Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing.

Technology for spatial multi-omics aids the discovery of new insights into cellular functions and disease mechanisms. Here we report the development and applicability of multi-omics in situ pairwise sequencing (MiP-seq), a method for the simultaneous detection of DNAs, RNAs, proteins and biomolecules at subcellular resolution. Compared with other in situ sequencing methods, MiP-seq enhances decoding capacity and reduces sequencing and imaging costs while maintaining the efficacy of detection of gene mutations, allele-specific expression and RNA modifications. MiP-seq can be integrated with in vivo calcium imaging and Raman imaging, which enabled us to generate a spatial multi-omics atlas of mouse brain tissues and to correlate gene expression with neuronal activity and cellular biochemical fingerprints. We also report a sequential dilution strategy for resolving optically crowded signals during in situ sequencing. High-throughput in situ pairwise sequencing may facilitate the multidimensional analysis of molecular and functional maps of tissues.

ZCHSound: Open-Source ZJU Paediatric Heart Sound Database With Congenital Heart Disease.

BACKGROUND: Congenital heart disease (CHD) is a common birth defect in children. Intelligent auscultation algorithms have been proven to reduce the subjectivity of diagnoses and alleviate the workload of doctors. However, the development of this algorithm has been limited by the lack of reliable, standardized, and publicly available pediatric heart sound databases. Therefore, the objective of this research is to develop a large-scale, high-standard, high-quality, and accurately labeled pediatric congenital heart disease (CHD) heart sound database, and perform classification tasks to evaluate its performance, filling this important research gap. METHOD: From 2020 to 2022, we collaborated with experienced cardiac surgeons from Zhejiang University Children's Hospital to collect heart sound signals from 1259 participants using electronic stethoscopes. To ensure accurate disease diagnosis, the cardiac ultrasound images for each participant were acquired by an experienced ultrasonographer, and the final diagnosis was confirmed through the consensus of two cardiac experts or cardiac surgeons. To establish the benchmark of ZCHSound, we extracted 84 time-frequency features from the heart sounds and evaluated the performance of the classification task using machine learning models. Additionally, we evaluated the importance scores of the 84 features in distinguishing between normal and pathological heart sounds in children using SHapley Additive exPlanations (SHAP) values. RESULTS: The ZCHSound database contains heart sound data from 1259 participants, with all data divided into two datasets: one is a high-quality, filtered clean heart sound dataset, and the other is a low-quality, noisy heart sound dataset. In the evaluation of the high-quality dataset, our random forest ensemble model achieved an F1 score of 90.3% in the classification task of normal and pathological heart sounds. Moreover, the SHAP analysis results demonstrate that frequency-domain features have a more significant impact on the model output compared to time-domain features. Features related to the cardiac diastolic period have a greater influence on the model's classification results compared to those related to the systolic period. CONCLUSION: This study has successfully established a large-scale, high-quality, rigorously standardized pediatric CHD sound database with precise disease diagnosis. This database not only provides important learning resources for clinical doctors in auscultation knowledge but also offers valuable data support for algorithm engineers in developing intelligent auscultation algorithms. Our data can be accessed and downloaded by the public at http://zchsound.ncrcch.org.cn/.

Interactome between ASFV and host immune pathway proteins.

IMPORTANCE: African swine fever (ASF), caused by African swine fever virus (ASFV), has become a major crisis for the pork industry in recent years. The mechanism for ASFV pathology and the clinical symptoms difference of ASF between domestic pigs and reservoir hosts remain to be elucidated. We deciphered the comprehensive protein-protein interaction (PPI) network between ASFV and host immune pathways. The intensive PPI network contained both ASFV-host immune pathway PPI and ASFV-ASFV PPI information, providing a comprehensive ASFV-host interaction landscape. Furthermore, the ASFV-host PPI difference between domestic pigs and warthogs was explored, which will be instructive for exploring essential candidates involved in ASFV pathology. Moreover, we screened the inhibitory effect of ASFV proteins in the PPI with cGAS-STING pathway on IFN-I and NF-κB, further providing possible functions of ASFV-host PPI network in innate immune regulation.

MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing.

Genomic abnormalities are strongly associated with cancer and infertility. In this study, we develop a simple and efficient method - multiple genetic abnormality sequencing (MGA-Seq) - to simultaneously detect structural variation, copy number variation, single-nucleotide polymorphism, homogeneously staining regions, and extrachromosomal DNA (ecDNA) from a single tube. MGA-Seq directly sequences proximity-ligated genomic fragments, yielding a dataset with concurrent genome three-dimensional and whole-genome sequencing information, enabling approximate localization of genomic structural variations and facilitating breakpoint identification. Additionally, by utilizing MGA-Seq, we map focal amplification and oncogene coamplification, thus facilitating the exploration of ecDNA's transcriptional regulatory function.

Children's Pain Identification Based on Skin Potential Signal.

Pain management is a crucial concern in medicine, particularly in the case of children who may struggle to effectively communicate their pain. Despite the longstanding reliance on various assessment scales by medical professionals, these tools have shown limitations and subjectivity. In this paper, we present a pain assessment scheme based on skin potential signals, aiming to convert subjective pain into objective indicators for pain identification using machine learning methods. We have designed and implemented a portable non-invasive measurement device to measure skin potential signals and conducted experiments involving 623 subjects. From the experimental data, we selected 358 valid records, which were then divided into 218 silent samples and 262 pain samples. A total of 38 features were extracted from each sample, with seven features displaying superior performance in pain identification. Employing three classification algorithms, we found that the random forest algorithm achieved the highest accuracy, reaching 70.63%. While this identification rate shows promise for clinical applications, it is important to note that our results differ from state-of-the-art research, which achieved a recognition rate of 81.5%. This discrepancy arises from the fact that our pain stimuli were induced by clinical operations, making it challenging to precisely control the stimulus intensity when compared to electrical or thermal stimuli. Despite this limitation, our pain assessment scheme demonstrates significant potential in providing objective pain identification in clinical settings. Further research and refinement of the proposed approach may lead to even more accurate and reliable pain management techniques in the future.

Trends in the prevalence of elevated cardiovascular risk and the control of its risk factors Among US adults, 2001-2020.

Background: An accurate assessment of current trends in cardiovascular risks could inform public health policy. This study aims to determine 20-year trends in the prevalence of elevated cardiovascular risk and its risk factors' control among US adults. Methods: In this serial cross-sectional analysis of 23,594 adults, aged 40-79 years, without clinical atherosclerotic cardiovascular disease (ASCVD) in the National Health and Nutrition Examination Survey from 2001 to 2020, we calculated the prevalence of elevated cardiovascular risk (10-year ASCVD risk ≥ 7.5%) for all participants and subgroups with their risk factors controlled for diabetes, hypertension, or dyslipidemia. Results: The age- and sex-adjusted prevalence of elevated cardiovascular risk slightly decreased from 41.5% (95% CI, 39.7-43.3%) in 2001-2004 to 38.6% (95% CI, 36.1-41.1%) in 2017-2020 (P for trend = 0.169) while the respective sex-adjusted prevalence significantly increased from 34.4% (95% CI, 32.8-36.0%) to 39.5% (95% CI, 37.0-42.0%; P for trend <0.001). Sex and race continued to show disparities in cardiovascular risk. Furthermore, a worsening disparity in age- and sex-adjusted prevalence of elevated cardiovascular risk between young and old and a narrowing gap among different education and poverty index levels (all P trend for interaction <0.05). Differential decomposition analysis found that demographic changes (primarily population aging) led to an 8.8% increase in the prevalence of elevated cardiovascular risk from 2001 to 2004 to 2017-2020, while risk factor control led to a 3.8% decrease. The rate of individuals receiving treatment for diabetes, hypertension, or dyslipidemia increased significantly between 2001 and 2020 (all P for trend <0.05). The rate of participants with hypertension who achieved blood pressure under 130/80 mmHg and those with dyslipidemia who achieved a non-high-density lipoprotein cholesterol level under 130 mg/dl increased significantly (all P for trend <0.001). Conclusions: There is a slight reduction in the prevalence of age- and sex-adjusted elevated cardiovascular risk among US adults without clinical ASCVD between 2001 and 2020, while the sex-adjusted prevalence significantly increased. The decrease in elevated cardiovascular risk prevalence was mainly attributed to risk factor control, while demographic changes contributed to an increase.

The influence of psychological factors on coronary heart disease: A review of the evidence and implications for psychological interventions.

This article reviews the evidence on the influence of psychological factors on coronary heart disease (CHD) and discusses the implications of these findings for psychological interventions. The review focuses on the role of work stress, depression, anxiety, and social support in the impact of CHD, as well as the effects of psychological interventions on CHD. The article concludes with recommendations for future research and clinical practice.

A deep learning-based method for pediatric congenital heart disease detection with seven standard views in echocardiography.

Background: With the aggregation of clinical data and the evolution of computational resources, artificial intelligence-based methods have become possible to facilitate clinical diagnosis. For congenital heart disease (CHD) detection, recent deep learning-based methods tend to achieve classification with few views or even a single view. Due to the complexity of CHD, the input images for the deep learning model should cover as many anatomical structures of the heart as possible to enhance the accuracy and robustness of the algorithm. In this paper, we first propose a deep learning method based on seven views for CHD classification and then validate it with clinical data, the results of which show the competitiveness of our approach. Methods: A total of 1411 children admitted to the Children's Hospital of Zhejiang University School of Medicine were selected, and their echocardiographic videos were obtained. Then, seven standard views were selected from each video, which were used as the input to the deep learning model to obtain the final result after training, validation and testing. Results: In the test set, when a reasonable type of image was input, the area under the curve (AUC) value could reach 0.91, and the accuracy could reach 92.3%. During the experiment, shear transformation was used as interference to test the infection resistance of our method. As long as appropriate data were input, the above experimental results would not fluctuate obviously even if artificial interference was applied. Conclusions: These results indicate that the deep learning model based on the seven standard echocardiographic views can effectively detect CHD in children, and this approach has considerable value in practical application.

Pulsatilla chinensis saponins ameliorated murine depression by inhibiting intestinal inflammation mediated IDO1 overexpression and rebalancing tryptophan metabolism.

BACKGROUND: Current antidepressant therapy remains unsatisfactory due to the complex pathogenesis. Emerging evidence suggested that depression is associated with inflammatory bowel disease (IBD), intestinal inflammation is an increasingly accepted factor that influences depression, but the mechanism is unclear. PURPOSE: In the current study, we determined whether Pulsatilla chinensis saponins (PRS), a phytomedicine from Pulsatilla chinensis (Bunge) Regel with excellent anti-IBD effect, could improve the depression. Furthermore, we investigated the mechanisms to explore the relationship between IBD and depression and provide new source for the urgent development of antidepressants from phytomedicine. METHODS: The antidepressant activity of PRS was accessed by behavioral test and multichannel technology in depression mice induced by Chronic Unpredictable Mild Stress (CUMS). 16S rDNA-based microbiota and RNA-seq in colon was used to explore potential intestinal metabolism affected by PRS. To illustrate the underlying mechanisms of anti-depression effect of PRS, targeted metabolomics, ELISA assay, immunofluorescence staining, Western Blot, and qPCR were carried out. RESULTS: The results clarified that CUMS induced depression with tryptophan (Trp) metabolism and intestinal inflammation. PRS effectively suppressed the depression and acted as a regulator of Trp/kynurenine (Kyn) metabolic and intestinal inflammation confirmed by analysis of microflora and colon RNA. Meanwhile PRS reduced interferon gamma (IFN-γ), inhibited JAK1-STAT1 phosphorylation, decreased IDO1 levels to protect against the overactivity of Trp/kyn path, suggesting that IFN-γ activated IDO1 probably a significant target for PRS to exert anti-depression effects. To further confirm the mechanism, this research expressed that PRS improved IDO1 activity and depressive behavior in mice with IFN-γ-induced depression. Furthermore, the therapeutic effect of 1-methyl-tryptophan (1-MT) well known as an IDO1 inhibitor in depression and clinically used anti-UC drug Mesalazine (MS) was demonstrated to confirm the potential mechanism. CONCLUSION: The study is the first to reveal the antidepressant effect of PRS and further demonstrate its potential therapeutic targets. In addition, it also clarifies that the Trp/kyn pathway is the crosstalk between IBD and depression and provides new choice for depression treatment. And it also provides an important basis for the follow-up development and exploration of anti-intestinal antidepressants.

Pulsatilla chinensis saponins improve SCFAs regulating GPR43-NLRP3 signaling pathway in the treatment of ulcerative colitis.

ETHNOPHARMACOLOGICAL RELEVANCE: Pulsatilla decoction has been extensively used to treat ulcerative colitis (UC) in recent years. Pulsatilla chinensis saponin (PRS), the active ingredient of its monarch medicine Pulsatilla chinensis (Bunge) Regel, plays a crucial role in the treatment of UC, but its specific mechanism of action has not been fully elucidated. AIM OF THE STUDY: This study aims to investigate the protective effect and possible mechanism of PRS on DSS-induced ulcerative colitis in rats. MATERIALS AND METHODS: In this study, the DSS-induced colitis model was used to explore the metabolism and absorption of PRS under UC, detect the content of short-chain fatty acids (SCFAs) in colon tissue, the expression of receptor G Protein-Coupled Receptor 43 (GPR43) protein and inflammasome NLRP3, and observe the expression level of IL-1ß, IL-6 and TNF-α in colon tissue. The protective effect of the PRS was also observed. RESULTS: It was found that in the UC group, the absorption rate and extent of drugs increased, and the elimination was accelerated. Compared with the control group, PRS increased the content of short-chain fatty acids (SCFAs) in colon tissue, promoted the expression of SCFAs receptor GPR43 protein, inhibited the activation of the NLRP3 inflammasome, and decreased the content of IL-1ß, IL-6 and TNF-α. PRS protects the colon in DSS-induced inflammatory bowel disease by increasing the content of SCFAs, promoting the expression of GPR43 protein, inhibiting the activation of the NLRP3 inflammasome, and reversing the increase in IL-1ß, IL-6 and TNF-α levels. CONCLUSIONS: PRS can increase the content of colonic SCFAs, activate the GPR43-NLRP3 signaling pathway, and reduce the levels of pro-inflammatory cytokines, thereby improving the symptoms of DSS-induced colitis.

The prenatal weekly temperature exposure and neonatal congenital heart disease: a large population-based observational study in China.

We aim to explore the link between maternal weekly temperature exposure and CHD in offspring and identify the relative contributions from heat and cold and from moderate and extreme atmospheric temperature. From January 2019 to December 2020, newborns who were diagnosed with CHD by echocardiography in the Network Platform for Congenital Heart Disease (NPCHD) from 11 cities in eastern China were enrolled in the present study. We appraised the exposure lag response relationship between temperature and CHDs in the distributed lag nonlinear model and further probed the pooled estimates by multivariate meta-analysis. We further performed the exposure-response curves in extreme temperature (5th percentile for cold and 95th for hot events). We also delve into the cumulative risk ratios (CRRs) of temperature on CHDs in general and subgroups. In this study, 5904 of 983, 523 infants were diagnosed with CHDs. The temperature-CHD combination performed positive significance in two exposure windows, gestational weeks 10-16 and 26-31, and reached the maximum effect in the 28th week. Compared with extreme cold (5th, 6.14℃), these effects were higher in extreme heat (95th, 29.26℃). The cumulative exposure-response curve showed a steep nonlinear rise in the hot tail but showed non-significance at low temperatures. In this range, the CRRs of temperature showed an increment to a ceiling of 3.781 (95% CI: 1.460-10.723). The temperature- CHD curves for both sex groups showed a general growth trend. No statistical significance was observed between these two groups (P = 0.106). The cumulative effect of the temperature related CHD was significant in regions with lower education levels (maximum CRR was 9.282 (3.019-28.535)). A degree centigrade increase in temperature exposure was associated with the increment of CHD risk in the first and second trimesters, especially in extreme heat. Neonates born in lower education regions were more vulnerable to temperature-related CHDs.

Prediction of congenital heart disease for newborns: comparative analysis of Holt-Winters exponential smoothing and autoregressive integrated moving average models.

OBJECTIVE: To describe the temporal trend of the number of new congenital heart disease (CHD) cases among newborns in Jinhua from 2019 to 2020 and explored an appropriate model to fit and forecast the tendency of CHD. METHODS: Data on CHD from 2019 to 2020 was collected from a health information system. We counted the number of newborns with CHD weekly and separately used the additive Holt-Winters ES method and ARIMA model to fit and predict the number of CHD for newborns in Jinhua. By comparing the mean square error, rooted mean square error and mean absolute percentage error of each approach, we evaluated the effects of different approaches for predicting the number of CHD in newborns. RESULTS: A total of 1135 newborns, including 601 baby girls and 534 baby boys, were admitted for CHD from HIS in Jinhua during the 2-year study period. The prevalence of CHD among newborns in Jinhua in 2019 was 0.96%. Atrial septal defect was diagnosed the most frequently among all newborns with CHD. The number of CHD cases among newborns remained stable in 2019 and 2020. There were fewer cases in spring and summer, while cases peaked in November and December. The ARIMA(2,1,1) model relatively offered advantages over the additive Holt-winters ES method in predicting the number of newborns with CHD, while the accuracy of ARIMA(2,1,1) was not very ideal. CONCLUSIONS: The diagnosis of CHD is related to many risk factors, therefore, when using temporal models to fit and predict the data, we must consider such factors' influence and try to incorporate them into the models.

Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation.

Immunocytes dynamically reprogram their gene expression profiles during differentiation and immunoresponse. However, the underlying mechanism remains elusive. Here, we develop a single-cell Hi-C method and systematically delineate the 3D genome and dynamic epigenetic atlas of macrophages during these processes. We propose "degree of disorder" to measure genome organizational patterns inside topologically-associated domains, which is correlated with the chromatin epigenetic states, gene expression, and chromatin structure variability in individual cells. Furthermore, we identify that NF-κB initiates systematic chromatin conformation reorganization upon Mycobacterium tuberculosis infection. The integrated Hi-C, eQTL, and GWAS analysis depicts the atlas of the long-range target genes of mycobacterial disease susceptible loci. Among these, the SNP rs1873613 is located in the anchor of a dynamic chromatin loop with LRRK2, whose inhibitor AdoCbl could be an anti-tuberculosis drug candidate. Our study provides comprehensive resources for the 3D genome structure of immunocytes and sheds insights into the order of genome organization and the coordinated gene transcription during immunoresponse.

Trends in the disease burden of congenital heart disease in China over the past three decades.

OBJECTIVE: To investigate the disease burden of congenital heart disease (CHD) in China from 1990 to 2019. METHODS: Using the data from Global Burden of Disease (GBD) study 2019, the incidence, age-standardized incidence rates, the mortality, age-standardized mortality rates, disability-adjusted life year (DALY) and age-standardized DALY rates of CHD were calculated. Time trend analysis of disease burden-related indicators was analyzed by Joinpoint regression model. Age-period-cohort model was used to describe age, period, and birth cohort effects in CHD mortality population. The relationship between age-standardized incidence, mortality, DALY rates of congenital heart disease and human development index (HDI) were analyzed by Pearson correlation. RESULTS: From 1990 to 2019, the mean annual percentage change (AAPC) in age-standardized incidence rate, mortality rate and DALY rate of CHD in China were -0.1%(95% CI: -0.7%-0.4%)、-3.5%(95% CI: -3.7%--3.2%) and -3.5%(95% CI: -3.7%--3.2%), respectively. CHD usually occurred in the first year of life. The mean incidence rate at birth was 2497.9/100 000, and the mean incidence rate under 1 year of age was 2626.6/100 000. During the period of 1995-2000, the incidence rate in newborn and <1 year children showed an exponential upward trend, then it remained a steady downward trend. However, there was an exponential increase in <1 year children during 2010-2013 and 2014-2015, followed by an exponential decrease to the lowest value in the last three decades. The mortality of CHD tended to decrease with age, with mortality of 101.67/100 000 for children under 5 years of age and a decrease after 5 years of age. However, there was a transient increase in mortality in age group 55-<60. From 1995 to 2019, the relative risk of death of patients with CHD showed a downward trend. Compared with 1995-1999, the rate ratio of death decreased by 24% in 2015-2019. Such downward trend was also observed in the birth cohort after 1945. Compared with the 1945-1949 birth cohort, the rate ratio of death for patients with CHD decreased by 75% in the 2015-2019 birth cohort. When HDI<0.58 (before 1999), the age-standardized incidence of CHD was positively correlated with HDI ( r=0.74, P<0.05). When HDI≥0.58 (after 1999), the age-standardized incidence of CHD was negatively correlated with HDI ( r=-0.76, P<0.01). The age-standardized mortality and DALY rates were negatively correlated with HDI ( r=-0.95 and -0.93, both P<0.01). CONCLUSIONS: During 1990 to 1999, the incidence of CHD increases and is positively correlated with the social development. During 1999 to 2019, the incidence of CHD decreases and is negatively correlated with the social development. The disease burden of CHD decreases and is negatively correlated with the social development. Some progress has been made in the field of prevention and control of CHD, but the disease burden remains high among younger population in China.

Geographical and Socioeconomic Factors Influence the Birth Prevalence of Congenital Heart Disease: A Population-based Cross-sectional Study in Eastern China.

Neonatal congenital heart disease (CHD) is the most common congenital anomaly. As a practical matter of people's livelihood, cardiac ultrasonography was performed on potential CHD children in 11 cities eastern China. In this study, we aimed to document the birth prevalence of CHD and its socioeconomic and geographical distribution, as supported by this public health policy. In this study, the diagnosis of CHD was made based on echocardiography. Geographical and socioeconomic factors were determined by the Statistical Bulletin on National Economic and Social Development (SBNESD). 51857 newborns from the Network Platform for Congenital Heart Disease (NPCHD) from January to December 2019 in 11 cities eastern China were included. The total birth prevalence of CHD was 5.79 per 1000 births. The study on the low-income areas, mountainous areas, areas with low medical institution bed level, and with high qualification of medical personnel reported a signifcantly higher birth prevalence of CHD compared with high-income cities, flat areas, areas with high medical institution bed level, and with low qualification of medical personnel. ASD, VSD, PDA, PS, TOF, atrioventricular septal defect, coarctation of the aorta, TAPVD, TGA and pulmonary atresia are the most frequent subtypes. ASD, VSD, PDA, PS, atrioventricular septal defect, coarctation of the aorta and pulmonary atresia showed a female preponderance, while TOF, TGA and TAPVD showed a male preponderance. Our study gives a relatively realistic prevalence of CHD after cardiac ultrasound examination of newborns suspected positive with CHD. Significant differences across geographical regions, income levels, and health service access were observed. In the future, population-wide cardiac ultrasound screening, prospective birth defect registries, and systematic medical follow-up programs covering the entire eastern or even China are needed to determine the exact birth prevalence.