Interventions to Prevent and Respond to Violence Against Justice-Involved Young Women: A Scoping Review

Young women who have had contact with the criminal justice system (justice-involved young women) have an increased risk of being a victim of violence. However, no reviews have synthesized the evidence on interventions to prevent or respond to violence against justice-involved young women. We conducted a scoping review to identify interventions designed to prevent or respond to violence against justice-involved young women. We searched Medline, Criminal Justice Abstracts, Web of Science, and Google Scholar for peer-reviewed and gray literature published in English from January 1, 2000 until March 23, 2021. Consistent with the public health approach to violence, we included primary, secondary, and tertiary interventions. Excluding duplicates, our search returned 5,603 records, 14 of which met our inclusion criteria. We narratively synthesized the included studies, all of which were conducted in the United States. Most included studies examined a tertiary intervention (n = 10), and few examined a primary (n = 2) or secondary (n = 2) intervention. Across the Joanna Briggs Institute Critical Appraisal Tools, the percentage of items met ranged from 0% to 78%. There was some limited evidence that tertiary interventions that included cognitive behavioral therapy reduced the mental health impacts of violence victimization among justice-involved young women. There was little evidence on primary and secondary interventions. Effective and evidence-based interventions to prevent violence victimization and revictimization against justice-involved young women remains a critical gap in knowledge.

Machine Learning of Physiologic Waveforms and Electronic Health Record Data: A Large Perioperative Data Set of High-Fidelity Physiologic Waveforms

Perioperative morbidity and mortality are significantly associated with both static and dynamic perioperative factors. The studies investigating static perioperative factors have been reported; however, there are a limited number of previous studies and data sets analyzing dynamic perioperative factors, including physiologic waveforms, despite its clinical importance. To fill the gap, the authors introduce a novel large size perioperative data set: Machine Learning Of physiologic waveforms and electronic health Record Data (MLORD) data set. They also provide a concise tutorial on machine learning to illustrate predictive models trained on complex and diverse structures in the MLORD data set.

Differential Oxidative Stress Responses in Type II Airway Epithelial Cells Impact Premature Senescence and Lung Fibrosis Susceptibility

PURPOSE/OBJECTIVE(S)

Radiation-Induced Pulmonary Fibrosis (RIPF) is a late toxicity characterized by premature senescence in Type II airway epithelial cells (AECII) and accumulation of alternatively activated (M2) macrophages. Differential susceptibility to RIPF is observed across mouse strains. Based on our prior study of the effects of macrophage variation on RIPF, we hypothesized that intrinsic differences in AECII oxidative stress response across mouse strains also impact susceptibility to RIPF.

MATERIALS/METHODS

Ten-week-old female mice from C57L, C57BL6 and C3H/HeN strains were exposed to thoracic irradiation (5x6 Gy, n>5 per group). Fifteen weeks after radiation, lung tissue was collected and examined with Masson-Trichrome staining (histologic changes) and β-galactosidase activity assay (senescence). AECII prepared from mice of each strain were exposed to irradiation. To assess differential gene expression, total RNA was extracted and assessed with a multiplex analysis platform and quantitative PCR. Senescence was assessed by β-galactosidase activity assay in primary AECII after irradiation or after co-culture with M2 macrophages polarized with IL13.

RESULTS

Susceptibility to radiation-induced lung injury, survival, and premature AECII senescence vary by mouse strain: C57L (fibrosis-prone), C57BL6J (-intermediate) and C3H/HeN (-resistant). Enriched AECII from each strain exhibited differential expression of genes related to inflammatory responses including SASP production after irradiation. Minimal increased expression of Il1r1 was observed in irradiated and unirradiated AECII from C3H/HeN, however Il1rn levels were markedly elevated in response to irradiation. The expression of Thioredoxin (Txn) and Thioredoxin reductase 1 (Txnrd1) in AECII from C3H/HeN was significantly higher than those observed in other strains. In Vivo, C3H/HeN mouse lungs exhibited the least premature senescence in AECII after irradiation. Premature senescence in AECII irradiated In Vitro or co-cultured with superoxide anion-producing M2 macrophages was substantially less in AECII from C3H/HeN compared to other strains.

CONCLUSION

A comparison of primary AECII from three different mouse strains identified intrinsic differences in expression of major inflammatory signaling (IL1R and IL1RN) and redox homeostasis status (TXN and TXNDR1) molecules. This study is the first to demonstrate that intrinsic differences in AECII impacts susceptibility to premature senescence and lung fibrosis after irradiation.

Strain-tunable Berry curvature in quasi-two-dimensional chromium telluride

Magnetic transition metal chalcogenides form an emerging platform for exploring spin-orbit driven Berry phase phenomena owing to the nontrivial interplay between topology and magnetism. Here we show that the anomalous Hall effect in pristine Cr₂Te₃ thin films manifests a unique temperature-dependent sign reversal at nonzero magnetization, resulting from the momentum-space Berry curvature as established by first-principles simulations. The sign change is strain tunable, enabled by the sharp and well-defined substrate/film interface in the quasi-two-dimensional Cr₂Te₃ epitaxial films, revealed by scanning transmission electron microscopy and depth-sensitive polarized neutron reflectometry. This Berry phase effect further introduces hump-shaped Hall peaks in pristine Cr₂Te₃ near the coercive field during the magnetization switching process, owing to the presence of strain-modulated magnetic layers/domains. The versatile interface tunability of Berry curvature in Cr₂Te₃ thin films offers new opportunities for topological electronics.

GalaxyDock2-HEME: Protein-ligand docking for heme proteins

Prediction of protein-ligand binding poses is an essential component for understanding protein-ligand interactions and computer-aided drug design. Various proteins involve prosthetic groups such as heme for their functions, and adequate consideration of the prosthetic groups is vital for protein-ligand docking. Here, we extend the GalaxyDock2 protein-ligand docking algorithm to handle ligand docking to heme proteins. Docking to heme proteins involves increased complexity because the interaction of heme iron and ligand has covalent nature. GalaxyDock2-HEME, a new protein-ligand docking program for heme proteins, has been developed based on GalaxyDock2 by adding an orientation-dependent scoring term to describe heme iron-ligand coordination interaction. This new docking program performs better than other noncommercial docking programs such as EADock with MMBP, AutoDock Vina, PLANTS, LeDock, and GalaxyDock2 on a heme protein-ligand docking benchmark set in which ligands are known to bind iron. In addition, docking results on two other sets of heme protein-ligand complexes in which ligands do not bind iron show that GalaxyDock2-HEME does not have a high bias toward iron binding compared to other docking programs. This implies that the new docking program can distinguish iron binders from noniron binders for heme proteins.

Structural basis for Y2 receptor-mediated neuropeptide Y and peptide YY signaling

Neuropeptide Y (NPY) and its receptors are expressed in various human tissues including the brain where they regulate appetite and emotion. Upon NPY stimulation, the neuropeptide Y1 and Y2 receptors (Y₁R and Y₂R, respectively) activate G_I signaling, but their physiological responses to food intake are different. In addition, deletion of the two N-terminal amino acids of peptide YY (PYY(3-36)), the endogenous form found in circulation, can stimulate Y₂R but not Y₁R, suggesting that Y₁R and Y₂R may have distinct ligand-binding modes. Here, we report the cryo-electron microscopy structures of the PYY(3-36)‒Y₂R‒G_i and NPY‒Y₂R‒G_i complexes. Using cell-based assays, molecular dynamics simulations, and structural analysis, we revealed the molecular basis of the exclusive binding of PYY(3-36) to Y₂R. Furthermore, we demonstrated that Y₂R favors G protein signaling over β-arrestin signaling upon activation, whereas Y₁R does not show a preference between these two pathways.

How Neighborhood Structural and Individual Characteristics Affect Frailty Progression: Evidence from the China Health and Retirement Longitudinal Study

OBJECTIVES

(1) To characterize the average trajectories of frailty over time in Chinese community-dwelling older adults; (2) To assess the effects of neighborhood structural and individual characteristics on frailty progression.

DESIGN

A nationally representative prospective cohort study.

SETTING

Communities in 28 provinces, China.

PARTICIPANTS

6238 respondents aged 60 and above in 447 communities from four waves of the China Health and Retirement Longitudinal Study.

MEASUREMENTS

Frailty was measured using the 61-item Frailty Index (FI).

RESULTS

The trajectory of FI was nonlinear, with an average growth rate of 0.025 that significantly slows down at the rate of 0.002 per year. Older, male, and uninsured respondents showed faster rates of growth in FI over time than younger, female, and insured counterparts. Respondents living in neighborhoods with a higher percentage of the older population and rural villages showed slower rates of growth in FI over time.

CONCLUSION

Expanding health insurance coverage and keeping a high clustering of the elderly in neighborhoods may be the potential strategies for population-level frailty prevention and interventions.

Sex differences in suicide, suicidal ideation, and self-harm after release from incarceration: a systematic review and meta-analysis

PURPOSE

People released from incarceration are at increased risk of suicide compared to the general population. We aimed to synthesise evidence on the incidence of and sex differences in suicide, suicidal ideation, and self-harm after release from incarceration.

METHODS

We searched MEDLINE, EMBASE, PsycINFO, Web of Science and PubMed between 1 January 1970 and 14 October 2021 for suicide, suicidal ideation, and self-harm after release from incarceration (PROSPERO registration: CRD42020208885). We calculated pooled crude mortality rates (CMRs) and standardised mortality ratios (SMRs) for suicide, overall and by sex, using random-effects models. We calculated a pooled incidence rate ratio (IRR) comparing rates of suicide by sex.

RESULTS

Twenty-nine studies were included. The pooled suicide CMR per 100,000 person years was 114.5 (95%CI 97.0, 132.0, I² = 99.2%) for non-sex stratified samples, 139.5 (95% CI 91.3, 187.8, I² = 88.6%) for women, and 121.8 (95% CI 82.4, 161.2, I² = 99.1%) for men. The suicide SMR was 7.4 (95% CI 5.4, 9.4, I² = 98.3%) for non-sex stratified samples, 14.9 for women (95% CI 6.7, 23.1, I² = 88.3%), and 4.6 for men (95% CI 1.3, 7.8, I² = 98.8%). The pooled suicide IRR comparing women to men was 1.1 (95% CI 0.9, 1.4, I² = 82.2%). No studies reporting self-harm or suicidal ideation after incarceration reported sex differences.

CONCLUSION

People released from incarceration are greater than seven times more likely to die by suicide than the general population. The rate of suicide is higher after release than during incarceration, with the elevation in suicide risk (compared with the general population) three times higher for women than for men. Greater effort to prevent suicide after incarceration, particularly among women, is urgently needed.

Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction

While deep learning (DL) has brought a revolution in the protein structure prediction field, still an important question remains how the revolution can be transferred to advances in structure-based drug discovery. Because the lessons from the recent GPCR dock challenge were inconclusive primarily due to the size of the dataset, in this work we further elaborated on 70 diverse GPCR complexes bound to either small molecules or peptides to investigate the best-practice modeling and docking strategies for GPCR drug discovery. From our quantitative analysis, it is shown that substantial improvements in docking and virtual screening have been possible by the advance in DL-based protein structure predictions with respect to the expected results from the combination of best pre-DL tools. The success rate of docking on DL-based model structures approaches that of cross-docking on experimental structures, showing over 30% improvement from the best pre-DL protocols. This amount of performance could be achieved only when two modeling points were considered properly: 1) correct functional-state modeling of receptors and 2) receptor-flexible docking. Best-practice modeling strategies and the model confidence estimation metric suggested in this work may serve as a guideline for future computer-aided GPCR drug discovery scenarios.

CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein-ligand docking

Structure prediction of protein-ligand complexes, called protein-ligand docking, is a critical computational technique that can be used to understand the underlying principle behind the protein functions at the atomic level and to design new molecules regulating the functions. Protein-ligand docking methods have been employed in structure-based drug discovery for hit discovery and lead optimization. One of the important technical challenges in protein-ligand docking is to account for protein conformational changes induced by ligand binding. A small change such as a single side-chain rotation upon ligand binding can hinder accurate docking. Here we report an increase in docking performance achieved by structure alignment to known complex structures. First, a fully flexible compound-to-compound alignment method CSAlign is developed by global optimization of a shape score. Next, the alignment method is combined with a docking algorithm to dock a new ligand to a target protein when a reference protein-ligand complex structure is available. This alignment-based docking method, called CSAlign-Dock, showed superior performance to ab initio docking methods in cross-docking benchmark tests. Both CSAlign and CSAlign-Dock are freely available as a web server at https://galaxy.seoklab.org/csalign.

HProteome-BSite: predicted binding sites and ligands in human 3D proteome

Atomic-level knowledge of protein-ligand interactions allows a detailed understanding of protein functions and provides critical clues to discovering molecules regulating the functions. While recent innovative deep learning methods for protein structure prediction dramatically increased the structural coverage of the human proteome, molecular interactions remain largely unknown. A new database, HProteome-BSite, provides predictions of binding sites and ligands in the enlarged 3D human proteome. The model structures for human proteins from the AlphaFold Protein Structure Database were processed to structural domains of high confidence to maximize the coverage and reliability of interaction prediction. For ligand binding site prediction, an updated version of a template-based method GalaxySite was used. A high-level performance of the updated GalaxySite was confirmed. HProteome-BSite covers 80.74% of the UniProt entries in the AlphaFold human 3D proteome. Predicted binding sites and binding poses of potential ligands are provided for effective applications to further functional studies and drug discovery. The HProteome-BSite database is available at https://galaxy.seoklab.org/hproteome-bsite/database and is free and open to all users.

Comparison of adhesive single-lead ECG device and Holter test for atrial fibrillation monitoring

Background

There is insufficient validation of diagnostic benefits of extended monitoring with an adhesive single-lead ECG device compared to Holter test for routine medical care of AF patients.

Purpose

The study aimed to compare AF detection rates between 72-hour monitoring using an adhesive single-lead ECG device (mobiCARE MC-100, Seers Technology, Republic of Korea) and 24-hour Holter test among AF patients at outpatient clinics.

Methods

A total of 200 AF patients indicated for Holter test at cardiology outpatient clinics enrolled in the study. Study participants equipped both Holter and MC-100 for the first 24 hours (Figure 1). After then, only MC-100 continued ECG monitoring for additional 48 hours. AF detection during the first 24 hours was compared between two devices. The diagnostic benefits of extended monitoring with MC-100 were evaluated.

Results

During the first 24 hours, both monitoring methods detected AF in the same 40/200 (20.0%) patients (20 patients with paroxysmal and persistent AF each). Compared to 24-hour Holter, MC-100 increased AF detection rate by 1.5-fold (58/200; 29.0%) and 1.6-fold (64/200; 32.0%) with 48- and 72-hour monitoring, respectively (Figure 2A). With MC-100, the number of newly discovered patients with paroxysmal AF was 20/44 (45.5%), 18/44 (40.9%), and 6/44 (13.6%) for 24-, 48-, and 72-hour monitoring. Compared to 24-hour Holter, 72-hour monitoring with MC-100 increased the detection rate of paroxysmal AF by 2.2-fold (44/20). If only the episodes lasting over 30 seconds were counted as AF with MC-100, the detection rate of paroxysmal AF was decreased by 9.1% (Figure 2B).

Conclusion

Compared to Holter, AF detection rates could be improved with an adhesive single-lead device, especially for patients with paroxysmal AF. This device is expected to be useful for AF detection among patients whose conventional ECG tests were ineffective in documenting AF episodes.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): The Korea Medical Device Development Fund grant funded by the Korean government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health & Welfare, Republic of Korea, the Ministry of Food and Drug Safety)

The left atrial low-voltage area and persistent atrial fibrillation treated with pulmonary vein isolation alone

Background

There are limited data regarding the association between the burden of the left atrial low-voltage area (LVA) and the outcome of pulmonary vein isolation (PVI) alone in persistent atrial fibrillation (PeAF).

Purpose

The study aimed to investigate the impact of the burden of LVA on the patients with PeAF treated with PVI alone.

Methods

Using a retrospective cohort of PeAF patients who underwent PVI alone, both clinical and the left atrial voltage mapping data were reviewed. LVA was defined as an area of ≤0.5 mV (bipolar) when mapped during sinus rhythm and ≤0.2 mV during AF. The high burden of LVA was defined as a case when the LVA constitutes ≥10% of the total left atrial body area. The patients were categorized into either the high or low burden groups. The recurrence of any atrial tachyarrhythmia was followed up, and multivariable Cox's regression analysis was performed.

Results

A total of 50 and 25 patients were investigated for the low burden (LVA<10%) and high burden (LVA≥10%) groups, respectively. Compared to the low burden group, the high burden group had a significantly less male proportion (56.0% versus 78.0%), a higher CHA2DS2-VASc score (median 3 versus 2), more chronic kidney disease (16.0% versus 2.0%), and a higher burden of LVA (20±11% versus 5±3%). During the median follow-up of 9.5 (6.2–16.2)months, there were 30.0% and 48.0% ofrecurrences for the low and high burden groups, respectively. Compared to the low burden group, the high burden group was associated with higher risks of both early and late recurrences (HR [95% CI] =2.67 [1.15–6.18] and 2.08 [1.03–4.20], respectively) (Figure 1). The best cut-off of LVA to predict 2-year recurrence was 10.1% (Figure 2).

Conclusion

The high burden of LVA was significantly associated with an increased risk of recurrence among PeAF patients treated with PVI alone. Tailored ablation in addition to PVI would be needed to improve outcomes in patients with PeAF having a high burden of LVA.

Funding Acknowledgement

Type of funding sources: None.

Protective effect of proton pump inhibitor against gastrointestinal bleeding in patients receiving oral anticoagulants: a systematic review and meta-analysis

Background

The concurrent use of proton pump inhibitor (PPI) in oral anticoagulant (OAC) treated patients may be associated with a lower risk of gastrointestinal bleeding (GIB), but evidence is still conflicting according to individual OACs.

Purpose

We conducted a meta-analysis to estimate the risk of GIB in patients with OAC and PPI co-therapy.

Methods

A systematic search of PubMed, EMBASE, and Cochrane was performed for studies reporting GIB risk in OAC and PPI co-therapy. Primary outcomes were total GIB and major GIB events. We calculated pooled estimates of GIB risk by a random-effect meta-analysis and reported as odds ratios (OR) and 95% CI. Stratified analyses according to the origin of GIB, ethnic groups, individual OACs, and the presence of underlying GIB risk factors were performed.

Results

A total of 10 studies (1 randomized controlled study and 9 observational studies) and 1,970,931 patients who received OAC were included. OAC and PPI co-therapy were associated with a lower risk of total GIB, and major GIB; OR (95% CI) was 0.67 (0.62–0.74) for total GIB and 0.68 (0.63–0.75) for major GIB, respectively. Among total GIB, only the risk of upper GIB was lower with OAC and PPI co-therapy (OR 0.67, 95% CI 0.64–0.70). No difference in the lower risk of primary GIB outcomes of PPI co-therapy was observed between Asians and non-Asians (p-for-difference, total GIB=0.695, major GIB=0.748, respectively) and among individual OACs except for edoxaban. The protective effect of PPI on total GIB was more significant in high-risk patients, defined as those with concurrent medication of antiplatelets or non-steroidal anti-inflammatory drugs (OR 0.62, 95% CI 0.52–0.73) and presence of high bleeding risk factors such as previous GIB history, HAS-BLED score ≥3, or underlying gastrointestinal diseases. (OR 0.65, 95% CI 0.61–0.70).

Conclusion

In patients who receive OAC, the use of PPI co-therapy was associated with a lower risk of total GIB and major GIB irrespective of ethnic group and OAC type except for edoxaban. PPI co-therapy can be considered particularly in patients on concomitant NSAID and antiplatelet use or patients with high GIB risk factors.

Funding Acknowledgement

Type of funding sources: None.

Impact of mental disease on the risk of atrial fibrillation in patients with diabetes mellitus: a nationwide population-based study

Background

Diabetes mellitus (DM) is known to increase the risk of mental disorders, which increases the health care burden in these patients. Also, DM is one of the risk factors leading to atrial fibrillation (AF), and the presence of concomitant AF and DM adds to the increased risks of stroke and death. It is uncertain whether mental disease is an independent risk factor of incident AF in patients with DM.

Purpose

To investigate whether diabetic patients with mental disease have an increased risk of AF.

Methods

Using the Korea National Health Insurance Service database, we enrolled 2,512,690 patients diagnosed with DM without AF between 2009 and 2021. Newly diagnosed AF was identified during the follow-up period. We compared the risk of AF between patients with mental disease and those without.

Results

Among the total population, 828,929 (32.99%; mean age 61.58±11.28; 56.71% female) patients were diagnosed with mental diseases (Figure 1). Anxiety (564,786 patients, 68.13%) was the most common mental disease, while depression was the second most common (313,773 patients, 37.85%). Diabetic patients with mental diseases had a higher percentage of women, hypertension, dyslipidemia, chronic kidney failure, congestive heart failure, obstructive sleep apnea, and thyroid disease. During a median 7.0 years (IQR 5.93–8.07) follow-up, 34,523 were diagnosed new-onset AF (4.66 per 1,000 person-year). In multivariate analysis, diabetic patients with mental disorders showed a higher risk of new-onset AF (HR 1.19; 95% CI 1.17–1.21; p-value <0.0001) (Figure 2). Among mental diseases, depression, insomnia, and anxiety were associated with increased risks of new-onset AF (HR 1.15; 95% CI 1.12–1.17; HR 1.15; 95% CI 1.13–1.18; and HR 1.19; 95% CI, 1.67–1.21; all p-value <0.0001, respectively), whereas bipolar disorder and schizophrenia showed non-statistically significant trends (due to small numbers). Subgroup analyses showed that younger age had significant interactions with depression, insomnia, and anxiety.

Conclusion

Mental diseases, especially depression, insomnia, and anxiety, showed an increased risk of AF in patients with DM. Awareness and prompt diagnosis and management of AF would be necessary for these high-risk populations at risk of incident AF.

Funding Acknowledgement

Type of funding sources: None.

Increased risk of atrial fibrillation in patients with uterine fibroids: a nationwide population-based study

Background

Uterine fibroid, the most common benign neoplasm of the uterus, is associated with an elevated risk of cardiovascular disease. The link between incident atrial fibrillation (AF) and the uterine fibroid is unclear because earlier studies focused primarily on the development of atherosclerosis and hypertension. We aimed to investigate the risk of AF in patients with uterine fibroid.

Methods

This is a retrospective cohort study using the Korean National Health Insurance Service database (NHIS). From 2009 to 2012, a total of 2,574,349 women (20 to 40 years old) who underwent general health examinations were included. Diagnosis of uterine fibroids and surgical treatment status was defined by the international classification of diseases, 10th revision codes, and procedural codes from the Korean NHIS. The primary outcome was newly diagnosed AF. The risk of AF according to the uterine fibroids and their surgical treatment status was evaluated using Cox proportional-hazard models.

Results

Of the total population, the mean age was 29.76±4.27 years, and 20,682 (0.8%) were identified to have uterine fibroid. Incident AF was identified in 3,868 patients (61 in the fibroid group, 3,807 in the control group) during a mean follow-up of 7.3±1.1 years. Patients of the uterine fibroid group showed a higher incidence of AF compared to the control group (0.41 and 0.20 per 1000 person-years, respectively, Figure 1). Multivariate Cox-regression analysis presented that uterine fibroid was an independent risk factor of AF: hazard ratio (HR) 1.50, 95% confidence interval (CI) 1.16–1.93, p=0.002. Compared to the control group, uterine fibroid patients who underwent surgical treatment tend to show a lower risk for AF (HR 1.22, 95% CI 0.79–1.90) than patients without surgical treatment (HR 1.69, 95% CI 1.24–2.30), though statistical significance was indeterminate (Figure 2). After propensity score matching, patients of the uterine fibroid group showed higher risk of AF when compared to the control group (HR 1.77, 95% CI 1.32–2.63, p<0.001), which was in line with our main results. The presence of uterine fibroid was consistently associated with higher risk of AF among all subgroups except for the stroke subgroup.

Conclusion

Patients with uterine fibroids are predisposed to an increased risk of AF compared to the control group. Careful monitoring of arrhythmia development would be warranted in patients of uterine fibroid and surgical treatment as it is associated with a modest risk decrement of incident AF.

Funding Acknowledgement

Type of funding sources: None.

Increased epicardial adipose tissue volume after anthracycline chemotherapy is associated with a low risk of cardiotoxicity in breast cancer

Introduction

Chemotherapy-induced cardiotoxicity is a critical issue for patients with breast cancer. Epicardial adipose tissue (EAT) is located between the myocardial surface and the visceral layer of the pericardium. Change of EAT is associated with cardiac dysfunction.

Purpose

Considering that early detection of patients at risk of developing cardiotoxicity during and after anthracycline-based chemotherapy is the most important factor in reducing and reversing cardiac function, there is a need to identify a simple and novel imaging marker that can predict cardiotoxicity at an early stage. Therefore, the objective of the present study was to investigate the relationship between EAT and chemotherapy-induced cardiotoxicity.

Methods

This retrospective study analyzed EAT on chest computed tomography (CT) of patients with early breast cancer using automatic, quantitative measurement software between November 2015 and January 2020. Changes in EAT before and after initiation of chemotherapy were compared according to the type of anticancer drug. Subclinical cardiotoxicity was defined as worsening ≥10% in left ventricular ejection fraction to an absolute value >50% with a lower limit of normal measured with standard echocardiography.

Results

Among 234 patients with breast cancer, 85 were treated with adjuvant anthracycline-based (AC) and 149 were treated with non-anthracycline based (non-AC) chemotherapy. There was a significant increase in EAT volume index (mL/kg/m2) at the end of chemotherapy compared to that at the baseline in the AC group (3.33±1.53 vs. 2.90±1.52, p<0.001), but not in the non-AC group. During the follow-up period, subclinical cardiotoxicity developed in 20 (8.6%) patients in the total population (15.3% in the AC group and 4.8% in the non-AC group). In the multivariable analysis, EAT volume index increment after chemotherapy was associated with a lower risk of subclinical cardiotoxicity in the AC group (Odds ratio: 0.364, 95% CI: 0.136–0.971, p=0.044).

Conclusions

Measurement of EAT during anthracycline-based chemotherapy might help identify subgroups who are vulnerable to chemotherapy-induced cardiotoxicity. Early detection of EAT volume change could enable tailored chemotherapy with cardiotoxicity prevention strategies.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Medical Technology Development Program of the National Research Foundation of Korea (NRF) funded by the Korean government (MSIT).

Paradoxical association between lipid levels and incident atrial fibrillation according to statin usage

Background

In epidemiology studies, a higher level of total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) is associated with a lower risk of atrial fibrillation (AF). Statin use might exert possible confounding effects in the paradoxical relationship; however, the inverse link between AF and cholesterol level that distinguishes statin users from non-users has not been evaluated.

Objective

We investigated the epidemiological relationships of TC–AF and LDL-C–AF in statin users and non-users, respectively.

Methods

From the Korean National Health Insurance Service database, we included 9,778,014 adults who underwent a health examination in 2009 and had no prior AF history. The levels of TC and LCL-C at the health exam were categorized in quartile (Q) and decile (D) values of the total study population. The study population was grouped into statin users and non-users, and TC–AF and LDL-C–AF relationships were evaluated.

Results

867,336 (8.9%) were on statin use among the total population. Statin users showed higher TC level (208.4±55.6 vs. 194.1±39.5 mg/dL, p<0.001) and LDL-C level (123.0±102.2 vs. 121.3±226.3, p<0.001) compared to non-users. Inverse associations of TC–AF and LCL-C–AF were observed; higher levels of TC and LDL-C were associated with a lower risk of AF. The hazard ratios (HR) and 95% confidence intervals (CI) were 0.797 (0.786–0.809) for the highest quartile of TC (Q4, TC ≥218) and 0.832 (0.82–0.843) for the highest quartile of LDL-C (Q4, LDL-C ≥135) when adjusted by age, sex, lifestyle behaviors, comorbidities, and low-income status. Statin users exhibited higher AF incidence rate than non-statin users, but the association in statin users generally tracked that seen among non-statin users demonstrating similar HR in Q4 of TC [0.812 (0.790–0.835) for statin users and 0.812 (0.798–0.826) for non-statin users] and LDL-C [0.842 (0.819–0.865) for statin users and 0.849 (0.835–0.863) for non-statin users].

Conclusion

The paradoxical relationship between lipid levels (TC and LDL-C) and incident AF remained consistent both in statin users and non-users. Further research is required to investigate an underlying mechanism for the cholesterol paradox of AF which still seems evident despite the pleiotropic effects of statin.

Funding Acknowledgement

Type of funding sources: None.

Impact of metabolic syndrome on the risk of ischemic stroke in non-anticoagulated atrial fibrillation patients having low CHA2DS2-VASc scores

Background

Metabolic syndrome (MetS) predisposes to a thromboembolic state. However, conflicting results have been reported on whether MetS confers an increased risk of ischemic stroke in atrial fibrillation (AF), especially in patients with low CHA2DS2-VASc score who are not indicated for oral anticoagulant therapy.

Purpose

We investigated the risk of ischemic stroke according to the presence of MetS, the number of MetS components (metabolic burden), and the individual metabolic components in non-anticoagulated AF patients with low CHA2DS2-VASc score.

Methods

A total of 76,015 oral anticoagulant-naïve AF patients with low CHA2DS2-VASc score (0,1 in male and 1 in female) were included from the Korean National Health Insurance Service database. The status of MetS and individual metabolic components were evaluated based on health examination data within two years of AF diagnosis. We estimated the risk of ischemic stroke according to MetS, metabolic burden, and an individual component of MetS using Cox proportional-hazards models.

Results

The mean age was 49.8±11.1 years and 52,388 (68.9%) were male. The average CHA2DS2-VASc score was 0.7±0.5 and MetS was prevalent among 21,570 (28.4%) of the study population. During a mean follow-up of 5.1 years, ischemic stroke was developed in 1,395 (1.84%) patients. MetS was associated with a higher risk of ischemic stroke after adjustment for age, sex, lifestyle behaviors, low income, and cardiovascular comorbidities: adjusted hazard ratio (aHR) 1.19, 95% confidence interval (CI) 1.06–1.33, p=0.002. A positive linear correlation was observed between metabolic burden and ischemic stroke risk. Patients with five MetS components showed the highest aHR of 1.55 (95% CI 1.14–2.11, Figure 1 and Figure 2), whereas those with a single MetS component had a marginal risk of ischemic stroke (aHR 1.18, 95% CI 0.99–1.41). Among individual metabolic components, elevated blood pressure and increased waist circumference was significantly associated with an increased risk of ischemic stroke: aHR (95% CI), 1.45 (1.30–1.62), p<0.001, and 1.15 (1.03–1.30), p=0.016, respectively.

Conclusions

Among AF patients initially with CHA2DS2-VASc score 0 and 1 with no anticoagulation, the presence of MetS is associated with an increased risk of ischemic stroke. Given the linear incremental correlation between metabolic burden and ischemic stroke, special attention to the care of metabolic derangements is required in AF patients who are not indicated for anticoagulation.

Funding Acknowledgement

Type of funding sources: None.

Atrial fibrillation detection in ambulatory patients using a smart ring powered by deep learning analysis of continuous photoplethysmography monitoring

Background

Atrial fibrillation (AF) detection could be effective with photoplethysmography (PPG) signal monitoring by a wearable device.

Purpose

We aimed to validate the performance of AF detection among ambulatory patients who underwent electrical cardioversion for AF using a smart ring capable of continuous PPG monitoring and deep learning analysis.

Methods

In this prospective single-arm study, participants who underwent successful electrical cardioversion for AF were enrolled. The participants equipped a smart ring (CardioTracker, Sky Labs Inc., Seongnam, Republic of Korea) after the electrical cardioversion. The smart ring then continuously monitored PPG over 14 days to detect AF recurrence. The smart ring alarmed AF episodes based on deep learning analysis of PPG. The participants were asked to measure at least three daily ECGs using the smart ring to validate AF recurrence detected by PPG. All ECG snapshots were recorded along with lead I and saved with simultaneous PPG. ECG data were examined by the three cardiologists independently (SK, SRL, and EKC). The monitoring time, analyzable proportions of monitored signals, detection rates of AF episodes, and the diagnostic performance of PPG-based deep learning were evaluated. At the end of the monitoring, a survey on the use of the smart ring was performed.

Results

A total of 35 participants (mean age 58.9 years, male 74.3%) were enrolled. Figure 1 illustrates an example of PPG monitoring and PPG-ECG snapshots by the smart ring. The study participation period was a median of 14 days and the wearing time of the smart ring was a median of 9.2 days (IQR 7.1–11.5 days). Signal artifacts during daily activity decreased the analyzable proportions of monitored PPG by 68.5%. Irregular pulse episodes were detected by the smart ring in 29 (82.9%) participants after a median of 1 day from the cardioversion (Figure 2). A total of 2532 PPG-ECG snapshots were acquired and 1623 (64.1%) were interpretable by both the cardiologists (using ECG) and the deep learning analysis (using PPG). Comparing PPG by simultaneous ECG, the performance of AF detection by the smart ring was 98.7% for sensitivity, 97.8% for specificity, 2.2% for false positives, and 1.3% for false negatives (Figure 2). After using the smart ring, 76.9% of the participants responded that they had no discomfort in using the smart ring in daily activity and another 76.9% responded that it was helpful to monitor their disease.

Conclusion

Despite the signal artifacts during daily activity, AF detection with PPG monitoring by a smart ring could be effective for AF screening among ambulatory patients.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): This work was supported by Sky Labs Inc, Seongnam, Republic of Korea, and by the grant No. 0320202040 from the Seoul National University Hospital Research Fund.

Machine learning based potentiating impacts of 12-lead ECG for classifying paroxysmal versus non-paroxysmal atrial fibrillation

Background

Conventional modality requires several days observation by Holter monitor to differentiate atrial fibrillation (AF) between Paroxysmal atrial fibrillation (PAF) and Non-paroxysmal atrial fibrillation (Non-PAF). Rapid and practical differentiating approach is needed.

Objective

To develop a machine learning model that observes 10-s of standard 12-lead electrocardiograph (ECG) for real-time classification of AF between PAF versus Non-PAF.

Methods

In this multicenter, retrospective cohort study, the model training and cross-validation was performed on a dataset consisting of 741 patients enrolled from Severance Hospital, South Korea. For cross-institutional validation, the trained model was applied to an independent data set of 600 patients enrolled from Ewha University Hospital, South Korea. Lasso regression was applied to develop the model.

Results

In the primary analysis, the Area Under the Receiver Operating Characteristic Curve (AUC) on the test set for the model that predicted AF subtype only using ECG was 0.72 (95% CI 0.65–0.80). In the secondary analysis, AUC only using baseline characteristics was 0.53 (95% CI 0.45–0.61), while the model that employed both baseline characteristics and ECG parameters was 0.72 (95% CI 0.65–0.80). Moreover, the model that incorporated baseline characteristics, ECG, and Echocardiographic parameters achieved an AUC of 0.76 (95% CI 0.678–0.855) on the test set.

Conclusions

Our machine learning model using ECG has potential for automatic differentiation of AF between PAF versus Non-PAF achieving high accuracy. The inclusion of  Echocardiographic parameters further increases model performance. Further studies are needed to clarify the next steps towards clinical translation of the proposed algorithm.

Association Between Aspirin Use and Gastric Adenocarcinoma: A Prospective Cohort Study

Prospective data examining the association of aspirin use, according to dose and duration, with long-term risk of gastric adenocarcinoma in non-Asian cohorts are lacking. We evaluated the association between aspirin use and risk of gastric adenocarcinoma in two large prospective U.S. cohort studies, the Nurses' Health Study and the Health Professionals Follow-up Study. Cox proportional hazards regression models were used to calculate multivariable adjusted HRs and 95% confidence intervals (CI). Among the 159,116 participants, we documented 316 gastric adenocarcinoma cases (176 women, 140 men) over 34 years encompassing 4.5 million person-years. Among women, regular aspirin use (at least two times or more per week) was significantly associated with lower risk of gastric adenocarcinoma (multivariable HR, 0.52; 95% CI, 0.37-0.73) compared with nonregular use. However, regular aspirin use was not associated with gastric adenocarcinoma risk among men (multivariable HR, 1.08; 95% CI, 0.77-1.52; Pheterogeneity for sex = 0.003). Among women, the lower risk of gastric adenocarcinoma was more apparent with increasing duration of aspirin use (Ptrend < 0.001) and more than five tablets per week (multivariable HR, 0.51; 95% CI, 0.31-0.84). Regular, long-term aspirin use was associated with lower risk of gastric adenocarcinoma among women, but not men. The benefit appeared after at least 10 years of use and was maximized at higher doses among women. The heterogeneity by sex in the association of aspirin use with risk of gastric adenocarcinoma requires further investigation.

PREVENTION RELEVANCE

Novel prevention is urgently needed to reduce incidence and mortality of gastric cancer. We found that regular aspirin use was associated with lower risk of gastric adenocarcinoma among women, but not men. The benefit appeared after at least 10 years of use and was maximized at higher doses among women. See related Spotlight, p. 213.

Self-reported COVID-19 vaccine hesitancy and uptake among participants from different racial and ethnic groups in the United States and United Kingdom

Worldwide, racial and ethnic minorities have been disproportionately impacted by COVID-19 with increased risk of infection, its related complications, and death. In the initial phase of population-based vaccination in the United States (U.S.) and United Kingdom (U.K.), vaccine hesitancy may result in differences in uptake. We performed a cohort study among U.S. and U.K. participants who volunteered to take part in the smartphone-based COVID Symptom Study (March 2020-February 2021) and used logistic regression to estimate odds ratios of vaccine hesitancy and uptake. In the U.S. (n = 87,388), compared to white participants, vaccine hesitancy was greater for Black and Hispanic participants and those reporting more than one or other race. In the U.K. (n = 1,254,294), racial and ethnic minority participants showed similar levels of vaccine hesitancy to the U.S. However, associations between participant race and ethnicity and levels of vaccine uptake were observed to be different in the U.S. and the U.K. studies. Among U.S. participants, vaccine uptake was significantly lower among Black participants, which persisted among participants that self-reported being vaccine-willing. In contrast, statistically significant racial and ethnic disparities in vaccine uptake were not observed in the U.K sample. In this study of self-reported vaccine hesitancy and uptake, lower levels of vaccine uptake in Black participants in the U.S. during the initial vaccine rollout may be attributable to both hesitancy and disparities in access.

A pGpG-specific phosphodiesterase regulates cyclic di-GMP signaling in Vibrio cholerae

The bacterial second messenger bis-(3′-5′)-cyclic diguanylate monophosphate (c-di-GMP) controls various cellular processes, including motility, toxin production, and biofilm formation. c-di-GMP is enzymatically synthesized by GGDEF domain–containing diguanylate cyclases and degraded by HD-GYP domain–containing phosphodiesterases (PDEs) to 2 GMP or by EAL domain–containing PDE-As to 5ʹ-phosphoguanylyl-(3ʹ,5ʹ)-guanosine (pGpG). Since excess pGpG feedback inhibits PDE-A activity and thereby can lead to the uncontrolled accumulation of c-di-GMP, a PDE that degrades pGpG to 2 GMP (PDE-B) has been presumed to exist. To date, the only enzyme known to hydrolyze pGpG is oligoribonuclease Orn, which degrades all kinds of oligoribonucleotides. Here, we identified a pGpG-specific PDE, which we named PggH, using biochemical approaches in the gram-negative bacteria Vibrio cholerae. Biochemical experiments revealed that PggH exhibited specific PDE activity only toward pGpG, thus differing from the previously reported Orn. Furthermore, the high-resolution structure of PggH revealed the basis for its PDE activity and narrow substrate specificity. Finally, we propose that PggH could modulate the activities of PDE-As and the intracellular concentration of c-di-GMP, resulting in phenotypic changes including in biofilm formation.

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70-75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70-80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.

Diet quality and risk and severity of COVID-19: a prospective cohort study

OBJECTIVE

Poor metabolic health and unhealthy lifestyle factors have been associated with risk and severity of COVID-19, but data for diet are lacking. We aimed to investigate the association of diet quality with risk and severity of COVID-19 and its interaction with socioeconomic deprivation.

DESIGN

We used data from 592 571 participants of the smartphone-based COVID-19 Symptom Study. Diet information was collected for the prepandemic period using a short food frequency questionnaire, and diet quality was assessed using a healthful Plant-Based Diet Score, which emphasises healthy plant foods such as fruits or vegetables. Multivariable Cox models were fitted to calculate HRs and 95% CIs for COVID-19 risk and severity defined using a validated symptom-based algorithm or hospitalisation with oxygen support, respectively.

RESULTS

Over 3 886 274 person-months of follow-up, 31 815 COVID-19 cases were documented. Compared with individuals in the lowest quartile of the diet score, high diet quality was associated with lower risk of COVID-19 (HR 0.91; 95% CI 0.88 to 0.94) and severe COVID-19 (HR 0.59; 95% CI 0.47 to 0.74). The joint association of low diet quality and increased deprivation on COVID-19 risk was higher than the sum of the risk associated with each factor alone (Pinteraction=0.005). The corresponding absolute excess rate per 10 000 person/months for lowest vs highest quartile of diet score was 22.5 (95% CI 18.8 to 26.3) among persons living in areas with low deprivation and 40.8 (95% CI 31.7 to 49.8) among persons living in areas with high deprivation.

CONCLUSIONS

A diet characterised by healthy plant-based foods was associated with lower risk and severity of COVID-19. This association may be particularly evident among individuals living in areas with higher socioeconomic deprivation.

Dual antithrombotic therapy on early clinical outcomes in patients with atrial fibrillation after percutaneous coronary intervention: a nationwide study in the era of NOAC

Background/Introduction

Recent evidence has confirmed low bleeding risk with double antithrombotic therapy, combining oral anticoagulant (OAC) and single platelet inhibitor, in patients with atrial fibrillation (AF) undergoing percutaneous coronary intervention (PCI). Among the Asian AF population, most of the patients received dual antiplatelet therapy (DAPT) without OACs, even after the introduction of non-vitamin K oral anticoagulants (NOACs).

Purpose

The current nationwide study assessed 3-month ischemic and bleeding risks of DAPT in comparison to triple antithrombotic therapy among the Korean AF population undergoing PCI.

Methods

We analyzed the claims records of 11,039 patients (mean age 70 years, 66.3% male, and mean CHA2DS2-VASc score 3.2) between 2013 to 2018. Patients were categorized into triple therapy group with vitamin K antagonists (VKAs-TT), or NOACs (NOACs-TT), and DAPT group according to the antithrombotic therapy after PCI. 3-month risks of ischemic stroke, non-fatal myocardial infarction, any in-hospital death, and major bleeding were compared between groups after baseline adjustment using inverse probability weighting.

Results

A total of 1,786, 1,997, and 7,256 patients were allocated to the VKAs-TT, NOACs-TT, and DAPT groups. The DAPT group had a higher prevalence of prior MI and coronary revascularization, but had lower thromboembolic and bleeding risks than the triple antithrombotic therapy groups (mean CHA2DS2-VASc score 3.8, 4.1, and 3.5; and mean HAS-BLED score 3.3, 3.4, and 3.1 for VKAs-TT, NOACs-TT, and DAPT groups, respectively). The NOACs-TT group was associated with a lower risk of ischemic stroke (hazard ratio [HR] 0.38, 95% confidence interval [CI] 0.20–0.70) and any in-hospital death (HR 0.70, 95% CI 0.49–0.98) compared with the VKAs-TT group. The DAPT group showed a lower risk of ischemic stroke (HR 0.41, 95% CI 0.27–0.63) and major bleeding (HR 0.55, 95% CI 0.37–0.84) than the VKAs-TT group, especially in patients without prior OAC treatment. The DAPT group showed a comparable ischemic risk against the NOACs-TT group, although the risk of major bleeding was lower in the DAPT group, especially among old age (HR 0.47, 95% CI 0.29–0.78) or OACs-naive patients (HR 0.50, 95% CI 0.29–0.86).

Conclusion

Among the Asian AF population, using short-term DAPT for 3-month after PCI was associated with a lower risk of bleeding without increasing ischemic risk compared to triple antithrombotic therapy with OAC. This may be a therapeutic option in very high bleeding risk patients who have had complex PCI necessitating focus on DAPT in the initial 3 month period.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): This study was supported by grant no 3020200200 from the Seoul National University Hospital Research Fund, by the Korea Medical Device Development Fund grant funded by the Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health & Welfare, Republic of Korea, the Ministry of Food and Drug Safety) (Project Number: 202013B14), and by the Korea National Research Foundation funded by the Ministry of Education, Science and Technology (grant 2020R1F1A106740). Figure 1Figure 2

Antithrombotic therapy for patients with atrial fibrillation and stable coronary artery disease of 1-year and 3-year after percutaneous coronary intervention: a nationwide population-based study

Background

In a recent trial, rivaroxaban monotherapy was noninferior for efficacy and superior for safety to rivaroxaban plus single antiplatelet therapy, as antithrombotic therapy for patients with atrial fibrillation (AF) and stable coronary artery disease (CAD). However, there are limited data regarding the comparative effectiveness and safety of oral anticoagulant (OAC) monotherapy versus OAC plus single antiplatelet therapy (SAPT) in real-world practice, especially after the introduction of direct oral anticoagulants (DOAC).

Purpose

To compare the effectiveness, safety, and net clinical benefit of OAC monotherapy to OAC plus SAPT in patients with AF and stable CAD of 1-year and 3-year after percutaneous coronary intervention (PCI) in a contemporary real-world observational cohort.

Methods

Using the Korean nationwide claims database, we included AF patients who underwent PCI from January 1, 2009 to February 28, 2019. Considering dynamic changes of antithrombotic therapy according to the period after receiving PCI, the index antithrombotic treatment was independently defined at the different time after receiving PCI and we conducted two cohort: 1-year and 3-year after PCI. In each cohort, the baseline characteristics of OAC monotherapy and OAC plus SAPT groups were balanced using inverse probability of treatment weighting (IPTW) methods. To assess clinical outcomes, ischemic stroke, myocardial infarction, major bleeding, and composite clinical outcomes of each outcome were analyzed.

Results

In cohort with 1-year after PCI, 678 patients with OAC monotherapy and 3159 patients with OAC plus SAPT were included. In cohort with 3-year after PCI, 1038 patients with OAC monotherapy and 2128 patients with OAC plus SAPT were enrolled. The baseline characteristics were well-balanced after IPTW between the two groups in both cohorts. Among total population, about 45% of patients prescribed DOAC as OAC treatment. Among patients with 1-year after PCI, OAC monotherapy and OAC plus SAPT showed comparable results for ischemic stroke, myocardial infarction, major bleeding, and composite clinical outcomes (Figure). In cohort with 3-year after PCI, OAC monotherapy and OAC plus SAPT showed comparable results for ischemic stroke and myocardial infarction, but OAC monotherapy was associated with a lower risk of the composite clinical outcome (hazard ratio [HR] 0.762, 95% confidence interval [CI] 0.607–0.950), mainly driven by reduction of major bleeding risk (HR 0.762, 95% CI 0.607–0.950) compared to OAC plus SAPT (Figure).

Conclusion

OAC monotherapy might be, at least, comparable choice for patients with AF and stable CAD compared to OAC plus SAPT. In patients with stable CAD more than 3-years after index PCI, OAC monotherapy could be better therapeutic choice to achieve less major bleeding and positive net clinical benefit.

Funding Acknowledgement

Type of funding sources: None.

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on 10 proteins. The resulting models were released to the public. CASP community members also worked together to provide estimates of local and global accuracy and identify structure-based domain boundaries for some proteins. Subsequently, two of these structures (ORF3a and ORF8) have been solved experimentally, allowing assessment of both model quality and the accuracy estimates. Models from the AlphaFold2 group were found to have good agreement with the experimental structures, with main chain GDT_TS accuracy scores ranging from 63 (a correct topology) to 87 (competitive with experiment).

Protein oligomer structure prediction using GALAXY in CASP14

Proteins perform their functions by interacting with other biomolecules. For these interactions, proteins often form homo- or hetero-oligomers as well. Thus, oligomer protein structures provide important clues regarding the biological roles of proteins. To this end, computational prediction of oligomer structures may be a useful tool in the absence of experimentally resolved structures. Here, we describe our server and human-expert methods used to predict oligomer structures in the CASP14 experiment. Examples are provided for cases in which manual domain-splitting led to improved oligomeric domain structures by ab initio docking, automated oligomer structure refinement led to improved subunit orientation and terminal structure, and manual oligomer modeling utilizing literature information generated a reasonable oligomer model. We also discussed the results of post-prediction docking calculations with AlphaFold2 monomers as input in comparison to our blind prediction results. Overall, ab initio docking of AlphaFold2 models did not lead to better oligomer structure prediction, which may be attributed to the interfacial structural difference between the AlphaFold2 monomer structures and the crystal oligomer structures. This result poses a next-stage challenge in oligomer structure prediction after the success of AlphaFold2. For successful protein assembly structure prediction, a different approach that exploits further evolutionary information on the interface and/or flexible docking taking the interfacial conformational flexibilities of subunit structures into account is needed.

Race, ethnicity, community-level socioeconomic factors, and risk of COVID-19 in the United States and the United Kingdom

BACKGROUND

There is limited prior investigation of the combined influence of personal and community-level socioeconomic factors on racial/ethnic disparities in individual risk of coronavirus disease 2019 (COVID-19).

METHODS

We performed a cross-sectional analysis nested within a prospective cohort of 2,102,364 participants from March 29, 2020 in the United States (US) and March 24, 2020 in the United Kingdom (UK) through December 02, 2020 via the COVID Symptom Study smartphone application. We examined the contribution of community-level deprivation using the Neighborhood Deprivation Index (NDI) and the Index of Multiple Deprivation (IMD) to observe racial/ethnic disparities in COVID-19 incidence. ClinicalTrials.gov registration: NCT04331509.

FINDINGS

Compared with non-Hispanic White participants, the risk for a positive COVID-19 test was increased in the US for non-Hispanic Black (multivariable-adjusted odds ratio [OR], 1.32; 95% confidence interval [CI], 1.18-1.47) and Hispanic participants (OR, 1.42; 95% CI, 1.33-1.52) and in the UK for Black (OR, 1.17; 95% CI, 1.02-1.34), South Asian (OR, 1.39; 95% CI, 1.30-1.49), and Middle Eastern participants (OR, 1.38; 95% CI, 1.18-1.61). This elevated risk was associated with living in more deprived communities according to the NDI/IMD. After accounting for downstream mediators of COVID-19 risk, community-level deprivation still mediated 16.6% and 7.7% of the excess risk in Black compared to White participants in the US and the UK, respectively.

INTERPRETATION

Our results illustrate the critical role of social determinants of health in the disproportionate COVID-19 risk experienced by racial and ethnic minorities.

Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges

In CASP, blind testing of model accuracy estimation methods has been conducted on models submitted by tertiary structure prediction servers. In CASP14, model accuracy estimation results were evaluated in terms of both global and local structure accuracy, as in the previous CASPs. Unlike the previous CASPs that did not show pronounced improvements in performance, the best single-model method (from the Baker group) showed an improved performance in CASP14, particularly in evaluating global structure accuracy when compared to both the best single-model methods in previous CASPs and the best multi-model methods in the current CASP. Although the CASP14 experiment on model accuracy estimation did not deal with the structures generated by AlphaFold2, new challenges that have arisen due to the success of AlphaFold2 are discussed.

Association of social distancing and face mask use with risk of COVID-19

Given the continued burden of COVID-19 worldwide, there is a high unmet need for data on the effect of social distancing and face mask use to mitigate the risk of COVID-19. We examined the association of community-level social distancing measures and individual face mask use with risk of predicted COVID-19 in a large prospective U.S. cohort study of 198,077 participants. Individuals living in communities with the greatest social distancing had a 31% lower risk of predicted COVID-19 compared with those living in communities with poor social distancing. Self-reported 'always' use of face mask was associated with a 62% reduced risk of predicted COVID-19 even among individuals living in a community with poor social distancing. These findings provide support for the efficacy of mask-wearing even in settings of poor social distancing in reducing COVID-19 transmission. Despite mass vaccination campaigns in many parts of the world, continued efforts at social distancing and face mask use remain critically important in reducing the spread of COVID-19.

Racial and ethnic differences in COVID-19 vaccine hesitancy and uptake

BACKGROUND

Racial and ethnic minorities have been disproportionately impacted by COVID-19. In the initial phase of population-based vaccination in the United States (U.S.) and United Kingdom (U.K.), vaccine hesitancy and limited access may result in disparities in uptake.

METHODS

We performed a cohort study among U.S. and U.K. participants in the smartphone-based COVID Symptom Study (March 24, 2020-February 16, 2021). We used logistic regression to estimate odds ratios (ORs) of COVID-19 vaccine hesitancy (unsure/not willing) and receipt.

RESULTS

In the U.S. ( n =87,388), compared to White non-Hispanic participants, the multivariable ORs of vaccine hesitancy were 3.15 (95% CI: 2.86 to 3.47) for Black participants, 1.42 (1.28 to 1.58) for Hispanic participants, 1.34 (1.18 to 1.52) for Asian participants, and 2.02 (1.70 to 2.39) for participants reporting more than one race/other. In the U.K. ( n =1,254,294), racial and ethnic minorities had similarly elevated hesitancy: compared to White participants, their corresponding ORs were 2.84 (95% CI: 2.69 to 2.99) for Black participants, 1.66 (1.57 to 1.76) for South Asian participants, 1.84 (1.70 to 1.98) for Middle East/East Asian participants, and 1.48 (1.39 to 1.57) for participants reporting more than one race/other. Among U.S. participants, the OR of vaccine receipt was 0.71 (0.64 to 0.79) for Black participants, a disparity that persisted among individuals who specifically endorsed a willingness to obtain a vaccine. In contrast, disparities in uptake were not observed in the U.K.

CONCLUSIONS

COVID-19 vaccine hesitancy was greater among racial and ethnic minorities, and Black participants living in the U.S. were less likely to receive a vaccine than White participants. Lower uptake among Black participants in the U.S. during the initial vaccine rollout is attributable to both hesitancy and disparities in access.

Cancer and Risk of COVID-19 Through a General Community Survey

Individuals with cancer may be at high risk for coronavirus disease 2019 (COVID-19) and adverse outcomes. However, evidence from large population-based studies examining whether cancer and cancer-related therapy exacerbates the risk of COVID-19 infection is still limited. Data were collected from the COVID Symptom Study smartphone application since March 29 through May 8, 2020. Among 23,266 participants with cancer and 1,784,293 without cancer, we documented 10,404 reports of a positive COVID-19 test. Compared with participants without cancer, those living with cancer had a 60% increased risk of a positive COVID-19 test. Among patients with cancer, current treatment with chemotherapy or immunotherapy was associated with a 2.2-fold increased risk of a positive test. The association between cancer and COVID-19 infection was stronger among participants >65 years and males. Future studies are needed to identify subgroups by tumor types and treatment regimens who are particularly at risk for COVID-19 infection and adverse outcomes.

Feasibility Study for an Automated Engineering Change Process

Engineering change is a significant cost sink in many projects. While avoiding and mitigating the risk of change is the ideal approach, mistakes and improvements are recognized inevitably as more is learned over time about the quality of the decisions made in a product's design. This paper presents a feasibility and performance analysis of automating engineering change requests to demonstrate the promise for increasing speed, efficiency, and effectiveness of product-lifecycle-wide engineering-change-request processes. To explore this idea, a comparatively simple case study is examined both to mimic the reduced set of alterable aspects of a typical change request and to highlight the need of appropriate search algorithms as brute force methods quickly prohibitively resource intensive. Although such cases may seem trivial for human agents, with the volume of expected change requests in a typical facility, the potential opportunity gain by eliminating or reducing the amount of human effort in low level change requests accumulate into significant returns for industry on time and money. Within this work, the genetic algorithm is selected to demonstrate feasibility due to its broad scope of applicability and low barriers to deployment. Future refinement of this or other sophisticated algorithms leveraging the nature of the standard representations and qualities of alterable design features could produce tools with strong implications for process efficiency and industry competitiveness in the execution of its projects.

Effectiveness of corticosteroids for post-extubation stridor and extubation failure in pediatric patients: a systematic review and meta-analysis

BACKGROUND

While the results of previous meta-analyses have shown beneficial effects of corticosteroid therapy on post-extubation stridor and extubation failure in adults, these results might not be generalizable to children because of the differences in anatomy and structure. We aimed to determine the benefits of corticosteroids on those outcomes in pediatric populations.

METHODS

We searched PubMed, EMBASE, and reference lists of articles from inception until February 2019. Randomized controlled trials and observational studies on the efficacy of systemic corticosteroid administration given prior to elective extubation in mechanically ventilated pediatrics were eligible. Outcomes included post-extubation stridor indicating laryngeal edema and extubation failures.

RESULTS

A total of ten randomized controlled trials with 591 pediatric patients were included: seven of the ten studies for post-extubation stridor/suspected upper airway obstruction and nine of the ten studies for extubation failure. The estimate of pooled odds ratios (ORs) for post-extubation stridor/suspected upper airway obstruction was 0.40 (95% CI: 0.21-0.79). When analysis was restricted to trials that had explicit data for infants and explicit data for pediatric patients under 5 years old excluding infants, the estimates of pooled ORs were 0.53 (95% CI: 0.20-1.40) and 0.68 (95% CI: 0.38-1.22), respectively. For pediatric patients who received corticosteroids, there was a 0.37-fold lower odds of extubation failure than that in pediatric patients who did not receive corticosteroids (OR, 0.37; 95% CI, 0.22-0.61). While three observational studies were included in this review, their estimates have a potential for bias and we did not perform a meta-analysis.

CONCLUSIONS

Despite a relatively small sample size in each randomized controlled trial and wide ranges of ages and steroid administration regimens, our results suggest that the use of corticosteroids for prevention of post-extubation stridor and extubation failure could be considered to be acceptable in pediatric patients.

Association of social distancing and masking with risk of COVID-19

Given the continued burden of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) disease (COVID-19) across the U.S., there is a high unmet need for data to inform decision-making regarding social distancing and universal masking. We examined the association of community-level social distancing measures and individual masking with risk of predicted COVID-19 in a large prospective U.S. cohort study of 198,077 participants. Individuals living in communities with the greatest social distancing had a 31% lower risk of predicted COVID-19 compared with those living in communities with poor social distancing. Self-reported masking was associated with a 63% reduced risk of predicted COVID-19 even among individuals living in a community with poor social distancing. These findings provide support for the efficacy of mask-wearing even in settings of poor social distancing in reducing COVID-19 transmission. In the current environment of relaxed social distancing mandates and practices, universal masking may be particularly important in mitigating risk of infection.

Risk of COVID-19 among front-line health-care workers and the general community: a prospective cohort study

BACKGROUND

Data for front-line health-care workers and risk of COVID-19 are limited. We sought to assess risk of COVID-19 among front-line health-care workers compared with the general community and the effect of personal protective equipment (PPE) on risk.

METHODS

We did a prospective, observational cohort study in the UK and the USA of the general community, including front-line health-care workers, using self-reported data from the COVID Symptom Study smartphone application (app) from March 24 (UK) and March 29 (USA) to April 23, 2020. Participants were voluntary users of the app and at first use provided information on demographic factors (including age, sex, race or ethnic background, height and weight, and occupation) and medical history, and subsequently reported any COVID-19 symptoms. We used Cox proportional hazards modelling to estimate multivariate-adjusted hazard ratios (HRs) of our primary outcome, which was a positive COVID-19 test. The COVID Symptom Study app is registered with ClinicalTrials.gov, NCT04331509.

FINDINGS

Among 2 035 395 community individuals and 99 795 front-line health-care workers, we recorded 5545 incident reports of a positive COVID-19 test over 34 435 272 person-days. Compared with the general community, front-line health-care workers were at increased risk for reporting a positive COVID-19 test (adjusted HR 11·61, 95% CI 10·93-12·33). To account for differences in testing frequency between front-line health-care workers and the general community and possible selection bias, an inverse probability-weighted model was used to adjust for the likelihood of receiving a COVID-19 test (adjusted HR 3·40, 95% CI 3·37-3·43). Secondary and post-hoc analyses suggested adequacy of PPE, clinical setting, and ethnic background were also important factors.

INTERPRETATION

In the UK and the USA, risk of reporting a positive test for COVID-19 was increased among front-line health-care workers. Health-care systems should ensure adequate availability of PPE and develop additional strategies to protect health-care workers from COVID-19, particularly those from Black, Asian, and minority ethnic backgrounds. Additional follow-up of these observational findings is needed.

FUNDING

Zoe Global, Wellcome Trust, Engineering and Physical Sciences Research Council, National Institutes of Health Research, UK Research and Innovation, Alzheimer's Society, National Institutes of Health, National Institute for Occupational Safety and Health, and Massachusetts Consortium on Pathogen Readiness.

The COronavirus Pandemic Epidemiology (COPE) Consortium: A Call to Action

The rapid pace of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; COVID-19) pandemic presents challenges to the real-time collection of population-scale data to inform near-term public health needs as well as future investigations. We established the COronavirus Pandemic Epidemiology (COPE) consortium to address this unprecedented crisis on behalf of the epidemiology research community. As a central component of this initiative, we have developed a COVID Symptom Study (previously known as the COVID Symptom Tracker) mobile application as a common data collection tool for epidemiologic cohort studies with active study participants. This mobile application collects information on risk factors, daily symptoms, and outcomes through a user-friendly interface that minimizes participant burden. Combined with our efforts within the general population, data collected from nearly 3 million participants in the United States and United Kingdom are being used to address critical needs in the emergency response, including identifying potential hot spots of disease and clinically actionable risk factors. The linkage of symptom data collected in the app with information and biospecimens already collected in epidemiology cohorts will position us to address key questions related to diet, lifestyle, environmental, and socioeconomic factors on susceptibility to COVID-19, clinical outcomes related to infection, and long-term physical, mental health, and financial sequalae. We call upon additional epidemiology cohorts to join this collective effort to strengthen our impact on the current health crisis and generate a new model for a collaborative and nimble research infrastructure that will lead to more rapid translation of our work for the betterment of public health.

GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds

Computational techniques for predicting interactions of proteins and druglike molecules have often been used to search for compounds that bind a given protein with high affinity. More recently, such tools have also been applied to the reverse procedure of searching protein targets for a given compound. Among methods for predicting protein-ligand interactions, ligand-based methods relying on similarity to ligands of known interactions are effective only when similar protein-ligand interactions are known. Receptor-based methods predicting protein-ligand interactions by molecular docking are effective only when high-accuracy receptor structures and binding sites are available. Moreover, the computational cost of molecular docking tends to be too high to be applied to the entire protein structure database. In this paper, an effective target prediction method, which combines ligand similarity-based and receptor structure-based approaches, is introduced. In this method, protein-ligand docking is performed after efficient structure- and similarity-based screening. The enriched protein target database by predicted binding ligands and sites allows detection of protein targets with previously unknown ligand interactions. The method, called GalaxySagittarius, is freely available as a web server at http://galaxy.seoklab.org/sagittarius.

Subnanosecond phase transition dynamics in laser-shocked iron

Iron is one of the most studied chemical elements due to its sociotechnological and planetary importance; hence, understanding its structural transition dynamics is of vital interest. By combining a short pulse optical laser and an ultrashort free electron laser pulse, we have observed the subnanosecond structural dynamics of iron from high-quality x-ray diffraction data measured at 50-ps intervals up to 2500 ps. We unequivocally identify a three-wave structure during the initial compression and a two-wave structure during the decaying shock, involving all of the known structural types of iron (α-, γ-, and ε-phase). In the final stage, negative lattice pressures are generated by the propagation of rarefaction waves, leading to the formation of expanded phases and the recovery of γ-phase. Our observations demonstrate the unique capability of measuring the atomistic evolution during the entire lattice compression and release processes at unprecedented time and strain rate.

1140 Sleep Disturbances, Lifestyle, And Self-Management In Adults With Subarachnoid Hemorrhage

Introduction

Subarachnoid hemorrhage (SAH) survivors often suffer sleep disturbances. Self-management strategies focusing on lifestyle changes and health-promoting behaviors may improve sleep in SAH survivors. Few studies have examined sleep in SAH survivors, and little is known about sleep management practices used to improve their sleep. The purposes of this study were to: 1) describe the prevalence of sleep disturbances using subjective and objective sleep measures, and 2) explore interest in and engagement with self-management practices to promote sleep health in SAH survivors.

Methods

We conducted a cross-sectional study with a convenience sample of 30 SAH survivors recruited from a university hospital. We assessed sleep quality using the Pittsburgh Sleep Quality Index (PSQI), daytime sleepiness using the Epworth Sleepiness Scale (ESS), and objective sleep using wrist actigraphy. We conducted content analysis of semi-structured interviews, with two authors each coding sleep disturbances and self-management practices addressing sleep.

Results

Seventy-three percent of SAH survivors reported poor sleep quality (PSQI &gt; 5) and 27% had daytime sleepiness (ESS &gt; 10). Actigraphy analysis indicated that 41% of SAH survivors slept less than 7 hours or more than 9 hours. Interview content analyses suggested 3 themes and 15 sub-categories: 1) Sleep disturbances (difficulties in falling asleep, wake after sleep onset, daytime sleepiness, too much or insufficient sleep, and poor sleep quality), 2) Sleep management practices (exercise, regular sleep schedule, relaxation, keeping busy and staying active, changing beverage intake, taking supplements, taking medication, recharging energy, and barriers to sleep management), and 3) Healthcare providers (discussing sleep problems with health care providers).

Conclusion

Sleep disturbances are highly prevalent and an urgent need exists to focus on improving sleep in SAH survivors. Developing tailored interventions that incorporate self-management and lifestyle change would be a critical next step to improve sleep and promote health in this at-risk population.

Support

This research was supported by grants from the National Institutes of Health/National Institute of Nursing Research (K23 NR017404), University of Washington Institute of Translational Health Science Translational Research Scholars Program (UL1 TR000423), and University of Washington School of Nursing Research and Intramural Funding Program.

Risk of COVID-19 among frontline healthcare workers and the general community: a prospective cohort study

Background

Data for frontline healthcare workers (HCWs) and risk of SARS-CoV-2 infection are limited and whether personal protective equipment (PPE) mitigates this risk is unknown. We evaluated risk for COVID-19 among frontline HCWs compared to the general community and the influence of PPE.

Methods

We performed a prospective cohort study of the general community, including frontline HCWs, who reported information through the COVID Symptom Study smartphone application beginning on March 24 (United Kingdom, U.K.) and March 29 (United States, U.S.) through April 23, 2020. We used Cox proportional hazards modeling to estimate multivariate-adjusted hazard ratios (aHRs) of a positive COVID-19 test.

Findings

Among 2,035,395 community individuals and 99,795 frontline HCWs, we documented 5,545 incident reports of a positive COVID-19 test over 34,435,272 person-days. Compared with the general community, frontline HCWs had an aHR of 11·6 (95% CI: 10·9 to 12·3) for reporting a positive test. The corresponding aHR was 3·40 (95% CI: 3·37 to 3·43) using an inverse probability weighted Cox model adjusting for the likelihood of receiving a test. A symptom-based classifier of predicted COVID-19 yielded similar risk estimates. Compared with HCWs reporting adequate PPE, the aHRs for reporting a positive test were 1·46 (95% CI: 1·21 to 1·76) for those reporting PPE reuse and 1·31 (95% CI: 1·10 to 1·56) for reporting inadequate PPE. Compared with HCWs reporting adequate PPE who did not care for COVID-19 patients, HCWs caring for patients with documented COVID-19 had aHRs for a positive test of 4·83 (95% CI: 3·99 to 5·85) if they had adequate PPE, 5·06 (95% CI: 3·90 to 6·57) for reused PPE, and 5·91 (95% CI: 4·53 to 7·71) for inadequate PPE.

Interpretation

Frontline HCWs had a significantly increased risk of COVID-19 infection, highest among HCWs who reused PPE or had inadequate access to PPE. However, adequate supplies of PPE did not completely mitigate high-risk exposures.

Funding

Zoe Global Ltd., Wellcome Trust, EPSRC, NIHR, UK Research and Innovation, Alzheimer's Society, NIH, NIOSH, Massachusetts Consortium on Pathogen Readiness.