Identifying and Extracting Rare Diseases and Their Phenotypes with Large Language Models

Purpose

Phenotyping is critical for informing rare disease diagnosis and treatment, but disease phenotypes are often embedded in unstructured text. While natural language processing (NLP) can automate extraction, a major bottleneck is developing annotated corpora. Recently, prompt learning with large language models (LLMs) has been shown to lead to generalizable results without any (zero-shot) or few annotated samples (few-shot), but none have explored this for rare diseases. Our work is the first to study prompt learning for identifying and extracting rare disease phenotypes in the zero- and few-shot settings.

Methods

We compared the performance of prompt learning with ChatGPT and fine-tuning with BioClinicalBERT. We engineered novel prompts for ChatGPT to identify and extract rare diseases and their phenotypes (e.g., diseases, symptoms, and signs), established a benchmark for evaluating its performance, and conducted an in-depth error analysis.

Results

Overall, fine-tuning BioClinicalBERT resulted in higher performance (F1 of 0.689) than ChatGPT (F1 of 0.472 and 0.610 in the zero- and few-shot settings, respectively). However, ChatGPT achieved higher accuracy for rare diseases and signs in the one-shot setting (F1 of 0.778 and 0.725). Conversational, sentence-based prompts generally achieved higher accuracy than structured lists.

Conclusion

Prompt learning using ChatGPT has the potential to match or outperform fine-tuning BioClinicalBERT at extracting rare diseases and signs with just one annotated sample. Given its accessibility, ChatGPT could be leveraged to extract these entities without relying on a large, annotated corpus. While LLMs can support rare disease phenotyping, researchers should critically evaluate model outputs to ensure phenotyping accuracy.

Plasma electron acceleration driven by a long-wave-infrared laser

Laser-driven plasma accelerators provide tabletop sources of relativistic electron bunches and femtosecond x-ray pulses, but usually require petawatt-class solid-state-laser pulses of wavelength λL ~ 1 μm. Longer-λL lasers can potentially accelerate higher-quality bunches, since they require less power to drive larger wakes in less dense plasma. Here, we report on a self-injecting plasma accelerator driven by a long-wave-infrared laser: a chirped-pulse-amplified CO2 laser (λL ≈ 10 μm). Through optical scattering experiments, we observed wakes that 4-ps CO2 pulses with <  1/2 terawatt (TW) peak power drove in hydrogen plasma of electron density down to 4 × 1017 cm-3 (1/100 atmospheric density) via a self-modulation (SM) instability. Shorter, more powerful CO2 pulses drove wakes in plasma down to 3 × 1016 cm-3 that captured and accelerated plasma electrons to relativistic energy. Collimated quasi-monoenergetic features in the electron output marked the onset of a transition from SM to bubble-regime acceleration, portending future higher-quality accelerators driven by yet shorter, more powerful pulses.

Empowering the Participant Voice (EPV): Design and implementation of collaborative infrastructure to collect research participant experience feedback at scale

Empowering the Participant Voice (EPV) is an NCATS-funded six-CTSA collaboration to develop, demonstrate, and disseminate a low-cost infrastructure for collecting timely feedback from research participants, fostering trust, and providing data for improving clinical translational research. EPV leverages the validated Research Participant Perception Survey (RPPS) and the popular REDCap electronic data-capture platform. This report describes the development of infrastructure designed to overcome identified institutional barriers to routinely collecting participant feedback using RPPS and demonstration use cases. Sites engaged local stakeholders iteratively, incorporating feedback about anticipated value and potential concerns into project design. The team defined common standards and operations, developed software, and produced a detailed planning and implementation Guide. By May 2023, 2,575 participants diverse in age, race, ethnicity, and sex had responded to approximately 13,850 survey invitations (18.6%); 29% of responses included free-text comments. EPV infrastructure enabled sites to routinely access local and multi-site research participant experience data on an interactive analytics dashboard. The EPV learning collaborative continues to test initiatives to improve survey reach and optimize infrastructure and process. Broad uptake of EPV will expand the evidence base, enable hypothesis generation, and drive research-on-research locally and nationally to enhance the clinical research enterprise.

Toroidal-spiral particles as a CAR-T cell delivery device for solid tumor immunotherapy

Chimeric antigen receptor (CAR) T cell therapy has resulted in positive effects on patients with hematologic malignancy but shows limited efficacy in solid tumor treatments due to insufficient trafficking and tumor infiltration, intensive CAR-T-related toxicities, and antigen escape. In this work, we developed and investigated a biodegradable and biocompatible polymeric toroidal-spiral particle (TSP) as a in vivo cell incubator and delivery device that can be implanted near tumor through a minimally invasive procedure or injected near or into solid tumors by using a biopsy needle. The main matrix structure of the millimeter-sized TSP is made from crosslinking of gelatin methacrylamine (GelMA) and poly (ethylene glycol) diacrylate (PEGDA) with a tunable degradation rate from a few days to months, providing appropriate mechanical properties and sustained release of co-encapsulated drugs and/or stimulation compounds. The toroidal-spiral layer of the particles, presenting an internal void volume for high-capacity cell loading and flexibility of co-encapsulating small and large molecular compounds with individually manipulated release schedules, is filled with collagen and suspended T cells. The TSPs promote cell proliferation, activation, and migration in the tumor micro-environment in a prolonged and sustained manner. In this study, the efficacy of mesothelin (MSLN) CAR-T cells released from the TSPs was tested in preclinical mouse tumor models. Compared to systemic and intratumoral injection, peritumoral delivery of MSLN CAR-T cells using the TSPs resulted in a superior antitumor effect. The TSPs made of FDA approved materials as an in vivo reactor may provide an option for efficiently local delivery of CAR-T cells to solid tumors for higher efficacy and lower toxicity, with a minimally invasive administration procedure.

Elevating nucleic acid delivery via a stable anionic peptide-dextran ternary system

Nucleic acid-based therapies hold promise for treating previously intractable diseases but require effective delivery vectors to protect the therapeutic agents and ensure efficient transfection. Cationic polymeric vectors are particularly notable for their adaptability, high transfection efficiency, and low cost, but their positive charge often attracts blood proteins, causing aggregation and reduced transfection efficiency. Addressing this, we designed an anionic peptide-grafted dextran (Dex-LipE5H) to serve as a cross-linkable coating to bolster the stability of cationic polymer/nucleic acid complexes. The Dex-LipE5H was synthesized through a Michael addition reaction, combining an anionic peptide (LipE5H) with dextran modified by divinyl sulfone. We demonstrated Dex-lipE5H utility in a novel ternary nucleic acid delivery system, CDex-LipE5H/PEI/nucleic acid. CDex-LipE5H/PEI/nucleic acid demonstrated lower cytotoxicity and superior anti-protein absorption ability compared to PEI/pDNA and Dex-LipE5H/PEI/pDNA. Most notably, the crosslinked CDex-LipE5H/PEI/pDNA demonstrated remarkable transfection performance in HepG2 cells, which poses significant transfection challenges, even in a medium with 20% serum. This system's effective siRNA interference performance was further validated through a PCSK9 gene knockdown assay. This investigation provides novel insights and contributes to the design of cost-effective, next-generation nucleic acid delivery systems with enhanced blood stability and transfection efficiency.

Simple Bioparticle Filtration Device Based on an Ultralow-Fouling Zwitterionic Polyurethane Membrane for Rapid Large-Volume Separation of Plasma and Viruses from Whole Blood

Plasma separation from whole blood is oftent required as an essential first step when performing blood tests with a viral assay. However, developing a point-of-care plasma extraction device with a large output and high virus recovery remains a significant obstacle to the success of on-site viral load tests. Here, we report a portable, easy-to-use, cost-efficient, membrane-filtration-based plasma separation device that enables rapid large-volume plasma extraction from whole blood, designed for point-of-care virus assays. The plasma separation is realized by a low-fouling zwitterionic polyurethane-modified cellulose acetate (PCBU-CA) membrane. The zwitterionic coating on the cellulose acetate membrane can decrease surface protein adsorption by 60% and increase plasma permeation by 46% compared with a pristine membrane. The PCBU-CA membrane, with its ultralow-fouling properties, enables rapid plasma separation. The device can yield a total of 1.33 mL plasma from 10 mL whole blood in 10 min. The extracted plasma is cell-free and exhibits a low hemoglobin level. In addition, our device demonstrated a 57.8% T7 phage recovery in the separated plasma. The results of real-time polymerase chain reaction analysis confirmed that the nucleic acid amplification curve of the plasma extracted by our device is comparable to that obtained by centrifugation. With its high plasma yield and good phage recovery, our plasma separation device provides an excellent replacement for traditional plasma separation protocols for point-of-care virus assays and a broad spectrum of clinical tests.

Pembrolizumab monotherapy versus chemotherapy in platinum-pretreated, recurrent or metastatic nasopharyngeal cancer (KEYNOTE-122): an open-label, randomized, phase III trial

BACKGROUND

Pembrolizumab previously demonstrated robust antitumor activity and manageable safety in a phase Ib study of patients with heavily pretreated, programmed death ligand 1 (PD-L1)-positive, recurrent or metastatic nasopharyngeal carcinoma (NPC). The phase III KEYNOTE-122 study was conducted to further evaluate pembrolizumab versus chemotherapy in patients with platinum-pretreated, recurrent and/or metastatic NPC. Final analysis results are presented.

PATIENTS AND METHODS

KEYNOTE-122 was an open-label, randomized study conducted at 29 sites, globally. Participants with platinum-pretreated recurrent and/or metastatic NPC were randomly assigned (1 : 1) to pembrolizumab or chemotherapy with capecitabine, gemcitabine, or docetaxel. Randomization was stratified by liver metastasis (present versus absent). The primary endpoint was overall survival (OS), analyzed in the intention-to-treat population using the stratified log-rank test (superiority threshold, one-sided P = 0.0187). Safety was assessed in the as-treated population.

RESULTS

Between 5 May 2016 and 28 May 2018, 233 participants were randomly assigned to treatment (pembrolizumab, n = 117; chemotherapy, n = 116); Most participants (86.7%) received study treatment in the second-line or later setting. Median time from randomization to data cut-off (30 November 2020) was 45.1 months (interquartile range, 39.0-48.8 months). Median OS was 17.2 months [95% confidence interval (CI) 11.7-22.9 months] with pembrolizumab and 15.3 months (95% CI 10.9-18.1 months) with chemotherapy [hazard ratio, 0.90 (95% CI 0.67-1.19; P = 0.2262)]. Grade 3-5 treatment-related adverse events occurred in 12 of 116 participants (10.3%) with pembrolizumab and 49 of 112 participants (43.8%) with chemotherapy. Three treatment-related deaths occurred: 1 participant (0.9%) with pembrolizumab (pneumonitis) and 2 (1.8%) with chemotherapy (pneumonia, intracranial hemorrhage).

CONCLUSION

Pembrolizumab did not significantly improve OS compared with chemotherapy in participants with platinum-pretreated recurrent and/or metastatic NPC but did have manageable safety and a lower incidence of treatment-related adverse events.

Interplay of Immunosuppression and Immunotherapy Among Patients With Cancer and COVID-19

Importance

Cytokine storm due to COVID-19 can cause high morbidity and mortality and may be more common in patients with cancer treated with immunotherapy (IO) due to immune system activation.

Objective

To determine the association of baseline immunosuppression and/or IO-based therapies with COVID-19 severity and cytokine storm in patients with cancer.

Design, Setting, and Participants

This registry-based retrospective cohort study included 12 046 patients reported to the COVID-19 and Cancer Consortium (CCC19) registry from March 2020 to May 2022. The CCC19 registry is a centralized international multi-institutional registry of patients with COVID-19 with a current or past diagnosis of cancer. Records analyzed included patients with active or previous cancer who had a laboratory-confirmed infection with SARS-CoV-2 by polymerase chain reaction and/or serologic findings.

Exposures

Immunosuppression due to therapy; systemic anticancer therapy (IO or non-IO).

Main Outcomes and Measures

The primary outcome was a 5-level ordinal scale of COVID-19 severity: no complications; hospitalized without requiring oxygen; hospitalized and required oxygen; intensive care unit admission and/or mechanical ventilation; death. The secondary outcome was the occurrence of cytokine storm.

Results

The median age of the entire cohort was 65 years (interquartile range [IQR], 54-74) years and 6359 patients were female (52.8%) and 6598 (54.8%) were non-Hispanic White. A total of 599 (5.0%) patients received IO, whereas 4327 (35.9%) received non-IO systemic anticancer therapies, and 7120 (59.1%) did not receive any antineoplastic regimen within 3 months prior to COVID-19 diagnosis. Although no difference in COVID-19 severity and cytokine storm was found in the IO group compared with the untreated group in the total cohort (adjusted odds ratio [aOR], 0.80; 95% CI, 0.56-1.13, and aOR, 0.89; 95% CI, 0.41-1.93, respectively), patients with baseline immunosuppression treated with IO (vs untreated) had worse COVID-19 severity and cytokine storm (aOR, 3.33; 95% CI, 1.38-8.01, and aOR, 4.41; 95% CI, 1.71-11.38, respectively). Patients with immunosuppression receiving non-IO therapies (vs untreated) also had worse COVID-19 severity (aOR, 1.79; 95% CI, 1.36-2.35) and cytokine storm (aOR, 2.32; 95% CI, 1.42-3.79).

Conclusions and Relevance

This cohort study found that in patients with cancer and COVID-19, administration of systemic anticancer therapies, especially IO, in the context of baseline immunosuppression was associated with severe clinical outcomes and the development of cytokine storm.

Trial Registration

ClinicalTrials.gov Identifier: NCT04354701.

Comparison of Wild Type DNA Sequence of Spike Protein from SARS-CoV-2 with Optimized Sequence on The Induction of Protective Responses Against SARS-Cov-2 Challenge in Mouse Model

Genetic optimization of Nucleic Acid immunogens is important for potentially improving their immune potency. A COVID-19 DNA vaccine is in phase III clinical trial which is based on a promising highly developable technology platform. Here, we show optimization in mice generating a pGX-9501 DNA vaccine encoding full-length spike protein, which results in induction of potent humoral and cellular immune responses, including neutralizing antibodies, that block hACE2-RBD binding of live CoV2 virus in vitro. Optimization resulted in improved induction of cellular immunity by pGX-9501 as demonstrated by increased IFN-γ expression in both CD8+ and CD4 + T cells and this was associated with more robust antiviral CTL responses compared to unoptimized constructs. Vaccination with pGX-9501 induced subsequent protection against virus challenge in a rigorous hACE2 transgenic mouse model. Overall, pGX-9501 is a promising optimized COVID-19 DNA vaccine candidate inducing humoral and cellular immunity contributing to the vaccine's protective effects.

Dynamic networks of psychotic symptoms in adults living in precarious housing or homelessness

BACKGROUND

People living in precarious housing or homelessness have higher than expected rates of psychotic disorders, persistent psychotic symptoms, and premature mortality. Psychotic symptoms can be modeled as a complex dynamic system, allowing assessment of roles for risk factors in symptom development, persistence, and contribution to premature mortality.

METHOD

The severity of delusions, conceptual disorganization, hallucinations, suspiciousness, and unusual thought content was rated monthly over 5 years in a community sample of precariously housed/homeless adults (n = 375) in Vancouver, Canada. Multilevel vector auto-regression analysis was used to construct temporal, contemporaneous, and between-person symptom networks. Network measures were compared between participants with (n = 219) or without (n = 156) history of psychotic disorder using bootstrap and permutation analyses. Relationships between network connectivity and risk factors including homelessness, trauma, and substance dependence were estimated by multiple linear regression. The contribution of network measures to premature mortality was estimated by Cox proportional hazard models.

RESULTS

Delusions and unusual thought content were central symptoms in the multilevel network. Each psychotic symptom was positively reinforcing over time, an effect most pronounced in participants with a history of psychotic disorder. Global connectivity was similar between those with and without such a history. Greater connectivity between symptoms was associated with methamphetamine dependence and past trauma exposure. Auto-regressive connectivity was associated with premature mortality in participants under age 55.

CONCLUSIONS

Past and current experiences contribute to the severity and dynamic relationships between psychotic symptoms. Interrupting the self-perpetuating severity of psychotic symptoms in a vulnerable group of people could contribute to reducing premature mortality.

Identification of a promiscuous conserved CTL epitope within the SARS-CoV-2 spike protein

The COVID-19 disease caused by infection with SARS-CoV-2 and its variants is devastating to the global public health and economy. To date, over a hundred COVID-19 vaccines are known to be under development, and the few that have been approved to fight the disease are using the spike protein as the primary target antigen. Although virus-neutralizing epitopes are mainly located within the RBD of the spike protein, the presence of T cell epitopes, particularly the CTL epitopes that are likely to be needed for killing infected cells, has received comparatively little attention. This study predicted several potential T cell epitopes with web-based analytic tools and narrowed them down from several potential MHC-I and MHC-II epitopes by ELIspot and cytolytic assays to a conserved MHC-I epitope. The epitope is highly conserved in current viral variants and compatible with a presentation by most HLA alleles worldwide. In conclusion, we identified a CTL epitope suitable for evaluating the CD8+ T cell-mediated cellular response and potentially for addition into future COVID-19 vaccine candidates to maximize CTL responses against SARS-CoV-2.

Breast Cancer Disparities Through the Lens of the COVID-19 Pandemic

Purpose of Review

The emergency medicine and critical care needs of the COVID-19 pandemic forced a sudden and dramatic disruption of cancer screening and treatment programs in the USA during the winter and spring of 2020. This review commentary addresses the impact of the pandemic on racial/ethnic minorities such as African Americans and Hispanic-Latina Americans, with a focus on factors related to breast cancer.

Recent Findings

African Americans and Hispanic-Latina Americans experienced disproportionately higher morbidity and mortality from COVID-19; many of the same socioeconomic and tumor biology/genetic factors that explain breast cancer disparities are likely to account for COVID-19 outcome disparities.

Summary

The breast cancer clinical and research community should partner with public health experts to ensure participation of diverse patients in COVID-19 treatment trials and vaccine programs and to overcome COVID-19-related breast health management delays that are likely to have been magnified among African Americans and Hispanic-Latina Americans.

Neutrophil-Lymphocyte Ratio and Absolute Lymphocyte Count as Prognostic Markers in Patients Treated with Curative-intent Radiotherapy for Non-small Cell Lung Cancer

AIMS

The neutrophil-lymphocyte ratio (NLR) and the absolute lymphocyte count (ALC) have been proposed as prognostic markers in non-small cell lung cancer (NSCLC). The objective of this study was to examine the association of NLR/ALC before and after curative-intent radiotherapy for NSCLC on disease recurrence and overall survival.

MATERIALS AND METHODS

A retrospective study of consecutive patients who underwent curative-intent radiotherapy for NSCLC across nine sites in the UK from 1 October 2014 to 1 October 2016. A multivariate analysis was carried out to assess the ability of pre-treatment NLR/ALC, post-treatment NLR/ALC and change in NLR/ALC, adjusted for confounding factors using the Cox proportional hazards model, to predict disease recurrence and overall survival within 2 years of treatment.

RESULTS

In total, 425 patients were identified with complete blood parameter values. None of the NLR/ALC parameters were independent predictors of disease recurrence. Higher pre-NLR, post-NLR and change in NLR plus lower post-ALC were all independent predictors of worse survival. Receiver operator curve analysis found a pre-NLR > 2.5 (odds ratio 1.71, 95% confidence interval 1.06-2.79, P < 0.05), a post-NLR > 5.5 (odds ratio 2.36, 95% confidence interval 1.49-3.76, P < 0.001), a change in NLR >3.6 (odds ratio 2.41, 95% confidence interval 1.5-3.91, P < 0.001) and a post-ALC < 0.8 (odds ratio 2.86, 95% confidence interval 1.76-4.69, P < 0.001) optimally predicted poor overall survival on both univariate and multivariate analysis when adjusted for confounding factors. Median overall survival for the high-versus low-risk groups were: pre-NLR 770 versus 1009 days (P = 0.34), post-NLR 596 versus 1287 days (P ≤ 0.001), change in NLR 553 versus 1214 days (P ≤ 0.001) and post-ALC 594 versus 1287 days (P ≤ 0.001).

CONCLUSION

NLR and ALC, surrogate markers for systemic inflammation, have prognostic value in NSCLC patients treated with curative-intent radiotherapy. These simple and readily available parameters may have a future role in risk stratification post-treatment to inform the intensity of surveillance protocols.

Embracing informed learner self-assessment during debriefing: the art of plus-delta

The healthcare simulation field has no shortage of debriefing options. Some demand considerable skill which serves as a barrier to more widespread implementation. The plus-delta approach to debriefing offers the advantages of conceptual simplicity and ease of implementation. Importantly, plus-delta promotes learners' capacity for a self-assessment, a skill vital for safe clinical practice and yet a notorious deficiency in professional practice. The plus-delta approach confers the benefits of promoting uptake of debriefing in time-limited settings by educators with both fundamental but also advanced skills, and enhancing essential capacity for critical self-assessment informed by objective performance feedback. In this paper, we describe the role of plus-delta in debriefing, provide guidance for incorporating informed learner self-assessment into debriefings, and highlight four opportunities for improving the art of the plus delta: (a) exploring the big picture vs. specific performance issues, (b) choosing between single vs. double-barreled questions, (c) unpacking positive performance, and (d) managing perception mismatches.

Differential effects of cannabis exposure during early versus later adolescence on the expression of psychosis in homeless and precariously housed adults

Longitudinal studies of cannabis exposure during early adolescence in the general population frequently report an increased risk of subsequently developing psychotic symptoms or a psychotic illness. However, there is a dearth of knowledge about the effects of early cannabis exposure on psychosis in homeless and precariously housed adults, who represent a population afflicted with high rates of psychosis. The aim of the present study was to examine how early cannabis exposure (by age 15) compared to later first use (after age 15) affected the expression of adult psychosis in this population. Secondary measures of psychopathology, drug use, cognition and brain structure were also collected. 437 subjects were recruited from single room occupancy hotels in the urban setting of the Downtown Eastside of Vancouver, Canada. Psychiatric diagnoses were determined, and psychotic symptom severity was measured with the 5-factor PANSS. Participants completed a battery of neurocognitive tests, and brain structure was assessed using structural and diffusion tensor imaging MRI scans. Results indicated that early cannabis exposure was associated with an increased risk (OR = 1.09, p < .05) of developing substance induced psychosis, whereas later first use increased risk (OR = 2.19, p < .01) of developing schizophrenia or schizoaffective disorder. There was no group difference in neurocognitive function, although differences were observed in the lateral orbitofrontal cortex and white matter tract diffusivity. These findings indicate that early cannabis exposure in this population may increase the risk of developing drug associated psychoses, which could potentially be mediated in part through altered neurodevelopmental brain changes.

Predicting the Risk of Disease Recurrence and Death Following Curative-intent Radiotherapy for Non-small Cell Lung Cancer: The Development and Validation of Two Scoring Systems From a Large Multicentre UK Cohort

AIMS

There is a paucity of evidence on which to produce recommendations on neither the clinical nor the imaging follow-up of lung cancer patients after curative-intent radiotherapy. In the 2019 National Institute for Health and Care Excellence lung cancer guidelines, further research into risk-stratification models to inform follow-up protocols was recommended.

MATERIALS AND METHODS

A retrospective study of consecutive patients undergoing curative-intent radiotherapy for non-small cell lung cancer from 1 October 2014 to 1 October 2016 across nine UK trusts was carried out. Twenty-two demographic, clinical and treatment-related variables were collected and multivariable logistic regression was used to develop and validate two risk-stratification models to determine the risk of disease recurrence and death.

RESULTS

In total, 898 patients were included in the study. The mean age was 72 years, 63% (562/898) had a good performance status (0-1) and 43% (388/898), 15% (134/898) and 42% (376/898) were clinical stage I, II and III, respectively. Thirty-six per cent (322/898) suffered disease recurrence and 41% (369/898) died in the first 2 years after radiotherapy. The ASSENT score (age, performance status, smoking status, staging endobronchial ultrasound, N-stage, T-stage) was developed, which stratifies the risk for disease recurrence within 2 years, with an area under the receiver operating characteristic curve (AUROC) for the total score of 0.712 (0.671-0.753) and 0.72 (0.65-0.789) in the derivation and validation sets, respectively. The STEPS score (sex, performance status, staging endobronchial ultrasound, T-stage, N-stage) was developed, which stratifies the risk of death within 2 years, with an AUROC for the total score of 0.625 (0.581-0.669) and 0.607 (0.53-0.684) in the derivation and validation sets, respectively.

CONCLUSIONS

These validated risk-stratification models could be used to inform follow-up protocols after curative-intent radiotherapy for lung cancer. The modest performance highlights the need for more advanced risk prediction tools.

RV Pacing Percentage

Introduction

Chronic right ventricular pacing (RVP) has been associated with dyssynchrony, leading to increased mortality. However, there have been discrepancies in previous reports in the effect of RVP levels.

Objective

To sub-stratify mortality risk by age for different RVP level groups within a large real-world ICD cohort.

Methods

Optum® de-identified electronic health records were linked to the Medtronic Carelink data to identify dual chamber ICD recipients (2007–2017). RVP level was based on median daily pacing during the first 90 days post-implant and categorized either into groups with a cutoff of 40%, or with groups of 0–9%, 10–19%, 20–29%, 30–39%, 40–49%, and 50–100%. The endpoint was death more than 90 days post-implant. Kaplan-Meier survival curves, log-rank tests, and Cox regression were used to analyze the relationship between RVP and risk of death.

Results

Among 14,832 ICD patients (median age 67; 74.0% male), there were 2,602 deaths within 10 years after implant. In unadjusted comparisons, high RVP (&gt;40%) increased the risk of death relative to low RVP (≤40%) (p&lt;0.001). This effect remained significant in older cohort (≥67 years old at implant) (p&lt;0.001), but not in younger cohort (&lt;67 years old) (p=0.955) (Figure). After controlling for age, gender, pacing mode, MI, SCA, HF hospitalization, diabetes, and renal dysfunction, similar or increased risk was associated with higher pacing groups relative to the 0–9% pacing group in the older cohort, but not in the younger cohort.

Conclusions

Our data from a large contemporaneous real-world source suggests that older age or characteristics associated with age make patients more sensitive to chronic RVP effects. These results help reconcile differences observed in prior studies.

Funding Acknowledgement

Type of funding source: Private company. Main funding source(s): Medtronic, Inc.

Clinical outcomes from out-of-hospital cardiac arrest in low-resource settings - A scoping review

AIM OF THE SCOPING REVIEW

Scientific recommendations on resuscitation are typically formulated from the perspective of an ideal resource environment, with little consideration of applicability in lower-income countries. We aimed to determine clinical outcomes from out-of-hospital cardiac arrest (OHCA) in low-resource countries, to identify shortcomings related to resuscitation in these areas and possible solutions, and to suggest future research priorities.

DATA SOURCES

This scoping review was part of the continuous evidence evaluation process of the International Liaison Committee on Resuscitation (ILCOR), and was performed following the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews. We identified low-resource countries as countries with a low- or middle gross national income per capita (World Bank data). We performed a literature search on outcomes after OHCA in these countries, and we extracted data on the outcome. We applied descriptive statistics and conducted a post-hoc correlation analysis of cohort size and ROSC rates.

RESULTS

We defined 24 eligible studies originating from middle-income countries, but none from low-income regions, suggesting a reporting bias. The number of reported patients in these studies ranged from 54 to 3214. Utstein-style reporting was rarely used. Return of spontaneous circulation varied from 0% to 62%. Fifteen studies reported on survival to hospital discharge (between 1.0 and 16.7%) or favourable neurological outcome (between 1.0 and 9.3%). An inverse correlation was found for study cohort size and the rate of return of spontaneous circulation (ρ = -0.48, p = 0.034).

CONCLUSION

Studies of OHCA outcomes in low-resource countries are heterogeneous and may be compromised by reporting bias. Minimum cardiopulmonary resuscitation standards for low-resource settings should be developed collaboratively involving local experts, respecting culture and context while balancing competing health priorities.

The prokaryotic expression, polyclonal antibody preparation, and subcellular localization of the transmembrane protein NS2A of the duck Tembusu virus

Duck Tembusu virus (DTMUV) is a single-stranded, positive-sense RNA arbovirus, belonging to the genus Flavivirus, the family Flaviviridae. As a transmembrane protein, non-structural protein 2A (NS2A) plays an important role in virion assembly, replication complex and antagonizing host immune response. Since NS2A protein contains many hydrophobic amino acids, it is hard to gain the full-length protein of NS2A for prokaryotic expression. Therefore, to make a deep study, prokaryotic expression and polyclonal antibody preparation of truncated DTMUV NS2A was performed. The truncated NS2A gene (178-450 bp) was obtained, and sub-cloned into the prokaryotic vector pGEX-4T-1 (pGEX-4T-1-NS2A178-450bp). Subsequently, the recombinant GST-NS2A60-150aa protein was successfully expressed in E. coli BL21 (DE3) with the induction by 0.3 mmol/l isopropyl β-D-thiogalactoside (IPTG) for 6 h at 37°C. The GST-NS2A60-150aa protein was extracted from the gel. The BALB/c mice were immunized with the purified recombinant NS2A protein to prepare polyclonal antibodies against the truncated NS2A protein. The titer of the polyclonal antibodies, determined by ELISA analysis, was 1:128,000. The specificity of the polyclonal antibodies (mPAb-DTMUV-NS2A60-150aa) were verified by Western blot analysis. Furthermore, the indirect immunofluorescence (IFA) was performed to explore the subcellular localization of NS2A. NS2A protein was, in the transfected cells, located mainly around nucleus in the endoplasmatic reticulum. Taken together, our study provided a useful tool for the further exploration of the biological functions and molecular mechanism of DTMUV NS2A. Keywords: duck Tembusu virus; non-structural protein 2A; prokaryotic expression; polyclonal antibodies; subcellular location.

Treatment workload by stage and subtype in patients with breast cancer: A SEER-Medicare analysis

e19328

Background: Patients with breast cancer experience significant disruption to their daily lives when undergoing treatment. When treatment workload exceeds the capacity to manage that treatment, patients are less likely to adhere to care plans and likelier to have worse outcomes. The purpose of this study was to assess treatment workload in patients with operable breast cancer in the SEER-Medicare dataset. Methods: Operable (stage I-III) breast cancer patients diagnosed from 2010-2016, > 65 years old at diagnosis, and with 18 months of continuous Medicare part A, B, and D coverage after diagnosis were included in the cohort. We calculated the number of outpatient appointment days, total cumulative inpatient lengths of stay, and distance traveled for patients in the cohort in the 18 months following diagnosis. We compared treatment workload outcomes between patients with stage I and stage III disease and between patients with HER2+ and HER2-/ER+ disease. Results: 35,071 patients met the inclusion criteria. Compared to stage I patients, stage III patients had more median outpatient appointment days (71 vs 50), more median inpatient days (2 vs 0), and greater median distance traveled (1846 vs 1332 miles). Compared to patients with HER2-/ER+ disease, patients with HER2+ disease had more median outpatient appointment days (70 vs 51), and greater median distance traveled (1775 vs 1350 miles). All comparisons were with Mann Whitney U and were statistically significant with P < .001. Conclusions: Patients with operable breast cancer experience a high amount of treatment workload in the first 18 months after diagnosis. These workload measures derived from SEER-Medicare claims differentiate significantly by stage and subtype, with stage III and HER2+ patients experiencing greater treatment workload than stage I and HER2-/ER+ patients respectively. We suspect that greater treatment workload in stage III is attributed to higher intensity of treatment for later stage cancer and associated complications, while greater treatment workload in HER2+ patients is attributed to the use of trastuzumab. [Table: see text]

Color, composition, and thermal environment of Kuiper Belt object (486958) Arrokoth

The outer Solar System object (486958) Arrokoth (provisional designation 2014 MU₆₉) has been largely undisturbed since its formation. We studied its surface composition using data collected by the New Horizons spacecraft. Methanol ice is present along with organic material, which may have formed through irradiation of simple molecules. Water ice was not detected. This composition indicates hydrogenation of carbon monoxide-rich ice and/or energetic processing of methane condensed on water ice grains in the cold, outer edge of the early Solar System. There are only small regional variations in color and spectra across the surface, which suggests that Arrokoth formed from a homogeneous or well-mixed reservoir of solids. Microwave thermal emission from the winter night side is consistent with a mean brightness temperature of 29 ± 5 kelvin.

P1445 DORv and window: a case of an uncorrected double outlet right ventricle with d-transposition of great arteries with concomitant aortopulmonary window in a 31-year-old female

Funding Acknowledgements

none

Double outlet right ventricle (DORV) is a rare type of ventriculo-arterial connection occurring in about 1-3% of congenital heart defects. Moreover, transposition of the great arteries, wherein the aorta is anterior and to the right of the pulmonary artery (D-TGA), accounts for only 26% of cases of DORV. An aortopulmonary window, on the other hand, represents approximately only 0.2% of all congenital cardiac lesions. A case of DORV with D-TGA and pulmonary stenosis with a concomitant aortopulmonary window has never been reported, particularly in an adult in the third decade of life and without any history of surgical repair.

We present the case of a 31-year-old female who had sought consult for left-sided weakness. On physical examination, a grade IV/VI systolic murmur was heard at the left anterior chest and cyanosis of the digits of the upper and lower extremities were noted. Transthoracic echocardiogram revealed a non-restrictive ventricular septal defect (VSD) and segmental approach showed atrial and visceral situs solitus, levocardia, and atrioventricular concordance. However, there was ventriculoarterial discordance with fusiform aneurysmal dilatation of the aorta, which was noted to be at the right of and anterior to the pulmonary artery. Both great vessels arose from the right ventricle. Other echocardiographic findings included dilated right atrium, dilated and hypertrophied right ventricle with volume and pressure overload, global left ventricular hypokinesia with mild systolic dysfunction, and moderate to severe aortic regurgitation. The above complex congenital anomalies were confirmed via transesophageal echocardiogram and cardiac magnetic resonance imaging (MRI). Furthermore, pulmonary valve stenosis and aortopulmonary window, that was 3.5 centimeters in length located at the level of the proximal ascending aorta and main pulmonary artery, were seen on the MRI.

Various cardiac imaging modalities aided in cinching the diagnosis for this very rare complex congenital case in an adult reaching the third decade of life. Palliative care was deemed best for this patient due to the severity of her cardiac condition.

Abstract P1445 Figure 1.

The financial burden of acute odontogenic infections: the South Australian experience

BACKGROUND

Acute odontogenic infections are a common surgical emergency managed by public hospitals in Australia which cause considerable patient morbidity and occasionally, mortality. Despite posing a significant public health burden, Australian data evaluating the cost of the management of these patients are lacking. This study assessed the patient and treatment variables associated with inpatient management of deep odontogenic infections, and their respective financial impact, at a statewide Oral & Maxillofacial service.

METHODS

A retrospective audit was carried out of patients with deep odontogenic infections at our institution, over a 7-year period. The primary outcome was the total cost of admission. Secondary outcomes included treatment received, operating room time, return-to-theatre, length of admission (LOS), and intensive care unit (ICU) use. Cost variables were assessed against the total LOS and ICU use to determine clinical predictors affecting outcome.

RESULTS

Four hundred and sixty two patients met the inclusion criteria. The average cost per patient was $12 228 Australian Dollars. After multivariate analysis, variables most significantly associated with increased cost of care and LOS were high-risk infections with airway compromise, high admission white cell count and age.

CONCLUSION

Hospital-based management of deep-space odontogenic infections engender significant costs compared to early primary care intervention such as a dental extraction ($181/extraction).

4113Glucose lowering drugs or strategies, major adverse cardiovascular events and heart failure outcomes, and association with weight loss - meta-analysis of large cardiovascular outcome trials

Background

Glucose lowering drugs or strategies (GLDS) have varied effects on major adverse cardiovascular events (MACE) and heart failure (HF) in cardiovascular outcomes trials. Mechanisms driving cardiovascular risk reduction remain elusive.

Methods

We searched MEDLINE, PubMed, and meeting abstracts up to 11/21/2018 for large GLDS cardiovascular outcome trials (CVOTs) in patients with or at risk for type 2 diabetes. Primary endpoints of MACE and HF were evaluated with random effects risk ratios (RR) and explored by baseline CVD subgroups and meta-regression by weight change across treatment arms.

Results

In 27 GLDS CVOTs, a total 207,820 patients, median age 63 years, 64% male, 64% CVD and 11% with prior HF were studied over a mean 3.8 years with 20,118 (10%) patients having MACE and 7,212 (4%) a HF event. Compared with standard care, GLDS overall lowered MACE (RR 0.92, P<0.ehz745.01171) but not HF (RR 1.01, P=0.91). Across GLDS, the magnitude and directionality varied modestly for MACE RR (P-int=0.07) but markedly for HF (P-int<0.ehz745.01171). Meta-regression showed a change in HF RR by 6% (95% CI 3%-9%) per 1 kg weight gain/loss between treatment arms (P=0.0006; Figure). In 9 trials of GLDS that achieved marked weight loss (lifestyle, GLP1 agonists, SGLT2 inhibitors), MACE benefit was confined to patients with baseline CVD (RR 0.89 [0.84–0.95] versus without (RR 1.02 [0.91–1.15]; P-int=0.01) with consistent HF effect (RR 0.80 [0.72–0.88] vs RR 0.76 [0.56–1.03]; P-int=0.74).

Heart Failure Risk and Changes in Weight

Conclusion

HF outcomes were improved with GLDS that lower weight. Among diabetes GLDS that lower weight, there was a robust risk reduction in atherothrombotic and heart failure events, with the MACE benefit confined to patients with established CVD.

Acknowledgement/Funding

Heart and Stroke Foundation

5970Morbidity and mortality in patients precluded for transvenous pacemaker implantation: experience with the Micra transcatheter pacemaker

Background

The Micra transcatheter pacemaker has proven to be a safe and effective alternative to transvenous pacemakers (TVPs). However, the safety profile after Micra implantation in patients deemed poor candidates for TVPs is poorly understood.

Purpose

To evaluate the safety and all-cause mortality outcomes in Micra recipients stratified by whether or not they were precluded for therapy with TVP.

Methods

Micra patients from the Micra Transcatheter Pacing (IDE) Study, Continued Access (CA) study, and Post-Approval Registry (PAR) were divided into groups based upon whether or not the implanting physician considered the patient to be precluded from receiving a transvenous pacing system. All-cause mortality was compared between the Micra patient groups and patients receiving a single-chamber transvenous pacing system (SC-TVP) since 2010 from the Medtronic product surveillance registry using univariate and multivariate Cox models.

Results

Among 2,819 patients who underwent a Micra implant attempt, the overall major complication rate through 24 months was 3.5%. In these patients, 548 were deemed precluded from TVP implantation. Prior device infection or bacteremia (38.9%), venous access issues (36.1%) and thrombosis (10.2%) were amongst the most common causes of preclusion for TVP implantation. These patients were younger (71.7 vs. 76.7 years), more frequently on hemodialysis (26.3% vs. 2.5%), and more often had a prior CIED implanted (38.4% vs. 4.4%) than non-precluded patients. Over an average follow-up of 13.5±11.1 months, all-cause mortality was significantly higher in precluded Micra patients compared with SC-TVP patients (HR: 2.16, 95% CI: 1.54–3.2, P<0.001) (Figure 1). However, there was no significant difference in all-cause mortality when comparing non-precluded Micra patients and SC-TVP patients (HR: 1.12, 95% CI: 0.86–1.44, P=0.401). Acute all-cause death (within 1 month) among Micra patients was 2.74% and 1.32% in the precluded and non-precluded TVP groups, respectively. The procedure-related death rate was 0.55% for the TVP precluded group and 0.13% for the not precluded group (P=0.092). The major complication rate through 24-months was similar between the two Micra groups (4.0% vs 3.4%, P=0.630).

All-cause mortality for Micra and SC-TVP

Conclusion

The overall safety profile of Micra remains is in line with previously reported data. All-cause mortality risk (both acute and long term) appears to be higher in patients who were precluded from receiving TVP.

Acknowledgement/Funding

Supported by Medtronic

Ultrastructure of duck Tembusu virus observed by electron microscopy with negative staining

Duck Tembusu virus (DTMUV) is a newly emerging enveloped flavivirus. This study shows the ultrastructure of DTMUV using viral purification, negative staining and electron microscopy. Electron microscopic examinations revealed mature DTMUV particles with 50 to 75 nm in diameter and typical enveloped flavivirus structure that consists of the internal nucleocapsid, an inner layer of lipid bilayer and an external layer of E glycoprotein ectodomain. Particles appear to be mostly spherical. In particular, RNA core is deep colored and dense, both capsid and lipid bilayer are clearly visible, the capsid forms regular hexagon, and E glycoprotein ectodomain forms a fringe instead of visible spikes. Thus, this report about the clear ultrastructure of the DTMUV particles will be the major driving forces behind structural biology of DTMUV.

[Impact of hypoxia-reoxygenation environment on autophagy level of osteoblasts]

Objective: To investigate the impact of hypoxia-reoxygenation environment on the level of autophagy in osteoblasts. Methods: Osteoblasts were purified from the skulls of newborn SD rats within 24-48 hours by tissue block adherence culture and differential centrifugation. The osteoblasts were identified by alizarin red staining and alkaline phosphatase staining. The third generation osteoblasts were cultured in normal state and randomly divided into four groups: group A was cultured under normal condition for 36 hours; group B was cultured under normal condition for 18 hours, then under hypoxia for 18 hours; group C was cultured under hypoxia for 36 hours; group D was cultured under hypoxia for 18 hours, and then under normal condition for 18 hours. The ability to form calcium nodules of osteoblasts in the four groups was observed after culture. The proliferation activity of osteoblasts was detected by CCK-8 assay. The expressions of autophagy specified gene Beclin 1, microtubule-associated protein light chain 3(LC3) and collagen Ⅰ(COL-Ⅰ), bone morphogenetic protein 2 (BMP-2) genes were detected by real time polymerase chain reaction (RT-PCR), and the protein expressions of Beclin 1, LC3-Ⅰ,LC3-Ⅱ and P62 were detected by immunoblotting. Results: Alizarin red staining showed that osteoblasts in group A had the strongest calcification ability, and calcification ability of osteoblasts in group B,C and D lowered gradually, and it was lowest in group D. The proliferative activity under the CCK-8 detection in group A, B, C and D was 98%±8%, 90%±8%,82%±9%,76%±8%, respectively (F=35.764, P=0.000). The mRNA expression of Beclin 1, LC3-Ⅱthe 4 groups increased gradurally (group D> group C> group B> group A)(F=38.327, 16.583, both P<0.05); and the mRNA expression of COL-Ⅰ, BMP-2 decreased gradually in the 4 groups (group A> group B> group C> group D) (F=20.387, 12.426, both P<0.05). The protein expression of Beclin 1,LC3-Ⅱ/LC3-Ⅰ increased gradually in the groups (group D>group C>group B>group A) (F=26.843, 28.576, bothP<0.05), and the expression of P62 protein decreased gradually (F=18.946, P=0.011). Conclusions: Hypoxia-reoxygenation environment can reduce the proliferation activity of osteoblasts and up-regulate the expression of autophagy-related genes in osteoblasts. Anoxic reoxygenation environment promotes the increasing of autophagy levels in osteoblasts.