Novel multi-cluster workflow system to support real-time HPC-enabled epidemic science: Investigating the impact of vaccine acceptance on COVID-19 spread

We present MacKenzie, a HPC-driven multi-cluster workflow system that was used repeatedly to configure and execute fine-grained US national-scale epidemic simulation models during the COVID-19 pandemic. Mackenzie supported federal and Virginia policymakers, in real-time, for a large number of "what-if" scenarios during the COVID-19 pandemic, and continues to be used to answer related questions as COVID-19 transitions to the endemic stage of the disease. MacKenzie is a novel HPC meta-scheduler that can execute US-scale simulation models and associated workflows that typically present significant big data challenges. The meta-scheduler optimizes the total execution time of simulations in the workflow, and helps improve overall human productivity. As an exemplar of the kind of studies that can be conducted using Mackenzie, we present a modeling study to understand the impact of vaccine-acceptance in controlling the spread of COVID-19 in the US. We use a 288 million node synthetic social contact network (digital twin) spanning all 50 US states plus Washington DC, comprised of 3300 counties, with 12 billion daily interactions. The highly-resolved agent-based model used for the epidemic simulations uses realistic information about disease progression, vaccine uptake, production schedules, acceptance trends, prevalence, and social distancing guidelines. Computational experiments show that, for the simulation workload discussed above, MacKenzie is able to scale up well to 10K CPU cores. Our modeling results show that, when compared to faster and accelerating vaccinations, slower vaccination rates due to vaccine hesitancy cause averted infections to drop from 6.7M to 4.5M, and averted total deaths to drop from 39.4K to 28.2K across the US. This occurs despite the fact that the final vaccine coverage is the same in both scenarios. We also find that if vaccine acceptance could be increased by 10% in all states, averted infections could be increased from 4.5M to 4.7M (a 4.4% improvement) and total averted deaths could be increased from 28.2K to 29.9K (a 6% improvement) nationwide.

Development and validation of the Atri-Risk Conduction Index risk score to predict risk of atrial fibrillation after typical atrial flutter ablation

BACKGROUND

Identification of patients at risk for atrial fibrillation (AF) after typical atrial flutter (tAFL) ablation is important to guide monitoring and treatment.

OBJECTIVE

The purpose of this study was to create and validate a risk score to predict AF after tAFL ablation METHODS: We identified patients who underwent tAFL ablation with no AF history between 2017 and 2022 and randomly allocated to derivation and validation cohorts. We collected clinical variables and measured conduction parameters in sinus rhythm on an electrophysiology recording system (CardioLab, GE Healthcare). Univariate and multivariate logistic regressions (LogR) were used to evaluate association with AF development.

RESULTS

A total of 242 consecutive patients (81% male; mean age 66 ± 11 years) were divided into derivation (n =142) and validation (n = 100) cohorts. Forty-two percent developed AF over median follow-up of 330 days. In multivariate LogR (derivation cohort), proximal to distal coronary sinus time (pCS-dCS) ≥70 ms (odds ratio [OR] 16.7; 95% confidence interval [CI] 5.6-49), pCS time ≥36 ms (OR 4.5; 95% CI 1.5-13), and CHADS2-VASc score ≥3 (OR 4.3; 95% CI 1.6-11.8) were independently associated with new AF during follow-up. The Atri-Risk Conduction Index (ARCI) score was created with 0 as minimal and 4 as high-risk using pCS-dCS ≥70 ms = 2 points; pCS ≥36 ms = 1 point; and CHADS2-VASc score ≥3 = 1 point. In the validation cohort, 0% of patients with ARCI score = 0 developed AF, whereas 89% of patients with ARCI score = 4 developed AF.

CONCLUSION

We developed and validated a risk score using atrial conduction parameters and clinical risk factors to predict AF after tAFL ablation. It stratifies low-, moderate-, and high-risk patients and may be helpful in individualizing approaches to AF monitoring and anticoagulation.

Guidance for the gastrointestinal evaluation and management of iron deficiency in Sub-Saharan Africa

BACKGROUND

Over 30% of the world's population is anaemic, with a significant proportion of these being iron deficient. As iron deficiency (ID) anaemia in men and post-menopausal women is mostly caused by gastrointestinal blood loss or malabsorption, the initial evaluation of a patient with ID anaemia involves referral to a gastroenterologist. The current drive towards patient blood management in sub-Saharan Africa (SSA)prescribes that we regulate not only the use of blood transfusion but also the management of patients in whom the cause of iron loss or inadequate iron absorption is sought. Recommendations have been developed to: (i) aid clinicians in the evaluation of suspected gastrointestinal iron loss and iron malabsorption, and often a combination of these; (ii) improve clinical outcomes for patients with gastrointestinal causes of ID; (iii) provide current, evidence-based, context-specific recommendations for use in the management of ID; and (iv) conserve resources by ensuring rational utilisation of blood and blood products.

METHOD

Development of the guidance document was facilitated by the Gastroenterology Foundation of Sub-Saharan Africa and the South African Gastroenterology Society. The consensus recommendations are based on a rigorous process involving 21 experts in gastroenterology and haematology in SSA. Following discussion of the scope and purpose of the guidance document among the experts, an initial review of the literature and existing guidelines was undertaken. Thereafter, draft recommendation statements were produced to fulfil the outlined purpose of the guidance document. These were reviewed in a round-table discussion and were subjected to two rounds of anonymised consensus voting by the full committee in an electronic Delphi exercise during 2022 using the online platform, Research Electronic Data Capture. Recommendations were modified by considering feedback from the previous round, and those reaching a consensus of over 80% were incorporated into the final document. Finally, 44 statements in the document were read and approved by all members of the working group.

CONCLUSION

The recommendations incorporate six areas, namely: general recommendations and practice, Helicobacter pylori, coeliac disease, suspected small bowel bleeding, inflammatory bowel disease, and preoperative care. Implementation of the recommendations is aimed at various levels from individual practitioners to healthcare institutions, departments and regional, district, provincial and national platforms. It is intended that the recommendations spur the development of centre-specific guidelines and that they are integrated with the relevant patient blood management protocols. Integration of the recommendations is intended to promote optimal evaluation and management of patients with ID, regardless of the presence of anaemia.

Motifs in SARS-CoV-2 evolution

We present a novel framework enhancing the prediction of whether novel lineage poses the threat of eventually dominating the viral population. The framework is based purely on genomic sequence data, without requiring prior established biological analysis. Its building blocks are sets of coevolving sites in the alignment (motifs), identified via coevolutionary signals. The collection of such motifs forms a relational structure over the polymorphic sites. Motifs are constructed using distances quantifying the coevolutionary coupling of pairs and manifest as coevolving clusters of sites. We present an approach to genomic surveillance based on this notion of relational structure. Our system will issue an alert regarding a lineage, based on its contribution to drastic changes in the relational structure. We then conduct a comprehensive retrospective analysis of the COVID-19 pandemic based on SARS-CoV-2 genomic sequence data in GISAID from October 2020 to September 2022, across 21 lineages and 27 countries with weekly resolution. We investigate the performance of this surveillance system in terms of its accuracy, timeliness, and robustness. Lastly, we study how well each lineage is classified by such a system.

Predicting metalwork following posterior fixation of thoracolumbar fractures

OBJECTIVES

Surgical fusion through posterior instrumentation and pedicle screw placement is a long established method for stabilising traumatic spinal fractures. Post-surgical complications include infection and metal work failure, the most common aetiology of which is pedicle screw fracture. Metal work failure rates vary from 15% to 60%. Research relating to factors which predict metal work failure in post-traumatic thoracolumbar spinal fixation is lacking. This study aimed to identify potential risk factors for metalwork failure in patients who had posterior fixation for traumatic thoracolumbar spine fractures.

METHODS

This retrospective cohort analysis was conducted by interrogating the hospital database for neurosurgical post-traumatic thoracolumbar fixation cases between 2015 and 2018 with at least 2 years follow up. Data was collected through electronic medical notes and PACS. Nineteen different patient factors (gender, age, mechanism of injury, presence of concomitant injury spinal or extra-spinal injury, pedicle cross-sectional area, pedicle cancellous bone density, pedicle total bone density, vertebral body bone density, erector spinae muscle density and lumbar spine subcutaneous fat thickness, Charlson comorbidity index, fracture location, surgical approach, long/short segment fixation, whether decompression was done, whether the index level was fixed, and presence of wound infection) were compared.

RESULTS

We identified 92 patients with 97 operations, and 9 cases of metal work failure. Two factors were statistically significantly associated with metal work failure: Post-operative wound infection (p = 0.029) and lumbar spine fat thickness (p = 0.024). The relative risk calculated in patients with a wound infection was 3.76. Lumbar spine fat thickness was on average 11.9 mm greater than patients not experiencing metal work failure.

CONCLUSIONS

This study has identified two factors associated with increased rates of metal work failure: Post-operative wound infection and lumbar spine fat thickness. When assessing surgical candidates these factors may be incorporated into surgical planning.

A radiological study of the natural history of diffuse idiopathic skeletal hyperostosis (DISH): a story of incomplete fusion

Introduction: DISH is an ankylosing disease, when fractured can be challenging to manage. A retrospective radiological study was conducted to evaluate the natural history and radiological characteristics of DISH on Computed tomography (CT).Methods: Paired CT scans with DISH that are separated at least two years apart were used to perform the following radiological measurements: Degree of disc space fusion, Osteophyte and vertebral body linear attenuation coefficients (LAC), and Osteophyte axial area size and location.Results: 164 patients were analysed with a mean duration of 4.49 years between scans. 38.14% (442/1159) of disc spaces had at least partial calcification. Most osteophytes were right sided before becoming more circumferential over time. The average fusion score was 54.17. Most of the changes in fusion occurred in the upper and lower thoracic regions. The thoracic region when compared to the lumbar region had a greater proportion of its disc spaced being fully fused. Disc level osteophyte areas were larger than Body level osteophytes. Disc osteophytes size growth rate drops over time from 10.89mm²/year in Stage 1 to 3.56mm²/year in Stage 3. Stage 3 disc spaces (-11.01HU/year) was also found to have had a reduction in their LAC over time when compared to Stage 1 disc spaces (17.04HU/year). This change in osteophyte LAC was not mirrored in the change in vertebral body LAC. We predict that the age of onset and complete thoracolumbar ankylosis of DISH to be 17.96 years and 100.59 years, respectively.Conclusion: DISH ankylosis of the spine a slow process that starts in the mid to lower thoracic region before extending cranially and caudally. After the bridging osteophyte has fully formed, remodelling of the osteophyte occurs.

Multicenter experience with andexanet alfa for refractory pericardial bleeding during catheter ablation of atrial fibrillation

INTRODUCTION

Pericardial bleeding is a rare but life-threatening complication of atrial fibrillation (AF) ablation. Patients taking uninterrupted oral anticoagulation (AC) may be at increased risk for refractory bleeding despite pericardiocentesis and administration of protamine. In such cases, andexanet alfa can be given to reverse rivaroxaban or apixaban. In this study, we aim to describe the rate of acute hemostasis and thromboembolic complications with andexanet for refractory pericardial bleeding during AF ablation.

METHODS AND RESULTS

In this multicenter, case series, participating centers identified patients who received a dose of apixaban or rivaroxaban within 24 h of AF ablation, developed refractory pericardial bleeding during the procedure despite pericardiocentesis and administration of protamine and received andexanet. Eleven patients met inclusion criteria, with mean age of 73.5 ± 5.3 years and median CHA₂ DS₂ -VASc score 4 [3-5]. All patients received protamine and pericardiocentesis, and 9 (82%) received blood products. All patients received a bolus of andexanet followed, in all but one, by a 2-h infusion. Acute hemostasis was achieved in eight patients (73%) while three required emergent surgery. One patient (9%) experienced acute ST-elevation myocardial infarction after receiving andexanet. Therapeutic AC was restarted after a mean of 2.2 ± 1.9 days and oral AC was restarted after a mean of 2.9 ± 1.6 days, with no recurrent bleeding.

CONCLUSION

In patients on uninterrupted apixaban or rivaroxaban, who develop refractory pericardial bleeding during AF ablation, andexanet can achieve hemostasis thereby avoiding the need for emergent surgery. However, there is a risk of thromboembolism following administration.

Evaluating temperature gradients across the posterior left atrium with radiofrequency ablation

INTRODUCTION

Esophageal injury is a well-known complication associated with catheter ablation. Though novel methods to mitigate esophageal injury have been developed, few studies have evaluated temperature gradients with catheter ablation across the posterior wall of the left atrium, interstitium, and esophagus.

METHODS

To investigate temperature gradients across the tissue, we developed a porcine heart-esophageal model to perform ex vivo catheter ablation on the posterior wall of the left atrium (LA), with juxtaposed interstitial tissue and esophagus. Circulating saline (5 L/min) was used to mimic blood flow along the LA and alteration of ionic content to modulate impedance. Thermistors along the region of interest were used to analyze temperature gradients. Varying time and power, radiofrequency (RF) ablation lesions were applied with an externally irrigated ablation catheter. Ablation strategies were divided into standard approaches (SAs, 10-15 g, 25-35 W, 30 s) or high-power short duration (HPSD, 10-15 g, 40-50 W, 10 s). Temperature gradients, time to the maximum measured temperature, and the relationship between measured temperature as a function of distance from the site of ablation was analyzed.

RESULTS

In total, five experiments were conducted each utilizing new porcine posterior LA wall-esophageal specimens for RF ablation (n = 60 lesions each for SA and HPSD). For both SA and HPSD, maximum temperature rise from baseline was markedly higher at the anterior wall (AW) of the esophagus compared to the esophageal lumen (SA: 4.29°C vs. 0.41°C, p < .0001 and HPSD: 3.13°C vs. 0.28°C, p < .0001). Across ablation strategies, the average temperature rise at the AW of the esophagus was significantly higher with SA relative to HPSD ablation (4.29°C vs. 3.13°C, p = .01). From the start of ablation, the average time to reach a maximum temperature as measured at the AW of the esophagus with SA was 36.49 ±  12.12 s, compared to 16.57 ±  4.54 s with HPSD ablation, p < .0001. Fit to a linear scale, a 0.37°C drop in temperature was seen for every 1 cm increase in distance from the site of ablation and thermistor location at the AW of the esophagus.

CONCLUSION

Both SA and HPSD ablation strategies resulted in markedly higher temperatures measured at the AW of the esophagus compared to the esophageal lumen, raising concern about the value of clinical intraluminal temperature monitoring. The temperature rise at the AW was lower with HPSD. A significant time delay was seen to reach the maximum measured temperature and a modest increase in distance between the site of ablation and thermistor location impacted the accuracy of monitored temperatures.

The arithmetic topology of genetic alignments

We propose a novel mathematical paradigm for the study of genetic variation in sequence alignments. This framework originates from extending the notion of pairwise relations, upon which current analysis is based on, to k-ary dissimilarity. This dissimilarity naturally leads to a generalization of simplicial complexes by endowing simplices with weights, compatible with the boundary operator. We introduce the notion of k-stances and dissimilarity complex, the former encapsulating arithmetic as well as topological structure expressing these k-ary relations. We study basic mathematical properties of dissimilarity complexes and show how this approach captures watershed moments of viral dynamics in the context of SARS-CoV-2 and H1N1 flu genomic data.

Association of Residual Ischemic Disease With Clinical Outcomes After Percutaneous Coronary Intervention

BACKGROUND

Anatomical scoring systems have been used to assess completeness of revascularization but are challenging to apply to large real-world datasets.

OBJECTIVES

The aim of this study was to assess the prevalence of complete revascularization and its association with longitudinal clinical outcomes in the U.S. Department of Veterans Affairs (VA) health care system using an automatically computed anatomic complexity score.

METHODS

Patients undergoing percutaneous coronary intervention (PCI) between October 1, 2007, and September 30, 2020, were identified, and the burden of prerevascularization and postrevascularization ischemic disease was quantified using the VA SYNTAX (Synergy Between PCI With Taxus and Cardiac Surgery) score. The association between residual VA SYNTAX score and long-term major adverse cardiovascular events (MACE; death, myocardial infarction, repeat revascularization, and stroke) was assessed.

RESULTS

A total of 57,476 veterans underwent PCI during the study period. After adjustment, the highest tertile of residual VA SYNTAX score was associated with increased hazard of MACE (HR: 2.06; 95% CI: 1.98-2.15) and death (HR: 1.50; 95% CI: 1.41-1.59) at 3 years compared to complete revascularization (residual VA SYNTAX score = 0). Hazard of 1- and 3-year MACE increased as a function of residual disease, regardless of baseline disease severity or initial presentation with acute or chronic coronary syndrome.

CONCLUSIONS

Residual ischemic disease was strongly associated with long-term clinical outcomes in a contemporary national cohort of PCI patients. Automatically computed anatomic complexity scores can be used to assess the longitudinal risk for residual ischemic disease after PCI and may be implemented to improve interventional quality.

Qualitative Evaluation of an Artificial Intelligence–Based Clinical Decision Support System to Guide Rhythm Management of Atrial Fibrillation: Survey Study

Background

Despite the numerous studies evaluating various rhythm control strategies for atrial fibrillation (AF), determination of the optimal strategy in a single patient is often based on trial and error, with no one-size-fits-all approach based on international guidelines/recommendations. The decision, therefore, remains personal and lends itself well to help from a clinical decision support system, specifically one guided by artificial intelligence (AI). QRhythm utilizes a 2-stage machine learning (ML) model to identify the optimal rhythm management strategy in a given patient based on a set of clinical factors, in which the model first uses supervised learning to predict the actions of an expert clinician and identifies the best strategy through reinforcement learning to obtain the best clinical outcome—a composite of symptomatic recurrence, hospitalization, and stroke.

Objective

We qualitatively evaluated a novel, AI-based, clinical decision support system (CDSS) for AF rhythm management, called QRhythm, which uses both supervised and reinforcement learning to recommend either a rate control or one of 3 types of rhythm control strategies—external cardioversion, antiarrhythmic medication, or ablation—based on individual patient characteristics.

Methods

Thirty-three clinicians, including cardiology attendings and fellows and internal medicine attendings and residents, performed an assessment of QRhythm, followed by a survey to assess relative comfort with automated CDSS in rhythm management and to examine areas for future development.

Results

The 33 providers were surveyed with training levels ranging from resident to fellow to attending. Of the characteristics of the app surveyed, safety was most important to providers, with an average importance rating of 4.7 out of 5 (SD 0.72). This priority was followed by clinical integrity (a desire for the advice provided to make clinical sense; importance rating 4.5, SD 0.9), backward interpretability (transparency in the population used to create the algorithm; importance rating 4.3, SD 0.65), transparency of the algorithm (reasoning underlying the decisions made; importance rating 4.3, SD 0.88), and provider autonomy (the ability to challenge the decisions made by the model; importance rating 3.85, SD 0.83). Providers who used the app ranked the integrity of recommendations as their highest concern with ongoing clinical use of the model, followed by efficacy of the application and patient data security. Trust in the app varied; 1 (17%) provider responded that they somewhat disagreed with the statement, “I trust the recommendations provided by the QRhythm app,” 2 (33%) providers responded with neutrality to the statement, and 3 (50%) somewhat agreed with the statement.

Conclusions

Safety of ML applications was the highest priority of the providers surveyed, and trust of such models remains varied. Widespread clinical acceptance of ML in health care is dependent on how much providers trust the algorithms. Building this trust involves ensuring transparency and interpretability of the model.

Prevention and Management of Hypertriglyceridemia-Induced Acute Pancreatitis During Pregnancy: A Systematic Review

Severe gestational hypertriglyceridemia can lead to acute pancreatitis, with maternal mortality rate of approximately 20%. The recent National Lipid Association part 2 expert panel recommendations provide guidance on monitoring pregnant women at high risk for hyperlipidemia. We suggest that high-risk women have triglyceride levels checked once every trimester. Fasting triglycerides >250 mg/dL should prompt monthly triglyceride levels, screening for gestational diabetes, and implementing a strict low-carbohydrate, low-fat diet, exercise. Fasting triglycerides >500 mg/dL, despite a strict dietary and lifestyle modifications, should prompt treatment with omega-3-fatty acids and continue a fat-restricted diet (<20 g total fat/d or <15% total calories) under the guidance of a registered dietician. The use of fibrates should be considered as a second-line therapy due to their unclear risk versus benefit and potential teratogenic effects. Plasmapheresis should be considered early in asymptomatic pregnant women with fasting triglyceride levels >1000 mg/dL or in pregnant women with clinical signs and symptoms of pancreatitis and triglyceride levels >500 mg/dL despite maximal lifestyle changes and pharmacologic therapy.

Limitations of Unipolar Signals in Guiding Successful Outflow Tract Premature Ventricular Contraction Ablation

OBJECTIVES

The authors sought to compare bipolar electrograms (BiEGMs) vs unipolar electrograms (UniEGMs) in guiding successful ablation of right ventricular outflow tract (RVOT) vs intramural outflow tract (OT) premature ventricular contractions (PVCs). The authors hypothesized that: 1) earliest bipolar local activation time (LAT_Bi) would better guide mapping and ablation, vs UniEGM dV/dt (LAT_Uni) or QS morphology; and 2) LAT differences using bipolar vs unipolar EGMs (ΔLAT_Bi-Uni) would be greater for intramural OT than RVOT PVCs.

BACKGROUND

UniEGMs are commonly used to annotate earliest local activation of focal arrhythmias. However, their utility in guiding PVC ablation may be limited when the PVC source is less superficial.

METHODS

Consecutive patients undergoing successful PVC ablation 2017 to2020 requiring only RVOT or RVOT+left ventricular OT (RVOT+LVOT) ablation were retrospectively analyzed. BiEGMs and UniEGMs at successful ablation sites were compared.

RESULTS

Of 70 patients, 50 required RVOT-only, and 20 required RVOT+LVOT ablation for acute and long-term PVC suppression. Mean ΔLAT_Bi-Uni was lower for RVOT vs RVOT+LVOT groups (9.3 ± 6.4 ms vs 17.4 ± 9.9 ms; P < 0.01). QS UniEGM was seen in 78% of RVOT, compared with 53% of RVOT+LVOT patients (P < 0.016). RVOT+LVOT sites most frequently included the posteroseptal RVOT and adjacent LVOT (73%), and 43% lacked a QS unipolar EGM. ΔLAT_Bi-Uni ≥15 ms best distinguished sites in which RVOT-only vs RVOT+LVOT ablation achieved acute PVC suppression (area under the curve: 0.77).

CONCLUSIONS

Earliest BiEGM activation guides successful ablation of OT PVCs better than UniEGM-guided analysis, especially when an intramural PVC source is present.

Phylogeography of the veined squid, Loligo forbesii, in European waters

The veined squid, Loligo forbesii Steenstrup, 1856, occurs at the European Shelf areas including the Azores and represents a valuable resource for the European commercial fishery in the North East Atlantic. However, very little is known about its population structure and phylogeography. This lack of knowledge also impedes the development of sustainable fishery management for this species. The present study combined the use of two types of markers that retrieve patterns of gene flow in different time spans; the analysis of 16 nuclear microsatellites and sequencing of the mitochondrial cytochrome oxidase subunit I (COI). Whereas the high mutation rate of microsatellites allows the description of recent patterns of connectivity in species, the lower mutation rate of COI provides phylogeographic patterns on a longer timescale. A total of 347 individuals of L. forbesii were investigated from nearly the entire distribution range of the species, including the North East Atlantic Shelf, the Azores and the Mediterranean. Individuals from the Western and Eastern Mediterranean Sea have never been included in a genetic study before. We were able to analyse COI sequences from all 12 sampling areas and define three clades of L. forbesii. Due to our large sampling area, we are presenting 13 COI-haplotypes that were previously unknown. The microsatellite analysis does not include the Azores but three main clades could be identified at the remaining 11 sampling sites. Low F_ST values indicate gene flow over large geographical distances. However, the genetically significant differences and an additional slight grouping in the microsatellite structure reveal that geographical barriers seem to influence the population structure and reduce gene flow. Furthermore, both markers provide strong evidence that the observed phylogeographic pattern reflects the geographical history of the Azores and the Mediterranean Sea.