The impact of non-pharmaceutical interventions on premature births during the COVID-19 pandemic: a nationwide observational study in Korea

BackgroundNon-pharmaceutical interventions (NPIs), such as social distancing and hand washing, have been associated with a decline in the preterm birth rate worldwide. We aimed to evaluate whether the preterm birth rate in Korea during the coronavirus disease 2019 lockdown has changed compared to that in previous years.MethodA birth registry from the Korea Statistical Information Service, which is a nationwide official database, was used to include all births claimed to have occurred between 2011 and 2020. Newborns with gestational age (GA) less than 22 weeks and birth weight less than 220 g were excluded. The pre-NPI period was designated as January 2011 to January 2020, and the NPI period was defined as February 2020 to December 2020. We assessed the effect of NPI on the incidence of prematurity per 100 births using an interrupted time-series quasi-experimental design and implementing an autoregressive integrated moving average (ARIMA) model.ResultsFrom 2011 to 2020, a total of 3,931,974 live births were registered, among which 11,416 were excluded. Consequently, the final study population included 3,920,558 live births (both singleton and multiple births) among which 275,009 (7.0%) were preterm. The preterm birth rate was significantly higher during the NPI period (8.68%) compared to that in the pre-NPI period (6.92%) (P < 0.001). The ARIMA model showed that in all singleton and multiple births, except those in July (observed 9.24, expected 8.54, [95% prediction interval {PI} 8.13–8.96], percent difference 7.81%), September (observed 7.89, expected 8.35, [95% PI 7.93–8.76], percent difference −5.66%), and December (observed 9.90, expected 9.40, [95% PI 8.98–9.82], percent difference 5.2%), most observed values were within the 95% PI of the expected values and showed an increasing trend.ConclusionIn this nationwide observational study, the trend in premature birth rate did not significantly change due to NPI implementation in Korea, as it had been increasing since 2011. The trend of Korea's birth rate appears to be unaffected by the implementation of NPIs; however, further studies with a longer follow-up period are needed

Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning.

Scoring model structure is an essential component of protein structure prediction that can affect the prediction accuracy tremendously. Users of protein structure prediction results also need to score models to select the best models for their application studies. In Critical Assessment of techniques for protein Structure Prediction (CASP), model accuracy estimation methods have been tested in a blind fashion by providing models submitted by the tertiary structure prediction servers for scoring. In CASP13, model accuracy estimation results were evaluated in terms of both global and local structure accuracy. Global structure accuracy estimation was evaluated by the quality of the models selected by the global structure scores and by the absolute estimates of the global scores. Residue-wise, local structure accuracy estimations were evaluated by three different measures. A new measure introduced in CASP13 evaluates the ability to predict inaccurately modeled regions that may be improved by refinement. An intensive comparative analysis on CASP13 and the previous CASPs revealed that the tertiary structure models generated by the CASP13 servers show very distinct features. Higher consensus toward models of higher global accuracy appeared even for free modeling targets, and many models of high global accuracy were not well optimized at the atomic level. This is related to the new technology in CASP13, deep learning for tertiary contact prediction. The tertiary model structures generated by deep learning pose a new challenge for EMA (estimation of model accuracy) method developers. Model accuracy estimation itself is also an area where deep learning can potentially have an impact, although current EMA methods have not fully explored that direction

Protein oligomer modeling guided by predicted interchain contacts in CASP14

For CASP14, we developed deep learning-based methods for predicting homo-oligomeric and hetero-oligomeric contacts and used them for oligomer modeling. To build structure models, we developed an oligomer structure generation method that utilizes predicted interchain contacts to guide iterative restrained minimization from random backbone structures. We supplemented this gradient-based fold-and-dock method with template-based and ab initio docking approaches using deep learning-based subunit predictions on 29 assembly targets. These methods produced oligomer models with summed Z-scores 5.5 units higher than the next best group, with the fold-and-dock method having the best relative performance. Over the eight targets for which this method was used, the best of the five submitted models had average oligomer TM-score of 0.71 (average oligomer TM-score of the next best group: 0.64), and explicit modeling of inter-subunit interactions improved modeling of six out of 40 individual domains (Delta GDT-TS > 2.0).N

Improved protein structure refinement guided by deep learning based accuracy estimation

We develop a deep learning framework (DeepAccNet) that estimates per-residue accuracy and residue-residue distance signed error in protein models and uses these predictions to guide Rosetta protein structure refinement. The network uses 3D convolutions to evaluate local atomic environments followed by 2D convolutions to provide their global contexts and outperforms other methods that similarly predict the accuracy of protein structure models. Overall accuracy predictions for X-ray and cryoEM structures in the PDB correlate with their resolution, and the network should be broadly useful for assessing the accuracy of both predicted structure models and experimentally determined structures and identifying specific regions likely to be in error. Incorporation of the accuracy predictions at multiple stages in the Rosetta refinement protocol considerably increased the accuracy of the resulting protein structure models, illustrating how deep learning can improve search for global energy minima of biomolecules. Here the authors present DeepAccNet, a deep learning framework that estimates per-residue accuracy and residue-residue distance signed error in protein models, which are used to guide Rosetta protein structure refinement. Benchmarking suggests an improvement of accuracy prediction and refinement compared to other related state of the art methods.N

The challenge of modeling protein assemblies: the CASP12-CAPRI experiment

International audienc

EPHA6 rs4857055 C > T polymorphism associates with hypertension through triglyceride and LDL particle size in the Korean population

Abstract Background Erythropoietin-producing human hepatocellular (Eph) receptors might contribute to the development of atherosclerosis. A genome-wide association study indicated that the Eph receptor A6 gene (EPHA6) associated with at least 1 blood pressure (BP) phenotype. The objective of the present study was to determine whether EPHA6 is a novel candidate gene for hypertension in a Korean population. Methods A total 2146 study participants with normotension and hypertension were included. Genotype data were obtained using a Korean Chip. To assess the association between single-nucleotide polymorphisms (SNPs) and BP, we performed a linear regression analysis, which showed that rs4850755 in the EPHA6 gene was the SNP most highly associated with both systolic and diastolic BP. Results The presence of the TT genotype of the EPHA6 rs4857055 C > T SNP was associated with a higher risk of hypertension after adjusting for age, sex, body mass index (BMI), smoking, and drinking [odds ratio 1.533, P = 0.001]. In the control group, significant associations were observed between systolic BP and the rs4857055 polymorphism and between diastolic BP and the rs4857055 polymorphism. In the hypertension group, a significant association was observed between systolic BP and the rs4857055 polymorphism. In the hypertension group, subjects with the TT genotype showed significantly higher systolic BP than CC subjects. Additionally, in the hypertension group, TT carriers showed a higher tendency of serum triglyceride (P = 0.069) and significantly higher apolipoprotein B (P = 0.015) and smaller low-density lipoprotein (LDL) particle size (P  T SNP is a novel candidate gene for hypertension in the Korean population. Additionally, the TT genotype could be associated with hypertriglyceridemia and small LDL particle size in hypertension