Additional file 1. Supplementary figures.

Additional file 11. Methods.

Additional file 12. Supplementary discussion.

Additional file 13. Supplementary results.

Additional file 2. Table S2: Adjuvant treatment information.

Additional file 3. Table S3: Performance of three strategies.

Additional file 7. Figure S4: ctDNA statuses and disease-related events of patients during follow-up periods. Swimmer plot illustrating the ctDNA statuses, adjuvant therapies, and pathological events of all patients. Abbreviations: LUAD – lung adenocarcinoma, LUSC - lung squamous-cell carcinoma, AT – adjuvant therapy.

Additional file 8. Figure S5: Prognostic values of ctDNA detection based on clonal and subclonal mutations. A). The recurrence-free survival analysis of patients stratified by ctDNA detection based on only clonal mutation profiles. B). The recurrence-free survival analysis of patients stratified by ctDNA detection based on all clonal and subclonal mutations.

Additional file 9. Figure S6: ctDNA testing, LDCT scans, and disease-related events of patients during follow-up periods. . Swimmer plot illustrating the first positive ctDNA testing, the last negative LDCT scans, and pathological events of patients that experienced recurrence or deceased. B). The original and adjusted time intervals between the first positive ctDNA testing and final LDCT scans that detected disease recurrence. Abbreviations: LDCT – low-dose computed tomography, LUAD – lung adenocarcinoma, LUSC - lung...

Additional file 9. Figure S6: ctDNA testing, LDCT scans, and disease-related events of patients during follow-up periods. . Swimmer plot illustrating the first positive ctDNA testing, the last negative LDCT scans, and pathological events of patients that experienced recurrence or deceased. B). The original and adjusted time intervals between the first positive ctDNA testing and final LDCT scans that detected disease recurrence. Abbreviations: LDCT – low-dose computed tomography, LUAD – lung adenocarcinoma, LUSC - lung...

Abstract Background Circulating tumor DNA (ctDNA) has been proven as a marker for detecting minimal residual diseases following systemic therapies in mid-to-late-stage non-small-cell lung cancers (NSCLCs) by multiple studies. However, fewer studies cast light on ctDNA-based MRD monitoring in early-to-mid-stage NSCLCs that received surgical resection as the standard of care. Methods We prospectively recruited 128 patients with stage I–III NSCLCs who received curative surgical resections in our Lung Cancer Tempo-spatial Heterogeneity prospective cohort. Plasma samples...

Identifying the latent cluster structure based on model heterogeneity is a fundamental but challenging task arises in many machine learning applications. In this paper, we study the clustered coefficient regression problem in the distributed network systems, where the data are locally collected and held by nodes. Our work aims to improve the regression estimation efficiency by aggregating the neighbors’ information while also identifying the cluster membership for nodes. To achieve efficient estimation and clustering, we...

Additional file 2. Odds of depression symptoms according to status and consumption of cigarette smoking stratified by age.

Additional file 3. Odds of depression symptoms according to status and consumption of alcohol drinking stratified by age.

Abstract Background Although association of depressive symptoms with cigarette or alcohol is well documented, the dose–response relationship between them is rarely studied. This study aims to evaluate dose–response relationships of cigarette and alcohol consumption with depressive symptoms in Chinese middle-aged and elderly men, providing evidence to guide cigarette and alcohol control. Methods This multiple-center, cross-sectional study including 5965 Chinese men aged 40–79 years was conducted in 2013–2016 in China. Depressive symptoms were evaluated by Beck...

Additional file 1: Supplementary Figure 1. Kaplan-Meier analysis for the cumulative incidence of dementia with log-rank test. Supplementary Figure 2. The survival curves of cumulative incidence of dementia and competing risk event for death. Supplementary Table 1. Association of cancer with dementia risk after additional adjustment for cognitive function. Supplementary Table 2. Association of site-specific cancers with dementia and its subtypes. Supplementary Table 3. Association of specific cancer sites with ACD, AD, and VD by...

Additional file 1: Supplementary Materials 1. Study workflow. Supplementary Materials 2. Initial analysis for the associations between resting heart rate and different cognitive tests. Supplementary Materials 3. Main analyses. Supplementary Materials 4. Testing for non-linearity of resting heart rate effects. Supplementary Materials 5. Sensitivity analyses of dementia. Supplementary Materials 6. Sensitivity analyses of cognitive decline. Supplementary Materials 7. Brain imaging analyses. Appendix 1. Field IDs and of UK Biobank. Appendix 2. Catalogue of rest heart...

Abstract Background Resting heart rate (RHR) has been linked with an increased risk of dementia. However, evidence characterizing the associations of RHR with different dementia subtypes and their underlying mechanisms remains scarce. This study aims to investigate the relationships of RHR with different dementia types, cognitive function, and brain structural abnormalities. Methods Three hundred thirty-nine thousand nine hundred one participants with no prior diagnosis of dementia from the UK biobank were analyzed. Cox regression and...

Additional file 10. Figure S10. (a) T-Distributed Stochastic Neighbor Embedding (t-SNE) plot depicting clusters of all immune and non-immune cells from 24 EMT-6 tumors analyzed by 10× genomics scRNA-seq. (b) Violin plot showing expression of Ptprc (encoding CD45) in all clusters from EMT-6 tumors.

Additional file 10. Figure S10. (a) T-Distributed Stochastic Neighbor Embedding (t-SNE) plot depicting clusters of all immune and non-immune cells from 24 EMT-6 tumors analyzed by 10× genomics scRNA-seq. (b) Violin plot showing expression of Ptprc (encoding CD45) in all clusters from EMT-6 tumors.

Additional file 11. Figure S11. Heatmap showing cluster-specific gene profiles. (a) Macrophage-specific gene profiles. (b) Neutrophil-specific gene profiles. (c) T cell-specific gene profiles. (d) NK cell-specific gene profiles. (e) B cell-specific gene profiles. (f) Monocyte-specific gene profiles. (g) cDC-specific gene profiles. (h) pDC-specific gene profiles. (i) Mast-specific gene profiles.

Additional file 4. Figure S4: The effects of MSA-2 and TGF-β on chemokine production in BMDM. (a-f) Unactivated BMDMs were cultured with MSA-2 for one day, and supernatants were collected for chemokine detection.

Additional file 5. Figure S5: MSA-2-stimulated IFN-β expression in cancer cells. Three cell lines B16, CT26, and EMT-6 were cultured with MSA-2 for one day, and supernatants were collected for IFN-β detection with ELISA. BMDM and BMDC were used as positive controls.

Additional file 2.

A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was...