers. Results: Genome sequencing costs £6841 per cancer case (comprising matched tumor and germline samples) and £7050 per rare disease case (three samples). The consumables used during sequencing are the most expensive component of testing (68–72$1000/genome in a single laboratory. This aspirational sequencing cost will likely only be achieved if consumable costs are considerably reduced and sequencing is performed at scale