Development and immune evaluation of LAMP1 chimeric DNA vaccine against Singapore grouper iridovirus in orange-spotted grouper, Epinephelus coioides.

Grouper is one of the most important and valuable mariculture fish in China, with a high economic value. As the production of grouper has increased, massive outbreaks of epidemic diseases have limited the development of the industry. Singapore grouper iridovirus (SGIV) is one of the most serious infectious viral pathogens and has caused huge economic losses to grouper farming worldwide due to its rapid spread and high lethality. To find new strategies for the effective prevention and control of SGIV, we constructed two chimeric DNA vaccines using Lysosome-associated membrane protein 1 (LAMP1) fused with major capsid proteins (MCP) against SGIV. In addition, we evaluated the immune protective effects of vaccines including pcDNA3.1-3HA, pcDNA3.1-MCP, pcDNA3.1-LAMP1, chimeric DNA vaccine pcDNA3.1-MLAMP and pcDNA3.1-LAMCP by intramuscular injection. Our results showed that compared with groups injected with PBS, pcDNA3.1-3HA, pcDNA3.1-LAMP1 or pcDNA3.1-MCP, the antibody titer significantly increased in the chimeric vaccine groups. Moreover, the mRNA levels of immune-related factors in groupers, including IRF3, MHC-I, TNF-α, and CD8, showed the same trend. However, MHC-II and CD4 were significantly increased only in the chimeric vaccine groups. After 28 days of vaccination, groupers were challenged with SGIV, and mortality was documented for each group within 14 days. The data showed that two chimeric DNA vaccines provided 87 % and 91 % immune protection for groupers which were significantly higher than the 52 % protection rate of pcDNA3.1-MCP group, indicating that both forms of LAMP1 chimeric vaccines possessed higher immune protection against SGIV, providing the theoretical foundation for the creation of novel DNA vaccines for fish.

Quantum Similarity Testing with Convolutional Neural Networks.

The task of testing whether two uncharacterized quantum devices behave in the same way is crucial for benchmarking near-term quantum computers and quantum simulators, but has so far remained open for continuous variable quantum systems. In this Letter, we develop a machine learning algorithm for comparing unknown continuous variable states using limited and noisy data. The algorithm works on non-Gaussian quantum states for which similarity testing could not be achieved with previous techniques. Our approach is based on a convolutional neural network that assesses the similarity of quantum states based on a lower-dimensional state representation built from measurement data. The network can be trained off-line with classically simulated data from a fiducial set of states sharing structural similarities with the states to be tested, with experimental data generated by measurements on the fiducial states, or with a combination of simulated and experimental data. We test the performance of the model on noisy cat states and states generated by arbitrary selective number-dependent phase gates. Our network can also be applied to the problem of comparing continuous variable states across different experimental platforms, with different sets of achievable measurements, and to the problem of experimentally testing whether two states are equivalent up to Gaussian unitary transformations.

Functional analysis of the Cystatin F gene response to SGIV infection in orange-spotted grouper, Epinephelus coioides.

Cystatin F (CyF), an inhibitor of cysteine protease, was widely studied in immune defense and cancer therapy. However, the function of CyF and its latent molecular mechanism during virus infection in fish remain vacant. In our research, we cloned the open reading frame (ORF) of CyF homology from orange-spotted grouper (Ec-CyF) consisting of 342 nucleotides and encoding a 114-amino acid protein. Ec-CyF included two cystatins family sequences containing one KXVXG sequence without the signal peptide, and a hairpin ring containing proline and tryptophan (PW). Tissue distribution analysis indicated that Ec-CyF was highly expressed in spleen and head kidney. Besides, further analysis showed that the expression of Ec-CyF increased during SGIV infection in grouper spleen (GS) cells. Subcellular localization assay demonstrated that Ec-CyF was mainly distributed in cytoplasm in GS cells. Overexpressed Ec-CyF demoted the mRNA level of viral genes MCP, VP19 and LITAF. Meanwhile, SGIV-induced apoptosis in fat head minnow (FHM) cells was impeded, as well as the restraint of caspase 3/7 and caspase 8. In addition, Ec-CyF overexpression up-regulated the expression of IFN related molecules including ISG15, IFN, IFP35, IRF3, IRF7, MYD88 and down-regulated proinflammatory factors such as IL-1ß, IL-8 and TNF-α. At the same time, Ec-CyF-overexpressing increased the activity of IFN3 and ISRE promoter, but impeded NF-κB promoter activity by luciferase reporter gene assay. In summary, our findings suggested that Ec-CyF was involved in innate immunity response and played a key role in DNA virus infection.

Modulatory effects of curcumin on Singapore grouper iridovirus infection-associated apoptosis and autophagy in vitro.

Singapore grouper iridovirus (SGIV) with high pathogenicity can cause great economic losses to aquaculture industry. Thus, it is of urgency to find effective antiviral strategies to combat SGIV. Curcumin has been demonstrated effective antiviral activity on SGIV infection. However, the molecular mechanism behind this action needs to be further explanations. In view of the fact that apoptosis (type I programmed cell death) and autophagy (type II programmed cell death) were key regulators during SGIV infection, we aimed to investigate the relevance between antiviral activity of curcumin and SGIV-associated programmed and clarify the role of potential signaling pathways. Our results showed that curcumin suppressed SGIV-induced apoptosis. At the same time, the activities of caspase-3/8/9 and activating protein-1 (AP-1), P53, nuclear factor-κB (NF-ΚB) promoters were inhibited. Besides, the activation of extracellular regulated protein kinases (ERK), c-Jun N-terminal kinase (JNK) and p38 mitogen activate protein kinase (p38 MAPK) signal pathways were suppressed in curcumin-treated cells. On the other hand, curcumin down-regulated protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling pathway to promote autophagy representing by increased LC3 II and Beclin1 expression. Curcumin also hindered the transition of cells from G1 to S phase, as well as down-regulating the expression of CyclinD1. Our findings revealed the resistance curcumin induced to the effects of DNA virus on cell apoptosis and autophagy and the insights gained from this study may be of assistance to understand the molecular mechanism of curcumin against DNA virus infection.

Co-overexpression of TRAIL and Smac sensitizes MDA-MB-231 cells to radiation through apoptosis depending on mitochondrial pathway.

Pro-apoptosis in cancer cells has been proposed as a beneficial therapeutic strategy for potentiating the anticancer effects of radiotherapy. TNF-related apoptosis inducing ligand (TRAIL) and Second mitochondria derived activator of caspase (Smac) can induce cell apoptosis. Herein, we designed a conditionally replicating adenoviral co-overexpression vector of TRAIL and Smac regulated by the Egr1 promoter, in which hTERT, E1A-E1B and E1B55K genes were inserted to achieve enhanced tumor targeting characteristics. After breast cancer MDA-MB-231 cells were infected and irradiated, cellular proliferation and colony formation were measured, apoptotic rate was detected by FCM after AnnexinV-FITC/PI staining. To explore the molecular mechanisms of apoptosis, mRNA and protein levels of TRAIL, Smac, Cytochrome c (Cyt c), death receptor 5 (DR5), caspase-8, -9 and -3 were measured by quantitative real-time PCR, ELISA and Western blot, and caspase-3 activity was detected using caspase-3 activity kits. The results showed that TRAIL and/or Smac overexpression enhanced proliferation inhibition and radio-sensitivity through apoptosis. In addition, the combination of IR and overexpression of TRAIL and/or Smac can activate more apoptosis in tumor cells, and the transcriptional levels and protein expressions of Cyt c, DR5, caspase-8, -9 and -3 had similar regularity with apoptotic changes, indicating the molecular mechanisms of TRAIL and Smac involves the mitochondrial pathway. Our findings may have implications for novel radiotherapy plans for breast tumor treatment.

The Advances in Epigenetics for Cancer Radiotherapy.

Cancer is an important factor threatening human life and health; in recent years, its morbidity and mortality remain high and demosntrate an upward trend. It is of great significance to study its pathogenesis and targeted therapy. As the complex mechanisms of epigenetic modification has been increasingly discovered, they are more closely related to the occurrence and development of cancer. As a reversible response, epigenetic modification is of great significance for the improvement of classical therapeutic measures and the discovery of new therapeutic targets. It has become a research focusto explore the multi-level mechanisms of RNA, DNA, chromatin and proteins. As an important means of cancer treatment, radiotherapy has made great progress in technology, methods, means and targeted sensitization after years of rapid development, and even research on radiotherapy based on epigenetic modification is rampant. A series of epigenetic effects of radiation on DNA methylation, histone modification, chromosome remodeling, RNA modification and non-coding RNA during radiotherapy affects the therapeutic effects and prognosis. Starting from the epigenetic mechanism of tumorigenesis, this paper reviews the latest progress in the mechanism of interaction between epigenetic modification and cancer radiotherapy and briefly introduces the main types, mechanisms and applications of epigenetic modifiers used for radiotherapy sensitization in order to explore a more individual and dynamic approach of cancer treatment based on epigenetic mechanism. This study strives to make a modest contribution to the progress of human disease research.

Enhancing the Therapeutic Efficacy of Gefitinib in Human Non-Small-Cell Lung Cancer through Drug Combination.

The interaction between tumor cells and the tumor microenvironment (TME) significantly influences tumorigenesis, so TME-targeted therapy has attracted widespread attention. We have previously demonstrated that the combination of dipyridamole, bestatin, and dexamethasone (DBD mix, DBDx) is effective against heterogeneous human pancreatic cancer and hepatocellular carcinoma in mouse xenograft models. To further expand the therapeutic potential of this drug combination, herein, we investigated the antitumor efficacy and the underlying mechanism of DBDx and the combination of DBDx and gefitinib in different mouse xenograft models of human non-small-cell lung cancer (NSCLC). Three human cancer cell lines H460, PG, and A431 were used to determine the apoptosis and growth inhibition induced by DBDx, gefitinib, and their combinations. Changes in epidermal growth factor receptor (EGFR) signaling pathway-related proteins were analyzed following treatment using western blotting. In vitro, DBDx strongly inhibited the proliferation of tumor cells, whereas the combined treatment exhibited a significant synergistic effect. Compared with DBDx, the combination treatment further induced apoptosis and downregulated the expression of molecules associated with EGFR signaling pathway. In vivo, compared with DBDx alone, the combination treatment distinctly inhibited tumor growth in mouse xenograft models of human NSCLC. Overall, our results indicate that the combination of DBDx and gefitinib in the treatment of human NSCLC is very promising, which warrants further translational studies.

A Low-Latency and Energy-Efficient Neighbor Discovery Algorithm for Wireless Sensor Networks.

Wireless sensor networks have been widely adopted, and neighbor discovery is an essential step to construct the networks. Most existing studies on neighbor discovery are designed on the assumption that either all nodes are fully connected or only two nodes compose the network. However, networks are partially connected in reality: some nodes are within radio range of each other, while others are not. Low latency and energy efficiency are two common goals, which become even more challenging to achieve at the same time in partially connected networks. We find that the collision caused by simultaneous transmissions is the main obstruction of achieving the two goals. In this paper, we present an efficient algorithm called Panacea to address these challenges by alleviating collisions. To begin with, we design Panacea-NCD (Panacea no collision detection) for nodes that do not have a collision detection mechanism.

A Practical Neighbor Discovery Framework for Wireless Sensor Networks.

Neighbor discovery is a crucial operation frequently executed throughout the life cycle of a Wireless Sensor Network (WSN). Various protocols have been proposed to minimize the discovery latency or to prolong the lifetime of sensors. However, none of them have addressed that all the critical concerns stemming from real WSNs, including communication collisions, latency constraints and energy consumption limitations. In this paper, we propose Spear, the first practical neighbor discovery framework to meet all these requirements. Spear offers two new methods to reduce communication collisions, thus boosting the discovery rate of existing neighbor discovery protocols. Spear also takes into consideration latency constraints and facilitates timely adjustments in order to reduce the discovery latency. Spear offers two practical energy management methods that evidently prolong the lifetime of sensor nodes. Most importantly, Spear automatically improves the discovery results of existing discovery protocols, on which no modification is required. Beyond reporting details of different Spear modules, we also present experiment evaluations on several notable neighbor discovery protocols. Results show that Spear greatly improves the discovery rate from 33.0% to 99.2%, and prolongs the sensor nodes lifetime up to 6.47 times.

Estimating Haplotype Structure and Frequencies: A Bayesian Approach to Unknown Design in Pooled Genomic Data.

The estimation of haplotype structure and frequencies provides crucial information about the composition of genomes. Techniques, such as single-individual haplotyping, aim to reconstruct individual haplotypes from diploid genome sequencing data. However, our focus is distinct. We address the challenge of reconstructing haplotype structure and frequencies from pooled sequencing samples where multiple individuals are sequenced simultaneously. A frequentist method to address this issue has recently been proposed. In contrast to this and other methods that compute point estimates, our proposed Bayesian hierarchical model delivers a posterior that permits us to also quantify uncertainty. Since matching permutations in both haplotype structure and corresponding frequency matrix lead to the same reconstruction of their product, we introduce an order-preserving shrinkage prior that ensures identifiability with respect to permutations. For inference, we introduce a blocked Gibbs sampler that enforces the required constraints. In a simulation study, we assessed the performance of our method. Furthermore, by using our approach on two distinct sets of real data, we demonstrate that our Bayesian approach can reconstruct the dominant haplotypes in a challenging, high-dimensional set-up.

Polysaccharides derived from Spirulina platensis inhibited Singapore grouper iridovirus by impeding the entry of viral particles.

Attributable to the rapid dissemination and high lethality of Singapore grouper iridovirus (SGIV), it has caused significant economic losses for marine fish aquaculture in China and Southeast Asian nations. Hence, there is an urgent need to find antiviral drugs that are both safe and effective. In this study, a novel heteropolysaccharide named Spirulina platensis polysaccharides (SPP) was purified and characterized from S. platensis. The molecular weight of SPP is 276 kDa and it mainly consists of Glc and Rha, followed by minor components such as Gal, Xyl, and Fuc. The backbone of SPP was determined to be →2) -ß-Rhap-(1 â†’ 4) -α-Fucp-(1 â†’ [2) -α-Rhap-(1] 2[→6)-α-Glcp-(1] 4[→ 4) -α-Glcp-(1] 8[→ 4) -ß-Glcp-(1]2→, with branches of ß-Galp, α-Xylp and α-Glcp. SPP significantly inhibited SGIV-induced cytopathic effects (CPEs), viral gene replication and viral protein expression. The antiviral mechanism of SPP was associated with the disruption of SGIV entry to host cells. Furthermore, it was not observed that SPP made statistically significant impact on the expression of interferon-related cytokines. Our results offered novel insights into the potential utilization of spirulina polysaccharides for combating aquatic animal viruses.

Depressive symptoms, lifestyle behaviors, and risk of cardiovascular disease and mortality in individuals of different socioeconomic status: A prospective cohort study.

BACKGROUND: Depression is a global health issue, associated with increased risk of cardiovascular disease (CVD) and premature death, but whether the association varied across different socioeconomic status (SES), and mechanisms responsible for this association is unclear. We aimed to evaluate the association of depressive symptoms with the risk of incident CVD and mortality in people of low, medium, and high SES, and determine the extent to which lifestyle behaviors could explain the association. METHODS: This study included 314,800 participants from the UK Biobank. Depressive symptoms were assessed using the Patient Health Questionnaire-2 (PHQ-2). Information on socioeconomic status and lifestyle was obtained from baseline assessment. RESULTS: During 12 years of follow-up, 29,074 incident CVD cases and 16,673 deaths were documented. The increased CVD risk in participants with depressive symptoms (versus without) was more pronounced as SES decreased, with hazard ratios (HRs) and 95% confidence intervals (CIs) of 1.30 (1.22, 1.39), 1.27 (1.17, 1.37), and 1.17 (0.97, 1.41) in participants of low, medium, and high SES, respectively. The corresponding HRs (95% CIs) for all-cause mortality were 1.16 (1.07, 1.26), 1.21 (1.08, 1.36), and 1.24 (0.95, 1.61). In addition, multiple lifestyle factors together explained 14.4% to 32.8% of the elevated CVD and mortality risk due to depressive symptoms. LIMITATIONS: Moderate sensitivity of PHQ-2, lacked information on the severity of depression, baseline measurement of lifestyle. CONCLUSIONS: Depressive symptoms were associated with higher risks of incident CVD and mortality, especially in low SES groups, and lifestyle behaviors only explained a moderate proportion of the association. These findings indicated that health policies targeting healthy lifestyle promotion alone might not be sufficient, and other measures tackling social inequity are warranted to attenuate the elevated health risk due to depression.

Exploring autism via the retina: Comparative insights in children with autism spectrum disorder and typical development.

Autism spectrum disorder (ASD) is a widely recognized neurodevelopmental disorder, yet the identification of reliable imaging biomarkers for its early diagnosis remains a challenge. Considering the specific manifestations of ASD in the eyes and the interconnectivity between the brain and the eyes, this study investigates ASD through the lens of retinal analysis. We specifically examined differences in the macular region of the retina using optical coherence tomography (OCT)/optical coherence tomography angiography (OCTA) images between children diagnosed with ASD and those with typical development (TD). Our findings present potential novel characteristics of ASD: the thickness of the ellipsoid zone (EZ) with cone photoreceptors was significantly increased in ASD; the large-caliber arteriovenous of the inner retina was significantly reduced in ASD; these changes in the EZ and arteriovenous were more significant in the left eye than in the right eye. These observations of photoreceptor alterations, vascular function changes, and lateralization phenomena in ASD warrant further investigation, and we hope that this work can advance interdisciplinary understanding of ASD.

Bayesian inference of polymerase dynamics over the exclusion process.

Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference over a paradigmatic mechanistic model of non-equilibrium statistical physics, i.e. the asymmetric exclusion processes in the hydrodynamic limit, assuming a Gaussian process prior for the polymerase progression rate as a latent variable. Our framework allows us to infer the speed of polymerases during transcription given their spatial distribution, while avoiding the explicit inversion of the system's dynamics. The results, which show processing rates strongly varying with genomic position and minor role of traffic-like congestion, may have strong implications for the understanding of gene expression.

The triple-drug combination DBDx enhances the antitumor efficacy of PD-1 antibody associated with Treg modulation.

OBJECTIVE: This study investigated the antitumor efficacy of programmed cell death protein-1 (PD-1) antibody and DBDx, a triple-drug combination of dipyridamole, bestatin, and dexamethasone, and their related immunomodulation. MATERIALS AND METHODS: Mouse melanoma B16, mouse Lewis lung carcinoma, and mouse breast carcinoma 4T1 were used for evaluating the in vivo therapeutic efficacy of DBDx, PD-1 antibody, and their combination. The peripheral blood and tumor tissues of 4T1 tumor-bearing mice were collected to analyze regulatory T cells and measured using flow cytometry. RESULTS: The combination of PD-1 antibody and DBDx enhanced the therapeutic efficacy against B16 melanoma. The suppression of tumor growth by PD-1 antibody and DBDx was more significant than that by anti-PD-1 monotherapy. The tumor growth inhibition rates of PD-1 antibody, DBDx, and their combination were 54.0%, 72.4%, and 83.1%, respectively, suggesting a synergistic effect as determined by the coefficient of drug interaction. No significant changes were found in the body weights in all the above groups, indicating that the treated mice tolerated the applied drug doses. Similarly, enhanced therapeutic efficacy of the PD-1 antibody and DBDx combination was observed in murine Lewis lung carcinoma and 4T1 breast cancer models. In 4T1 breast cancer-bearing mice, the immunotherapy-related changes in lymphocytes in peripheral blood and tumor microenvironment were evaluated with flow cytometry. Compared with anti-PD-1 monotherapy, peripheral blood and tumor-infiltrating lymphocytes were found a lower ratio of regulatory T cell (Treg) subset cells and a higher ratio of CD8+/Treg cells. CONCLUSIONS: The combination of PD-1 antibody and DBDx could achieve enhanced therapeutic antitumor efficacy than anti-PD-1 monotherapy, suggesting potential for using the triple-drug combination DBDx in cancer immunotherapy.

Systematic Exploration of the Potential Material Basis and Molecular Mechanism of the Mongolian Medicine Shudage-4 in Attenuating Stress-Induced Gastric Ulcer in Rat.

Shudage-4, an ancient and well-known formula in traditional Mongolian medicine comprising four different types of traditional Chinese medicine, is widely used in the treatment of gastric ulcers. However, the potential material basis and molecular mechanism of Shudage-4 in attenuating stress-induced gastric ulcers remain unclear. This study aimed to first explore the potential material basis and molecular mechanism of Shudage-4 in attenuating gastric ulcers in rats. The chemical constituents and transitional components in the blood of Shudage-4 were identified by ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS). The rat gastric ulcer model was induced by water immersion restraint stress (WIRS). The ulcer damage to gastric tissue was measured at the gross anatomical level and pathological level by hematoxylin-eosin (HE) staining of gastric tissue. RNA sequencing of gastric tissue and plasma metabolomics were performed to analyze the mechanism of Shudage-4 against gastric ulcers. A Pearson correlation analysis was performed to explore the association between serum metabolites and gene expression of gastric tissue. A total of 30 chemical constituents were identified in Shudage-4 by UPLC-TOF-MS. Among 30 constituents, 13 transitional components in the blood were considered as the potential material basis. Shudage-4 treatment had a significant effect on WIRS-induced gastric ulcers in rats. HE staining of gastric tissue illustrated that WIRS-induced ulcer damage was suppressed by Shudage-4 treatment. RNA sequencing of gastric tissue showed that 282 reversed expression genes in gastric tissue were related to Shudage-4 treatment, and gene set enrichment analysis revealed that Shudage-4 treatment significantly inhibited gene set expression related to reactive oxygen species (ROS), which was also validated by detecting rat gastric tissue MDA, GSH, SOD, GSH-Px, and CAT activities. The plasma metabolomic data demonstrated that 23 significantly differential metabolites were closely associated with the Shudage-4 treatment. The further multiomics joint analysis found that significantly upregulated 5 plasma metabolites in Shudage-4-treated rats compared to model rats were negatively correlated with gene set expression related to ROS in gastric tissue. Shudage-4 alleviated WIRS-induced gastric ulcers by inhibiting ROS generation, which was achieved by regulating plasma metabolites level.

Curcumin Alleviates Singapore Grouper Iridovirus-Induced Intestine Injury in Orange-Spotted Grouper (Epinephelus coioides).

Singapore grouper iridovirus (SGIV) is a new ranavirus species in the Iridoviridae family, whose high lethality and rapid spread have resulted in enormous economic losses for the aquaculture industry. Curcumin, a polyphenolic compound, has been proven to possess multiple biological activities, including antibacterial, antioxidant, and antiviral properties. This study was conducted to determine whether curcumin protected orange-spotted grouper (Epinephelus coioides) from SGIV-induced intestinal damage by affecting the inflammatory response, cell apoptosis, oxidative stress, and intestinal microbiota. Random distribution of healthy orange-spotted groupers (8.0 ± 1.0 cm and 9.0 ± 1.0 g) into six experimental groups (each group with 90 groupers): Control, DMSO, curcumin, SGIV, DMSO + SGIV, and curcumin + SGIV. The fish administered gavage received DMSO dilution solution or 640 mg/L curcumin every day for 15 days and then were injected intraperitoneally with SGIV 24 h after the last gavage. When more than half of the groupers in the SGIV group perished, samples from each group were collected for intestinal health evaluation. Our results showed that curcumin significantly alleviated intestine damage and repaired intestinal barrier dysfunction, which was identified by decreased intestine permeability and serum diamine oxidase (DAO) activity and increased expressions of tight junction proteins during SGIV infection. Moreover, curcumin treatment suppressed intestinal cells apoptosis and inflammatory response caused by SGIV and protected intestinal cells from oxidative injury by enhancing the activity of antioxidant enzymes, which was related to the activation of nuclear factor erythroid 2-related factor 2 (Nrf2) signaling. Moreover, we found that curcumin treatment restored the disruption of the intestinal microbiota caused by SGIV infection. Our study provided a theoretical basis for the functional development of curcumin in aquaculture by highlighting the protective effect of curcumin against SGIV-induced intestinal injury.

Ultra-low-coverage genome-wide association study-insights into gestational age using 17,844 embryo samples with preimplantation genetic testing.

BACKGROUND: Very low-coverage (0.1 to 1×) whole genome sequencing (WGS) has become a promising and affordable approach to discover genomic variants of human populations for genome-wide association study (GWAS). To support genetic screening using preimplantation genetic testing (PGT) in a large population, the sequencing coverage goes below 0.1× to an ultra-low level. However, the feasibility and effectiveness of ultra-low-coverage WGS (ulcWGS) for GWAS remains undetermined. METHODS: We built a pipeline to carry out analysis of ulcWGS data for GWAS. To examine its effectiveness, we benchmarked the accuracy of genotype imputation at the combination of different coverages below 0.1× and sample sizes from 2000 to 16,000, using 17,844 embryo PGT samples with approximately 0.04× average coverage and the standard Chinese sample HG005 with known genotypes. We then applied the imputed genotypes of 1744 transferred embryos who have gestational ages and complete follow-up records to GWAS. RESULTS: The accuracy of genotype imputation under ultra-low coverage can be improved by increasing the sample size and applying a set of filters. From 1744 born embryos, we identified 11 genomic risk loci associated with gestational ages and 166 genes mapped to these loci according to positional, expression quantitative trait locus, and chromatin interaction strategies. Among these mapped genes, CRHBP, ICAM1, and OXTR were more frequently reported as preterm birth related. By joint analysis of gene expression data from previous studies, we constructed interrelationships of mainly CRHBP, ICAM1, PLAGL1, DNMT1, CNTLN, DKK1, and EGR2 with preterm birth, infant disease, and breast cancer. CONCLUSIONS: This study not only demonstrates that ulcWGS could achieve relatively high accuracy of adequate genotype imputation and is capable of GWAS, but also provides insights into the associations between gestational age and genetic variations of the fetal embryos from Chinese population.

Differences in HDL-related mortality risk between individuals with and without hypertension: a prospective cohort study in UK Biobank.

BACKGROUND AND AIMS: Very high levels of high-density lipoprotein cholesterol (HDL-C) have been paradoxically linked to increased mortality risk. The present study aimed to examine associations of HDL-C and varied sizes of the HDL particle (HDL-P) with mortality risk stratified by hypertension. METHODS AND RESULTS: This prospective cohort study included 429 792 participants (244 866 with hypertension and 184 926 without hypertension) from the UK Biobank. During a median follow-up of 12.7 years, 23 993 (9.8%) and 8142 (4.4%) deaths occurred among individuals with and without hypertension, respectively. A U-shaped association of HDL-C with all-cause mortality was observed in individuals with hypertension after multivariable adjustment, whereas an L-shape was observed in individuals without hypertension. Compared with individuals with normal HDL-C of 50-70 mg/dL, those with very high HDL-C levels (>90 mg/dL) had a significantly higher risk of all-cause mortality among individuals with hypertension (hazard ratio, 1.47; 95% confidence interval, 1.35-1.61), but not among those without hypertension (1.05, 0.91-1.22). As for HDL-P, among individuals with hypertension, a larger size of HDL-P was positively whereas smaller HDL-P was negatively associated with all-cause mortality. After additional adjustment for larger HDL-P in the model, the U-shaped association between HDL-C and mortality risk was altered to an L-shape among individuals with hypertension. CONCLUSIONS: The increased risk of mortality associated with very high HDL-C existed only in individuals with hypertension, but not in those without hypertension. Moreover, the increased risk at high HDL-C levels in hypertension was likely driven by larger HDL-P.

This study examined the potential modification of hypertension on associations of high-density lipoprotein cholesterol (HDL-C), especially at a very high level, and varied sizes of HDL particle (HDL-P) with the risk of mortality.Very high HDL-C levels were associated with increased risk of mortality in individuals with hypertension, but not in those without hypertension.In individuals with hypertension, the increased risk at a high HDL-C level was attributed to a larger size of HDL-P, which was directly associated with mortality risk. An inverse association with mortality was observed for a smaller size of HDL-P.

Association of healthy sleep pattern with risk of recurrent cardiovascular events among patients with coronary heart disease.

AIMS: To examine the association of a healthy sleep pattern with the risk of recurrent cardiovascular events among patients with coronary heart disease (CHD). METHODS AND RESULTS: This prospective cohort study included 21 193 individuals with CHD from the UK Biobank. A healthy sleep score was generated based on a combination of chronotype, sleep duration, insomnia, and excessive daytime sleepiness. Cox proportional hazards regression models were applied to estimate the associations between healthy sleep score and recurrent cardiovascular events. During a median of 11.1 years of follow up, we documented 3771 recurrent cardiovascular events, including 1634 heart failure cases and 704 stroke cases. After multivariable adjustment, including lifestyle factors, medical history, and CHD duration, sleep 7-8 h/day, never/rarely insomnia, and no frequent daytime sleepiness were each significantly associated with a 12-22% lower risk of heart failure. In addition, compared with participants who had a healthy sleep score of 0-1, the multivariable-adjusted HR (95% CI) for participants with a healthy sleep score of 4 was 0.86 (0.75, 0.99) for recurrent cardiovascular events, 0.71 (0.57, 0.89) for heart failure, and 0.72 (0.51, 1.03) for stroke. CONCLUSIONS: Adherence to a healthy sleep pattern was significantly associated with a lower risk of recurrent cardiovascular events among patients with CHD, especially for heart failure. These findings indicate that healthy sleep behaviours could be beneficial in the prevention of cardiovascular event recurrence.