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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The lifetime risk and impact of vitiligo across sociodemographic groups: a UK population-based cohort study

Abstract Background Vitiligo is an autoimmune skin disorder characterized by depigmented patches of skin, which can have significant psychological impacts. Objectives To estimate the lifetime incidence of vitiligo, overall, by ethnicity and across other sociodemographic subgroups, and to investigate the impacts of vitiligo on mental health, work and healthcare utilization. Methods Incident cases of vitiligo were identified in the Optimum Patient Care Database of primary care records in the UK between 1 January 2004 and 31 December 2020. The lifetime incidence of vitiligo was estimated at age 80 years using modified time-to-event models with age as the timescale, overall and stratified by ethnicity, sex and deprivation. Depression, anxiety, sleep disturbance, healthcare utilization and work-related outcomes were assessed in the 2 years after vitiligo diagnosis and compared with matched controls without vitiligo. The study protocol for this retrospective observational study was registered with ClinicalTrials.gov (NCT06097494). Results In total, 9460 adults and children were newly diagnosed with vitiligo during the study period. The overall cumulative lifetime incidence was 0.92% at 80 years of age [95% confidence interval (CI) 0.90–0.94]. Cumulative incidence was similar in female (0.94%, 95% CI 0.92–0.97) and male patients (0.89%, 95% CI 0.86–0.92). There were substantial differences in lifetime incidence across ethnic groups, listed by Office for National Statistics criteria [Asian 3.58% (95% CI 3.38–3.78); Black 2.18% (95% CI 1.85–2.50); Mixed/multiple 2.03% (95% CI 1.58–2.47); Other 1.05% (95% CI 0.94–1.17); and White 0.73% (95% CI 0.71–0.76)]. Compared with matched controls, people with vitiligo had an increased risk of depression [adjusted odds ratio (aOR) 1.08, 95% CI 1.01–1.15]; anxiety (aOR 1.19, 95% CI 1.09–1.30); depression or anxiety (aOR 1.10, 95% CI 1.03–1.17); and sleep disturbance [adjusted hazard ratio (aHR) 1.15, 95% CI 1.02–1.31]. People with vitiligo also had a greater number of primary care encounters (adjusted incidence rate ratio 1.29, 95% CI 1.26–1.32) and a greater risk of time off work (aHR 1.15, 95% CI 1.06–1.24). There was little evidence of disparities in vitiligo-related impacts across ethnic subgroups. Conclusions Clinicians should be aware of the markedly increased incidence of vitiligo in people belonging to Asian, Black, Mixed/multiple and Other groups. The negative impact of vitiligo on mental health, work and healthcare utilization highlights the importance of monitoring people with vitiligo to identify those who need additional support.

Eleftheriadou, Viktoria↗
DOE OSTI2023

Symptoms and Systemic Drug Reactions in Persons Receiving Weekly Rifapentine Plus Isoniazid (3HP) Treatment for Latent Tuberculosis Infection

Abstract Background Three months of weekly rifapentine plus isoniazid (3HP) therapy for latent tuberculosis infection (LTBI) is recommended worldwide. The development of symptoms and systemic drug reactions (SDRs) on 3HP have not been fully characterized. We aimed to determine the patterns of symptom development and identify SDRs and associated factors in patients taking 3HP. Methods We analyzed symptoms data in participants receiving 3HP in the Tuberculosis Trials Consortium's iAdhere study (Study 33). We examined the patterns of symptom reporting across participants from baseline and 4 monthly visits. Bivariate analyses and multivariable regression models were used to identify factors associated with SDRs. Risk ratios (RRs) and 95% confidence intervals (CIs) were calculated. Results Among 1002 participants receiving 3HP, 768 (77%) reported at least 1 symptom; 97% of these symptoms were grade 1 (79%) or grade 2 (18%). Most symptoms developed in the first month and resolved. A total of 111 (11%) participants had symptoms that met criteria for SDRs; however, 53 (48%) of these participants completed therapy. Factors associated with SDRs and discontinuation included female sex (RR: 2.05; 95% CI: 1.19–3.54), age ≥45 years (RR: 1.99; 95% CI: 1.19–3.31), and use of concomitant medications (RR: 2.26; 95% CI: 1.15–4.42). Conclusions Although most patients receiving 3HP reported symptoms, most were mild, occurred early, and resolved without stopping treatment. Among patients experiencing SDRs, nearly half were able to complete therapy. Patient and provider education should focus on differentiating severe reactions where 3HP should be stopped from minor symptoms that will resolve. Clinical Trials Registration. NCT01582711.

Immunology↗
DOE OSTI2022

Efficacy and safety of warfarin in patients with non-valvular atrial fibrillation and CKD G3–G5D

ABSTRACT Background Observational data comparing warfarin with no treatment for patients with non-valvular atrial fibrillation (NVAF) and severely reduced glomerular filtration rate (GFR) are conflicting and randomized controlled trials (RCTs) are lacking. Most studies do not provide information on warfarin treatment quality, making them difficult to compare. Methods This national cohort study investigates the risk of ischaemic stroke and major bleeding during warfarin treatment compared with no oral anticoagulants in patients with NVAF, GFR category 3–5 (G3–G5) or on dialysis (G5D), with kidney transplant recipients excluded, between 2009 and 2018. Data extracted from high-quality Swedish national healthcare registries, including the Swedish Renal Registry, AuriculA—the Swedish national quality registry for atrial fibrillation and anticoagulation—and the Stroke Registry. Results At enrolment of 12 106 patients, 21.4% were G3, 43.5% were G4, 11.6% were G5 and 23.6% were G5D. The mean time in the therapeutic range was 70%. Warfarin compared with no treatment showed a lower risk for ischaemic stroke for G3 {hazard ratio [HR] 0.37 [95% confidence interval (CI) 0.18–0.76]}, G4 [0.53 (0.38–0.74)] and G5D [0.49 (0.30–0.79)] and an increased risk of major bleeding in G4 [HR 1.22 (1.02–1.46)], G5 [1.52 (1.15–2.01)] and G5D [1.23 (1.00–1.51)]. All-cause mortality was more than halved on warfarin compared with no treatment in all GFR categories. Conclusions Warfarin treatment is associated with a lower risk of ischaemic stroke for patients with NVAF and G3, G4 and G5D at the cost of a higher risk of major bleeding for G4–G5D. Existing observational data are conflicting, stressing the need for RCTs on warfarin compared with no treatment in G4–G5D. Awaiting RCTs, it seems reasonable to treat selected patients on dialysis and NVAF with warfarin.

Welander, Frida (ORCID:0000000311117215)↗
DOE OSTI2022

Lipoprotein(a) is associated with the onset but not the progression of aortic valve calcification

Abstract Aim Lipoprotein(a) [Lp(a)] is a potential causal factor in the pathogenesis of aortic valve disease. However, the relationship of Lp(a) with new onset and progression of aortic valve calcium (AVC) has not been studied. The purpose of the study was to assess whether high serum levels of Lp(a) are associated with AVC incidence and progression. Methods and results A total of 922 individuals from the population-based Rotterdam Study (mean age 66.0±4.2 years, 47.7% men), whose Lp(a) measurements were available, underwent non-enhanced cardiac computed tomography imaging at baseline and after a median follow-up of 14.0 [interquartile range (IQR) 13.9–14.2] years. New-onset AVC was defined as an AVC score >0 on the follow-up scan in the absence of AVC on the first scan. Progression was defined as the absolute difference in AVC score between the baseline and follow-up scan. Logistic and linear regression analyses were performed to evaluate the relationship of Lp(a) with baseline, new onset, and progression of AVC. All analyses were corrected for age, sex, body mass index, smoking, hypertension, dyslipidaemia, and creatinine. AVC progression was analysed conditional on baseline AVC score expressed as restricted cubic splines. Of the 702 individuals without AVC at baseline, 415 (59.1%) developed new-onset AVC on the follow-up scan. In those with baseline AVC, median annual progression was 13.5 (IQR = 5.2–37.8) Agatston units (AU). Lipoprotein(a) concentration was independently associated with baseline AVC [odds ratio (OR) 1.43 for each 50 mg/dL higher Lp(a); 95% confidence interval (CI) 1.15–1.79] and new-onset AVC (OR 1.30 for each 50 mg/dL higher Lp(a); 95% CI 1.02–1.65), but not with AVC progression (β: −71 AU for each 50 mg/dL higher Lp(a); 95% CI −117; 35). Only baseline AVC score was significantly associated with AVC progression (P < 0.001). Conclusion In the population-based Rotterdam Study, Lp(a) is robustly associated with baseline and new-onset AVC but not with AVC progression, suggesting that Lp(a)-lowering interventions may be most effective in pre-calcific stages of aortic valve disease.

Kaiser, Yannick (ORCID:0000000168690042)↗
DOE OSTI2022

Effectiveness of supervised exercise, home-based exercise, or walk advice strategies on walking performance and muscle endurance in patients with intermittent claudication (SUNFIT trial): a randomized clinical trial

Abstract Aims Supervised exercise is a guideline-recommended treatment in intermittent claudication (IC). Hospital-based supervised exercise programmes (SEPs) are underutilized, while home-based structured exercise programmes (HSEPs) have attracted interest. The results from HSEP in IC are inconsistent and may confer no benefit over walk advice (WA) and be less effective than SEP. The aim of the study was to compare the effectiveness of best medical treatment, including Nordic pole WA alone, or WA + SEP or WA + HSEP for patients with IC. Methods and results This three-armed, multicentre randomized clinical trial enrolled patients with IC; all patients received best medical treatment including walking poles and the advice of regular Nordic pole walking (WA). For HSEP and SEP, additional exercise programmes were provided. The primarily investigated hypothesis was a non-inferiority analysis of SEP vs. HSEP regarding the 6-min walk test (6MWT) maximum distance, with a pre-defined non-inferiority margin of 50 m. Supporting outcomes included muscle endurance tests and the walking impairment questionnaire. Outcomes were assessed at baseline, 3, 6, and 12 months by a blinded evaluator. Altogether 166 patients (mean age 72 years; 59% males) were randomized. In HSEP and SEP, 24 and 26% patients, respectively, were fully exercise adherent. All three groups improved pain-free walking distance over time, but there were no significant intergroup differences. The intergroup 6MWT difference between SEP and HSEP from 0 to 12 months was –11.6 m, 95% confidence interval: –36.4 to 13.0 m (i.e. within the pre-specified non-inferiority margin). Conclusion The HSEP was non-inferior to SEP in patients with IC. There were no significant differences observed between the three groups at 1 year. Registration ClinicialTrials.gov: NCT02341716.

Sandberg, Anna (ORCID:0000000258432784)↗
DOE OSTI2022

Association mapping across a multitude of traits collected in diverse environments in maize

Abstract Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data—18M markers—from 2 partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least 7 US states and scored for 162 distinct trait data sets enabled the identification of of 2,154 suggestive marker-trait associations and 697 confident associations in the maize genome using a resampling-based genome-wide association strategy. The precision of individual marker-trait associations was estimated to be 3 genes based on a reference set of genes with known phenotypes. Examples were observed of both genetic loci associated with variation in diverse traits (e.g., above-ground and below-ground traits), as well as individual loci associated with the same or similar traits across diverse environments. Many significant signals are located near genes whose functions were previously entirely unknown or estimated purely via functional data on homologs. This study demonstrates the potential of mining community association panel data using new higher-density genetic marker sets combined with resampling-based genome-wide association tests to develop testable hypotheses about gene functions, identify potential pleiotropic effects of natural genetic variants, and study genotype-by-environment interaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Illuminating the North Korean nuclear explosion test in 2017 using remote infrasound observations

North Korea conducted its sixth underground nuclear explosion test (mb 6.3) on 2017 September 3. The underground explosion produced substantial low-frequency atmospheric waves, which were detected by infrasound arrays located up to a distance of 566 km. These infrasound waves are formed by the conversion of seismic energy to acoustic energy across the lithosphere–atmosphere interface. While infrasound records at regional distances produce estimates of ground motion amplitude over spatially extended regions covering about 26 500 km 2 , 3-D full seismo-acoustic simulations within the lithosphere and atmosphere provide quantitative information about seismo-acoustic energy partitioning. Our results demonstrate the capability of remote infrasound observations combined with 3-D propagation modelling to further develop discrimination methods for underground sources. These results contribute to enhance the confidence of source identification and characterization in nuclear test monitoring research, which is essential for the enforcement of the Comprehensive Nuclear-Test-Ban Treaty.

58 GEOSCIENCES↗
DOE OSTI2022

Evaluating the location capabilities of a regional infrasonic network in Utah, US, using both ray tracing-derived and empirical-derived celerity-range and backazimuth models

SUMMARY More realistic models for infrasound signal propagation across a region can be used to improve the precision and accuracy of spatial and temporal source localization estimates. Motivated by incomplete infrasound event bulletins in the Western US, the location capabilities of a regional infrasonic network of stations located between 84–458 km from the Utah Test and Training Range, Utah, USA, is assessed using a series of near-surface explosive events with complementary ground truth (GT) information. Signal arrival times and backazimuth estimates are determined with an automatic F-statistic based signal detector and manually refined by an analyst. This study represents the first application of three distinct celerity-range and backazimuth models to an extensive suite of realistic signal detections for event location purposes. A singular celerity and backazimuth deviation model was previously constructed using ray tracing analysis based on an extensive archive of historical atmospheric specifications and is applied within this study to test location capabilities. Similarly, a set of multivariate, season and location specific models for celerity and backazimuth are compared to an empirical model that depends on the observations across the infrasound network and the GT events, which accounts for atmospheric propagation variations from source to receiver. Discrepancies between observed and predicted signal celerities result in locations with poor accuracy. Application of the empirical model improves both spatial localization precision and accuracy; all but one location estimates retain the true GT location within the 90 per cent confidence bounds. Average mislocation of the events is 15.49 km and average 90 per cent error ellipse areas are 4141 km2. The empirical model additionally reduces origin time residuals; origin time residuals from the other location models are in excess of 160 s while residuals produced with the empirical model are within 30 s of the true origin time. We demonstrate that event location accuracy is driven by a combination of signal propagation model and the azimuthal gap of detecting stations. A direct relationship between mislocation, error ellipse area and increased station azimuthal gaps indicate that for sparse networks, detection backazimuths may drive location biases over traveltime estimates.

58 GEOSCIENCES↗
DOE OSTI2022

Probabilistic inversion of circular phase spectra: application to two-station phase-velocity dispersion estimation in western Canada

SUMMARY Periodic directional and temporal measurements are common in seismology, and necessitate specific statistical analyses that are appropriate for circular quantities. In this work, we explore the use of a von Mises distribution as a representation of errors on circular seismological observations. Specifically, we automate the estimation of surface-wave phase-velocity dispersion for the teleseismic two-station method, which generally suffers from a 2π phase ambiguity. The use of Bayesian inverse techniques, which aim to rigorously quantify model parameter uncertainty, have become widespread throughout seismology over the last decade. Here, we apply Bayesian inversion to measurements of surface-wave phase spectra in order to estimate 1-D, path-averaged Earth structure between station pairs. The dispersion curve and associated uncertainties are additional results of the inversion, which can then be used as input for subsequent analyses (e.g. tomography). We demonstrate this technique through application to surface-wave recordings from long-running seismic stations throughout western Canada. Our results for over 10 000 station pairs reveal first-order tectonic features consistent with previous studies, which provides confidence in our approach as well as an initial step towards resolving a full 3-D seismic velocity model for the region. This work also presents a foundation for the inversion of surface-wave phase spectra to estimate 3-D Earth structure directly. Finally, the ideas presented in this work are not limited to the inversion of surface-wave phase spectra, but can also be considered for Bayesian geophysical inversion of any circular quantities.

Gosselin, Jeremy M. (ORCID:0000000203754102)↗
DOE OSTI2024

A Pn magnitude scale m b ( Pn ) for earthquakes along the equatorial Mid-Atlantic Ridge

We developed a short-period Pn magnitude scale m b (Pn) for earthquakes along the equatorial Mid-Atlantic Ridge. Due to low signal-to-noise ratios, teleseismic body wave magnitude and long-period surface wave magnitude cannot be confidently determined for small earthquakes of m b < 4. Local magnitude scales are also not useful for these events because the oceanic environment does not allow the propagation of crustal phases. However, regional high-frequency Pn waves from these small- to moderate-size (m b 3–6) earthquakes are well recorded in the equatorial Atlantic region and can be used to assign magnitudes. We measured over 2041 Pn peak amplitudes on vertical records from about 21 stations in northeastern Brazil and 11 stations in western Africa in the distance range of 700–3700 km. We analysed data from 189 events from the global centroid moment tensor catalogue to tie our m b (Pn) scale to M w so that seismic moments can be readily estimated. Pn arrivals show apparent group velocity between 7.9 km s –1 at short ranges (~1000 km) and up to 9.1 km s –1 at 3500 km. The measured peak amplitudes have a frequency between 0.8 and 3 Hz at 1000–1800 km, but at greater distances, 1800–3700 km, they show a remarkably consistent frequency of about 0.8 Hz. The peak amplitude attenuates at a higher rate at short distances (~0.65 magnitude units between 700 and 2000 km) but attenuates at a lower rate at long distances (~0.35 magnitude units between 2000 and 3700 km). The low rate of amplitude decay with distance and nearly constant frequency content of the peak amplitudes suggest that Pn waves propagate efficiently in the lower part of the upper mantle in the equatorial Atlantic Ocean basins. Furthermore, these are important attributes of oceanic Pn waves that can be used to assign magnitude for small- to moderate-size earthquakes in the equatorial mid-Atlantic region. The estimated station corrections correlate well with upper mantle low-velocity anomalies, especially in Brazil.

58 GEOSCIENCES↗
DOE OSTI2024

Localization of infrasonic sources via Bayesian back projection

SUMMARY A Bayesian framework is investigated for event-specific localization of infrasonic sources using back projection ray tracing. Direction-of-arrival information from array-based detection analysis is used to initialize a back projection ray path originating from the detecting array location and quantifying propagation characteristics from hypothetical source locations. The Fisher statistic, computed from the array’s beam coherence, is mapped into uncertainty in the launch angles of the ray path. Auxiliary parameters previously introduced for solving the Transport equation to compute geometric spreading along ray paths are used to map uncertainty in the ray launch angles into spatial and temporal uncertainties in the ray path. An atmospheric ensemble approach is applied to account for atmospheric uncertainty, and the relation between uncertainties in the atmospheric state and confidence in estimated localization are evaluated using several ensembles with specified variances. The method is evaluated using a synthetic event in the western United States constructed via forward propagation simulations as well as a single-station, multi-arrival detection from a surface explosion in the western United States. Localization results using this event-specific approach are more accurate and exhibit improved precision than existing Bayesian localization methods that leverage generalized, pre-computed propagation statistics.

58 GEOSCIENCES↗
DOE OSTI2025

Divide and conquer: separating the two probabilities in seismic phase picking

There are two fundamental probabilities in the seismic phase picking process—the probability of the existence of a seismic phase (detection probability) and the probability associated with the phase arrival time estimation (timing probability). The nearly ubiquitous approach in developing deep learning phase picking models is to use a kernel, such as a truncated Gaussian, to mask the labelled phase arrival time and train a segmentation model. Once a model is trained, the times of the peaks in the output are taken as phase arrival times (picks), and the height of the peaks are taken as ‘probability’ of the picks. Here, we show that this ‘probability’ represents neither the detection nor the timing probability because this approach forces the output to follow the shape of the kernel. We introduce an approach using two models to estimate these two distinct probabilities. We use a binary classifier with a calibrated confidence to address the detection probability and a multiclass classifier to obtain a probability mass function to address the timing probability. This new approach can make the deep learning-based phase picking process more interpretable and provide options to logically control seismic monitoring workflows.

58 GEOSCIENCES↗
DOE OSTI2020

The effect of school intervention programs on the body mass index of adolescents: a systematic review with meta-analysis

Abstract Effective obesity interventions in adolescent populations have been identified as an immediate priority action to stem the increasing prevalence of adult obesity. The purpose of this meta-analysis was to make a quantitative analysis of the impact of school-based interventions on body mass index during adolescence. Studies were retrieved from PubMed, Scopus, Science Direct and Web of Science databases. Results were pooled using a random-effects model with 95% confidence interval considered statistically significant. Of the 18 798 possible relevant articles identified, 12 articles were included in this meta-analysis. The global result showed a low magnitude effect, though it was statistically significant (N = 14 428), global e.s. = −0.055, P = 0.004 (95% CI = −0.092, −0.017). Heterogeneity was low among the studies (I2 = 9.017%). The funnel plot showed no evidence of publication bias. The rank-correlation test of Begg (P = 0.45641) and Egger’s regression (P = 0.19459) confirmed the absence of bias. This meta-analysis reported a significant effect favoring the interventions; however, future research are needed since the reported the evidence was of low magnitude, with the studies following a substantial range of approaches and mostly had a modest methodological quality.

Saavedra Dias, R.↗
DOE OSTI2021

Reduction in total and major cause-specific mortality from tobacco smoking cessation: a pooled analysis of 16 population-based cohort studies in Asia

Little is known about the time course of mortality reduction following smoking cessation in Asians who have smoking behaviours distinct from their Western counterparts. We evaluated the level of reduction in all-cause, cardiovascular disease (CVD) and lung cancer mortality by years since quitting smoking, in Asia. Using Cox regression, we analysed individual participant data (n = 709 151) from 16 prospective cohorts conducted in China, Japan, Korea/Singapore, and India/Bangladesh, separately by cohorts. Cohort-specific hazard ratios (HRs) were combined using a random-effects meta-analysis. During a mean follow-up of 12.0 years, 108 287 deaths were ascertained—35 658 from CVD and 7546 from lung cancer. Among Asian men, a dose-response relationship of risk reduction in deaths from all causes, CVD and lung cancer was observed with an increase in years after smoking cessation. Compared with never smokers, however, all-cause and CVD mortality among former smokers remained elevated 10–14 years after quitting [multivariable-adjusted HR (95% confidence interval (CI) = 1.25 (1.13–1.37) and 1.20 (1.02–1.41), respectively]. Lung cancer mortality stayed almost 2-fold higher than among never smokers 15–19 years after smoking cessation [1.97 (1.41–2.73)], particularly among former heavy smokers [2.62 (1.71–4.00)]. Women who quitted for ≥5 years retained a significantly elevated mortality from all causes, CVD and lung cancer. Overall patterns of the cessation-mortality associations were similar across countries. Our findings suggest that adverse effects of tobacco smoking persist for an extended time period, even for more than two decades, which is beyond the time windows defined in current clinical guidelines for risk assessment of lung cancer and CVD.

Public, Environmental & Occupational Health↗
DOE OSTI2021

Excess deaths reveal the true spatial, temporal and demographic impact of COVID-19 on mortality in Ecuador

Accepted Background In early 2020, Ecuador reported one of the highest surges of per capita deaths across the globe. Methods We collected a comprehensive dataset containing individual death records between 2015 and 2020, from the Ecuadorian National Institute of Statistics and Census and the Ecuadorian Ministry of Government. We computed the number of excess deaths across time, geographical locations and demographic groups using Poisson regression methods. Results Between 1 January and 23 September 2020, the number of excess deaths in Ecuador was 36 402 [95% confidence interval (CI): 35 762–36 827] or 208 per 100 000 people, which is 171% of the expected deaths in that period in a typical year. Only 20% of the excess deaths are attributable to confirmed COVID-19 deaths. Strikingly, in provinces that were most affected by COVID-19 such as Guayas and Santa Elena, the all-cause deaths are more than double the expected number of deaths that would have occurred in a normal year. The extent of excess deaths in men is higher than in women, and the number of excess deaths increases with age. Indigenous populations had the highest level of excess deaths among all ethnic groups. Conclusions Overall, the exceptionally high level of excess deaths in Ecuador highlights the enormous burden and heterogeneous impact of COVID-19 on mortality, especially in older age groups and Indigenous populations in Ecuador, which was not fully revealed by COVID-19 death counts. Together with the limited testing in Ecuador, our results suggest that the majority of the excess deaths were likely to be undocumented COVID-19 deaths.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Identification of 2 Novel Subtypes of Hepatitis C Virus Genotype 8 and a Potential New Genotype Successfully Treated With Direct Acting Antivirals

Abstract Background Hepatitis C virus (HCV) has high genetic diversity and is classified into 8 genotypes and >90 subtypes, with some endemic to specific world regions. This could compromise direct-acting antiviral efficacy and global HCV elimination. Methods We characterized HCV subtypes “rare” in the United Kingdom (non-1a/1b/2b/3a/4d) by means of whole-genome sequencing via a national surveillance program. Genetic analyses to determine the genotype of samples with unresolved genotypes were undertaken by comparison with International Committee on Taxonomy of Viruses HCV reference sequences. Results Two HCV variants were characterized as being closely related to the recently identified genotype (GT) 8, with >85% pairwise genetic distance similarity to GT8 sequences and within the typical intersubtype genetic distance range. The individuals infected by the variants were UK residents originally from Pakistan and India. In contrast, a third variant was only confidently identified to be more similar to GT6 compared with other genotypes across 6% of the genome and was isolated from a UK resident originally from Guyana. All 3 were cured with pangenotypic direct-acting antivirals (sofosbuvir-velpatasvir or glecaprevir-pibrentasvir) despite the presence of resistance polymorphisms in NS3 (80K/168E), NS5A (28V/30S/62L/92S/93S) and NS5B (159F). Conclusions This study expands our knowledge of HCV diversity by identifying 2 new GT8 subtypes and potentially a new genotype.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

In with the old, in with the new: machine learning for time to event biomedical research

The predictive modeling literature for biomedical applications is dominated by biostatistical methods for survival analysis, and more recently some out of the box machine learning approaches. In this article, we show a presentation of a machine learning method appropriate for time-to-event modeling in the area of prostate cancer long-term disease progression. Using XGBoost adapted to long-term disease progression, we developed a predictive model for 118 788 patients with localized prostate cancer at diagnosis from the Department of Veterans Affairs (VA). Our model accounted for patient censoring. Harrell’s c-index for our model using only features available at the time of diagnosis was 0.757 95% confidence interval [0.756, 0.757]. Our results show that machine learning methods like XGBoost can be adapted to use accelerated failure time (AFT) with censoring to model long-term risk of disease progression. Furthermore, the long median survival justifies and requires censoring. Overall, we show that an existing machine learning approach can be used for AFT outcome modeling in prostate cancer, and more generally for other chronic diseases with long observation times.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2022

Using ensembles and distillation to optimize the deployment of deep learning models for the classification of electronic cancer pathology reports

One of the goals of the Surveillance, Epidemiology, and End Results (SEER) program is to estimate incidence, prevalence, and mortality of all cancers. To that end, cancer registries across the country maintain a massive database of cancer pathology reports which contain rich information to understand cancer trends. However, these reports are stored in the form of unstructured text, and human annotators are required to read and extract relevant information. In this article, we show that existing deep learning models for automating information extraction from cancer pathology reports can be significantly improved by using ensemble model distillation. We found that by training multiple predictive models and transferring their knowledge to a single, low-resource model, we can reduce the number of highly confident wrong predictions. Our results show that our implemented methods could save 1000s of manual annotation hours.

60 APPLIED LIFE SCIENCES↗