Impact of Stochastic Convection on the Ensemble Transform

Abstract The impact of stochastic convection on ensembles produced using the ensemble transform (ET) initial perturbation scheme is examined. This note compares the behavior of ensemble forecasts based only on initial ET perturbations with the behavior of ensemble forecasts based on the ET initial perturbations and forecasts that include stochastic convection. It is illustrated that despite the fact that stochastic convection occurs only after the forecast integrations have started, it induces changes in the initial perturbations as well. This is because the ET is a "cycling" scheme, in which previous short-term forecasts are used to produce the initial perturbations for the current forecast. The stochastic convection scheme induces rapid perturbation growth in regions where convection is active, primarily in the tropics. When combined with the ET scheme, this results in larger initial perturbation variance in the tropics, and, because of a global constraint on total initial perturbation variance, smaller initial perturbation variance in the extratropics. Thus, the inclusion of stochastic convection helps to mitigate a problem found in the practical implementation of the ET, namely, that of too little initial variance in the tropics and too much in the extratropics. Various skill scores show that stochastic convection improves ensemble performance in the tropics, with little impact to modest improvement in the extratropics. Experiments performed using the initial perturbations from the control ensemble run but forecast integrations using the stochastic convection scheme indicate that the improved performance of the stochastic convection ensemble at early forecast times is due to both "indirect" changes in the initial perturbations and "direct" changes in the forecast. At later forecast times, it appears that most of the improvement can be gained through stochastic convection alone

Examining the predictability of the Stratospheric Sudden Warming of January 2013 using multiple NWP systems

The first multi-model study to estimate the predictability of a boreal Sudden Stratospheric Warming (SSW) is performed using five NWP systems. During the 2012-2013 boreal winter, anomalous upward propagating planetary wave activity was observed towards the end of December, which followed by a rapid deceleration of the westerly circulation around 2 January 2013, and on 7 January 2013 the zonal mean zonal wind at 60°N and 10 hPa reversed to easterly. This stratospheric dynamical activity was followed by an equatorward shift of the tropospheric jet stream and by a high pressure anomaly over the North Atlantic, which resulted in severe cold conditions in the UK and Northern Europe. In most of the five models, the SSW event was predicted 10 days in advance. However, only some ensemble members in most of the models predicted weakening of westerly wind when the models were initialized 15 days in advance of the SSW. Further dynamical analysis of the SSW shows that this event was characterized by the anomalous planetary wave-1 amplification followed by the anomalous wave-2 amplification in the stratosphere, which resulted in a split vortex occurring between 6 January 2013 and 8 January 2013. The models have some success in reproducing wave-1 activity when initialized 15 days in advance, they but generally failed to produce the wave-2 activity during the final days of the event. Detailed analysis shows that models have reasonably good skill in forecasting tropospheric blocking features that stimulate wave-2 amplification in the troposphere, but they have limited skill in reproducing wave-2 amplification in the stratosphere

Identifying best approaches for engaging patients and family members in health informatics initiatives: a case study of the Group Priority Sort technique

Background Patient engagement strategies in health service delivery have become more common in recent years. However, many healthcare organizations are challenged in identifying the best methods to engage patients in health information technology (IT) initiatives. Engaging with important stakeholders to identify effective opportunities can inform the development of a resource that addresses this issue and supports organizations in their endeavors. The purpose of this paper is to share our experience and lessons learned from applying a novel consensus-building technique in order to identify key elements for effective patient engagement in health IT initiatives. This will be done through a case study approach. Methods Patients, family members of patients, health professionals, researchers, students, vendor representatives and individuals who work in health IT roles in health organizations were engaged through a one-day symposium in Toronto, Canada in September, 2018. During the symposium, the Group Priority Sort technique was used to obtain structured feedback from symposium attendees in the context of small group discussions. Descriptive statistics and a content analysis were undertaken to analyze the data collected through the Group Priority Sort as well as participant feedback following the symposium. Results A total of 37 participants attended the symposium from a variety of settings and organizations. Using the Group Priority Sort technique, 30 topics were classified by priority to be included in a future resource. Participant feedback pertaining to the symposium and research methods was largely positive. Several areas of improvement, such as clarity of items, were identified from this case study. Conclusions The Group Priority Sort technique was an efficient method for obtaining valuable suggestions from a diverse group of stakeholders, including patients and family members. The specific priorities and feedback obtained from the symposium will be incorporated into a resource for healthcare organizations to aid them in engaging patients in health IT initiatives. Additionally, five important considerations were identified when conducting future work with the Group Priority Sort technique and are outlined in this paper

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Species-specific basecallers improve actual accuracy of nanopore sequencing in plants

Background: Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is basecalling, the process of converting raw electrical signals produced by the sequencing device into nucleotide sequences. This is challenging as current basecallers are primarily based on mixtures of model species for training. Here we utilise both ONT PromethION and higher accuracy PacBio Sequel II HiFi sequencing on two plants, Phebalium stellatum and Xanthorrhoea johnsonii, to train species-specifc basecaller models with the aim of improving per-base accuracy. We investigate sequencing accuracies achieved by ONT basecallers and assess accuracy gains by training single-species and species-specifc basecaller models. We also evaluate accuracy gains from ONT’s improved fowcells (R10.4, FLO-PRO112) and sequencing kits (SQK-LSK112). For the truth dataset for both model training and accuracy assessment, we developed highly accurate, contiguous diploid reference genomes with PacBio Sequel II HiFi reads. Results: Basecalling with ONT Guppy 5 and 6 super-accurate gave almost identical results, attaining read accuracies of 91.96% and 94.15%. Guppy’s plant-specifc model gave highly mixed results, attaining read accuracies of 91.47% and 96.18%. Species-specifc basecalling models improved read accuracy, attaining 93.24% and 95.16% read accuracies. R10.4 sequencing kits also improve sequencing accuracy, attaining read accuracies of 95.46% (super-accurate) and 96.87% (species-specifc). Conclusions: The use of a single mixed-species basecaller model, such as ONT Guppy super-accurate, may be reducing the accuracy of nanopore sequencing, due to conflicting genome biology within the training dataset and study species. Training of single-species and genome-specifc basecaller models improves read accuracy. Studies that aim to do large-scale long-read genotyping would primarily benefit from training their own basecalling models. Such studies could use sequencing accuracy gains and improving bioinformatics tools to improve study outcomes

Secondary sources

Secondary Sources, a Dublin Dance Festival 2010 commission, by choreographer Liz Roche that brings together renowned collaborators and performers from the US, Australia, New Zealand, UK, Spain and Ireland. Liz Roche creates a tapestry of movements that reflect on the performers' embodied connections between primary and secondary sources of inspiration, exploring the influences that we carry in our bodies that come from other people, places and events. The work began nearly two years ago in New York as a quartet made during a residency at Movement Research NY and has been developing ever since through an on-going process between Liz Roche and an exceptional group of dancers/collaborators who are joined in performance by musician/composers Justin Carroll and Edward RosenBerg with lighting by Nick McCall and costumes by Jeni Roddy.

Identifying best approaches for engaging patients and family members in health informatics initiatives: a case study of the Group Priority Sort technique

Abstract Background Patient engagement strategies in health service delivery have become more common in recent years. However, many healthcare organizations are challenged in identifying the best methods to engage patients in health information technology (IT) initiatives. Engaging with important stakeholders to identify effective opportunities can inform the development of a resource that addresses this issue and supports organizations in their endeavors. The purpose of this paper is to share our experience and lessons learned from applying a novel consensus-building technique in order to identify key elements for effective patient engagement in health IT initiatives. This will be done through a case study approach. Methods Patients, family members of patients, health professionals, researchers, students, vendor representatives and individuals who work in health IT roles in health organizations were engaged through a one-day symposium in Toronto, Canada in September, 2018. During the symposium, the Group Priority Sort technique was used to obtain structured feedback from symposium attendees in the context of small group discussions. Descriptive statistics and a content analysis were undertaken to analyze the data collected through the Group Priority Sort as well as participant feedback following the symposium. Results A total of 37 participants attended the symposium from a variety of settings and organizations. Using the Group Priority Sort technique, 30 topics were classified by priority to be included in a future resource. Participant feedback pertaining to the symposium and research methods was largely positive. Several areas of improvement, such as clarity of items, were identified from this case study. Conclusions The Group Priority Sort technique was an efficient method for obtaining valuable suggestions from a diverse group of stakeholders, including patients and family members. The specific priorities and feedback obtained from the symposium will be incorporated into a resource for healthcare organizations to aid them in engaging patients in health IT initiatives. Additionally, five important considerations were identified when conducting future work with the Group Priority Sort technique and are outlined in this paper