Additional file 10. Table S7. Recurrent CNVs in previously published syndromic CHD cohorts and our study.

Additional file 24: Table S2. The Impacts of Somatic Copy Number Alterations in PDAC Cohort. Table S2A Matrix of amplification peaks, followed by the genes contained in them, 95% confidence level. Table S2B Matrix of deletion peaks, followed by the genes contained in them, 95% confidence level. Table S2C Matrix of the top 10 mutated genes in PDAC of Fudan cohort. Table S2D Matrix of the 10 mutated genes used in Figure 1C of ICGC,...

Additional file 27: Table S5. 8p11.22 Amplification Associated with PDAC Metastasis. Table S5A The matrix describing mutations in PDAC metastatic patients and non-metastatic patients. Table S5B Matrix of GSVA scores of pathways significantly altered in PDAC metastatic patients and non-metastatic patients, proteome level. Table S5C Matrix of xCell signatures significantly altered in PDAC metastatic patients and non-metastatic patients, transcriptome level. Table S5D Matrix describing the cis-effects of genes located on chromosome 8p11.22. Table S5E Matrix...

Additional file 27: Table S5. 8p11.22 Amplification Associated with PDAC Metastasis. Table S5A The matrix describing mutations in PDAC metastatic patients and non-metastatic patients. Table S5B Matrix of GSVA scores of pathways significantly altered in PDAC metastatic patients and non-metastatic patients, proteome level. Table S5C Matrix of xCell signatures significantly altered in PDAC metastatic patients and non-metastatic patients, transcriptome level. Table S5D Matrix describing the cis-effects of genes located on chromosome 8p11.22. Table S5E Matrix...

Additional file 29: Table S7. Characterization of Immune Infiltration in PDAC. Table S7A Matrix of xCell signatures significantly altered in 5 immune subgroups. Table S7B Matrix describing the expression of proteins in 5 immune subgroups. Table S7C Matrix of GSVA scores of pathways significantly altered in 5 immune subgroups, transcriptome level. Table S7D Matrix of amplification/deletion events of genes in 5 immune subgroups. Table S7E Matrix describing the expression of proteins involved in TCA cycle.

Many patients need repeated bronchoscopies with tissue sampling to obtain the final pathological results and guide the optimal subsequent treatment of pulmonary lesions. However, few studies have explored the safety of repeated biopsies. The records of patients who underwent bronchoscopy-guided tissue sampling because of pulmonary lesions at the respiratory department between 1 January 2008 and 31 December 2019 were revised. The patients’ clinical characteristics, information about bronchoscopy and incidence of complications were collected and analyzed....

Lamprophyre is one of the most important probes to understand the enrichment and depletion processes of the lithospheric evolution. Determining the age and petrogenesis of lamprophyres could provide critical data for deducing the timing and process of lithospheric revolution of the Sulu Orogenic Belt (SOB) and North China Craton (NCC). In this study, the Taolin lamprophyre in SOB was delineated by zircon U–Pb dating with the ages of 126 Ma. This lamprophyre is characterized by...

The chemical warfare agent sulfur mustard (SM) causes severe cutaneous lesions characterized by epidermal cell death, apoptosis, and inflammation. At present, the molecular mechanisms underlying SM-induced injury are not well understood, and there is no standard treatment protocol for SM-exposed patients. Here, we conducted a high-content screening of the Food and Drug Administration (FDA)-approved drug library of 1018 compounds against SM injury on an immortal human keratinocyte HaCaT cell line, focusing on cell survival. We...

Platycodon grandiflorus, a perennial flowering plant widely distributed in China and South Korea, is an excellent resource for both food and medicine. The main active compounds of P. grandiflorus are triterpenoid saponins. WRKY transcription factors (TFs) are among the largest gene families in plants and play an important role in regulating plant terpenoid accumulation, physiological metabolism, and stress response. Numerous studies have been reported on other medicinal plants; however, little is known about WRKY genes...

Seagrass meadows are virtual blue carbon ecosystems facing a dramatic decline on a global scale. Tracking the status and trends of seagrass meadows, which is still pending on large scales, is an emerging priority for their conservation and restoration. Here, we develop a semi-automatic procedure to identify and map seagrass meadows. Using Sentinel-2 data in Google Earth Engine (GEE) platform, a map is generated, showing a total of 11113.4 ha of seagrass meadows in coastal...

Macroautophagy/autophagy, a major catabolic pathway in eukaryotes, participates in plant sexual reproduction including the processes of male gametogenesis and the self-incompatibility response. Rapid pollen tube growth is another essential reproductive process that is metabolically highly demanding to drive the vigorous cell growth for delivery of male gametes for fertilization in angiosperms. Whether and how autophagy operates to maintain the homeostasis of pollen tubes remains unknown. Here, we provide evidence that autophagy is elevated in growing...

Age-related macular degeneration (AMD), the leading cause of blindness among the elderly, is without treatment for early disease. Degenerative retinal pigment epithelial (RPE) cell heterogeneity is a well-recognized but understudied pathogenic factor. Due to the daily phagocytosis of photoreceptor outer segments, unique photo-oxidative stress, and high metabolism for maintaining vision, the RPE has robust macroautophagy/autophagy, and mitochondrial and antioxidant networks. However, the autophagy subtype, mitophagy, in the RPE and AMD is understudied. Here, we found...

Age-related macular degeneration (AMD), the leading cause of blindness among the elderly, is without treatment for early disease. Degenerative retinal pigment epithelial (RPE) cell heterogeneity is a well-recognized but understudied pathogenic factor. Due to the daily phagocytosis of photoreceptor outer segments, unique photo-oxidative stress, and high metabolism for maintaining vision, the RPE has robust macroautophagy/autophagy, and mitochondrial and antioxidant networks. However, the autophagy subtype, mitophagy, in the RPE and AMD is understudied. Here, we found...

The northern areas of China are traditional endemic regions for brucellosis in both animals and humans, while occasional outbreaks of brucellosis have been observed in neglected southern provinces. On 16 December 2020, Chongqing Center for Disease Control and Prevention (CQCDC) received a report of 15 Brucella seropositive employees in a biological products company. The CQCDC and the local health administrative department launched an investigation that included identification of cases, laboratory testing of samples, and employees’...

Talaromyces marneffei tends to induce systemic infection in immunocompromised individuals, which is one of the causes of the high mortality. The underlying molecular mechanisms of T.marneffei-induced abnormal liver function are still poorly understood. In this study, we found that T.marneffei-infected patients could develop abnormal liver function, evidenced by reduced albumin and increased levels of aspartate aminotransferase (AST) and AST/alanine aminotransferase (ALT). T. marneffei-infected mice exhibited similar characteristics. In vitro investigations showed that T.marneffei induced the...

To evaluate changes in conjunctiva-associated lymphoid tissues (CALTs) in patients with type 2 diabetic mellitus (T2DM). Thirty-two patients with T2DM and 32 healthy volunteers underwent comprehensive examinations. In vivo confocal microscopy and Image J were used to observe and evaluate the patients’ CALT-related parameters. Conjunctival impression cytology (CIC) samples of the tarsal conjunctiva were collected from the patients, and CD4+ and CD8+ cells were evaluated by immunofluorescence staining. The diabetes group showed higher diffuse lymphocyte...

To evaluate changes in conjunctiva-associated lymphoid tissues (CALTs) in patients with type 2 diabetic mellitus (T2DM). Thirty-two patients with T2DM and 32 healthy volunteers underwent comprehensive examinations. In vivo confocal microscopy and Image J were used to observe and evaluate the patients’ CALT-related parameters. Conjunctival impression cytology (CIC) samples of the tarsal conjunctiva were collected from the patients, and CD4+ and CD8+ cells were evaluated by immunofluorescence staining. The diabetes group showed higher diffuse lymphocyte...

The present systematic review and meta-analysis of randomized clinical trials (RCTs) aimed to investigate the effects of pulmonary rehabilitation in individuals with chronic obstructive pulmonary disease (COPD). The RCTs of pulmonary rehabilitation programs published between 1999 and 2021 were retrieved from electronic databases (PubMed, Cochrane Library, and Embase). Two reviewers independently assessed the topical relevance and trial quality and extracted data for meta-analysis using the Stata software version 14.0. A total of 39 trials involving...

This study is designed to explore the role of long non-coding RNAs (lncRNAs) NCK1-AS1 in proliferative and invasive activities of esophageal squamous cell carcinoma (ESCC) cells by binding to microRNA-133b (miR-133b) to regulate ENPEP. Differentially expressed lncRNAs, miRs, genes and their targeting relationships were screened on ESCC-related gene expression datasets GSE17351 and GSE6188. The targeting relationships among NCK1-AS1, miR-133b, and ENPEP were verified using functional assays. Loss- and gain- of function assays were carried out...

The Himalaya-Hengduan Mountain region is one of the hotspots of biodiversity research. The uplift of the Qinghai-Tibetan Plateau (QTP) and the Quaternary glaciation caused great environmental changes in this region, and the responses of many species in the QTP to the Quaternary climate are still largely unknown. The genetic structure and phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an endemic Chinese alpine species in this area, were investigated based on four chloroplast fragments and...

Additional file 4: Table S1. Detailed information of the microarray used in this study.

Additional file 1. Table S1. Summary of tools for candidate gene prioritization, including VarElect, OVA, AMELIE, and ToppGene.

Additional file 1: Supplementary Figures. The full-length blots of WB in Fig. 5B. Whole-cell extracts were resolved on 10% SDS-PAGE by bio-rad Mini-PROTEAN with 10 sample Wells (1Marker, 2space, 3Blank group, 4CSP I-plus group, 5Endostar group, 6rES-CSP group, 7rES-CSP+ heparin group, 8DDP group, 9space, 10Marker), and then electrotransferred onto a polyvinylidene difluoride (PVDF) membrane (Millipore). The membranes were then probed with respective primary antibodies against VEGFA, MMP2, integrinβ1, and E-cadherin procured from Abcam, β-actin from...

Supplement 2: the size of pyrite and goethite from the SMG.

This document describes the basic drawing data of Figure 5