Additional file 1: of Evaluation of the ocular surface characteristics and Demodex infestation in paediatric and adult blepharokeratoconjunctivitis

Raw data for BKC study. Clinical data of ocular surface characteristics in controls and BKC patients. (XLSX 17 kb

Screening of candidate genes at GLC3B and GLC3C loci in Chinese primary congenital glaucoma patients with targeted next generation sequencing

Primary congenital glaucoma (PCG) is characterized by developmental abnormalities of the anterior chamber angle. Although several genes have been associated with PCG, pathogenic mutations could only be detected in about 20% of Chinese patients. GLC3B (1p36.2–36.1) and GLC3C (14q24.3) loci were previously identified in PCG pedigrees via linkage analysis. However, no causative genes were reported in these loci. This study was designed to search for novel PCG-related genes in these genetic regions. DNA samples from 100 PCG patients and 200 normal controls were pooled and sequenced using a customized panel of 133 positional candidate genes located around GLC3B and GLC3C loci (±1Mb). PCG-related genes were prioritized by the distribution of variants between patients and controls. Confirmation of selected variants and co-segregation analysis were performed using Sanger sequencing. Patient and control group contained 116 and 147 rare variants respectively after screening. Three genes (ZC2HC1C, VPS13D, and PGF) were prioritized according to the distribution of variants between the two groups. Rare variants of PGF were only identified in PCG patients. To the best of our knowledge, this is the first study aiming at exploring novel PCG-related genes at GLC3B and GLC3C loci. Our preliminary results suggest that there are potential associations between ZC2HC1C, VPS13D, PGF, and PCG. However, larger cohort studies and functional assays are required to provide further evidence for the proposed genotype-phenotype association.</p

Table1_Chemical composition, biological activities, and quality standards of hawthorn leaves used in traditional Chinese medicine: a comprehensive review.docx

Hawthorn leaves also known as crataegi foilum, are a combination of botanical drugs used commonly in Traditional Chinese Medicine. Hawthorn, the plant from which hawthorn leaves are prepared, is distributed in Northeast China, North China, and other regions in China. Hawthorn leaves are known to activate blood circulation and eliminate stasis, invigorating Qi, eliminating turbidity, and reducing the levels of lipids. So far, over a hundred compounds have been isolated from hawthorn leaves, including flavonoids, terpenoids, lignans, organic acids, and nitrogenous compounds. Hawthorn leaves are used for the treatment of hypertension, protecting against ischemic injury, angina, hyperglycemia, hyperlipidemia, and certain other conditions. Several of the currently available clinical preparations also use hawthorn leaves as raw materials, such as Yixintong capsules, Xinan capsules, etc. The present report systematically reviews the chemical composition, biological activities, and quality standards of hawthorn leaves, to provide a scientific basis and reference for detailed research on hawthorn leaves.</p

Table_1_Peripapillary Vascular Reactivity in Primary Open-Angle Glaucoma With High Myopia by Using Optical Coherence Tomography Angiography.pdf

PurposeTo evaluate peripapillary vascular reactivity in primary open-angle glaucoma (POAG) with and without high myopia (HM) by using optical coherence tomography angiography (OCTA).MethodsThis prospective study enrolled 48 eyes with POAG, including 16 and 32 eyes with and without HM, respectively. The retinal peripapillary vessel density (VD) was repeatedly assessed using OCTA at baseline and after a hyperoxia test (breathing 80% oxygen). The VD changes between different oxygenation conditions were calculated to reflect the vasoreactivity. Linear regression was performed to determine the relationship between myopia and retinal vascular reactivity in patients with POAG. Systemic hemodynamic characteristics were also evaluated under both conditions.ResultsThe VD was significantly reduced after hyperoxia in the whole image (baseline and hyperoxia: 41.4 ± 4.5 and 38.8 ± 4.4, respectively, P 2 = 0.31) and axial length (AL) (β = −0.72, P 2 = 0.33).ConclusionRetinal vasoreactivity of peripapillary capillaries in POAG eyes with HM was significantly impaired in comparison with that in POAG eyes without HM. A lower peripapillary vascular response was significantly associated with worse SE and elongated AL.</p

Presentation_1_Prognostic Nutritional Index Predicts Response and Prognosis in Cancer Patients Treated With Immune Checkpoint Inhibitors: A Systematic Review and Meta-Analysis.pdf

ObjectiveTo investigate the association between pretreatment prognostic nutritional index (PNI) and clinical survival outcomes for advanced-stage cancer patients treated with immune checkpoint inhibitors (ICIs).MethodsWe conducted a comprehensive literature search to identify eligible studies concerning the relationship between pretreatment PNI and survival outcomes in advanced cancer patients treated with ICIs. Published data were extracted and pooled odds ratio (pOR) for objective response rate (ORR), disease control rate (DCR), and pooled hazard ratio (pHR) for overall survival (OS), progressive-free survival (PFS), along with 95% confidence intervals (95% CIs) were calculated.ResultsTwelve studies with 1,359 participants were included in our study. A higher level of PNI indicated a greater ORR (pOR = 2.17, 95% CI = 1.52–3.10) and favorable DCR (pOR = 2.48, 95% CI = 1.87–3.29). Low PNI was associated with a shorter OS (pHR = 2.24, 95% CI = 1.57–3.20) and unfavorable PFS (pHR = 1.61, 95% CI = 1.37–1.88).ConclusionLow PNI might be an effective biomarker of poor tumor response and adverse prognosis of advanced cancer patients with ICIs. Further studies are needed to verify the prognostic value of PNI in clinical practice.</p

Data_Sheet_1_Transcriptomic Analyses for Identification and Prioritization of Genes Associated With Alzheimer’s Disease in Humans.docx

Long non-coding RNAs (lncRNAs), as important ncRNA regulators, play crucial roles in the regulation of various biological processes, and their aberrant expression is related to the occurrence and development of diseases, which is gradually validated by more and more studies. Alzheimer’s disease (AD) is a chronic neurodegenerative disease that often develops slowly and gradually deteriorates over time. However, which functions the lncRNAs perform in AD are almost unknown. In this study, we performed transcriptome analysis in AD, containing 12,892 known lncRNAs and 19,053 protein-coding genes (PCGs). Further, 14 down-regulated and 39 up-regulated lncRNAs were identified, compared with normal brain samples, which indicated that these lncRNAs might play critical roles in the pathogenesis of AD. In addition, 19 down-regulated and 28 up-regulated PCGs were also detected. Using the differentially expressed lncRNAs and PCGs through the WGCNA method, an lncRNA–mRNA co-expressed network was constructed. The results showed that lncRNAs RP3-522J7, MIR3180-2, and MIR3180-3 were frequently co-expressed with known AD risk PCGs. Interestingly, PCGs in the network are significantly enriched in brain- or AD-related biological functions, including the brain renin–angiotensin system, cell adhesion, neuroprotective role of THOP1 in AD, and so on. Furthermore, it was shown that 18 lncRNAs and 7 PCGs were highly expressed in normal brain tissue relative to other normal tissue types, suggesting their potential as diagnostic markers of AD, especially RP3-522J7, MIR3180-2, MIR3180-3, and CTA-929C8. In total, our study identified a compendium of AD-related dysregulated lncRNAs and characterized the corresponding biological functions of these lncRNAs in AD, which will be helpful to understand the molecular basis and pathogenesis of AD.</p

Additional file 3 of MIR22HG acts as a tumor suppressor via TGFβ/SMAD signaling and facilitates immunotherapy in colorectal cancer

Additional file 3. Table S1. Correlation of the expression of MIR22HG in colorectal cancer with clinic pathologic features

Additional file 2 of MIR22HG acts as a tumor suppressor via TGFβ/SMAD signaling and facilitates immunotherapy in colorectal cancer

Additional file 2. Supplementary figures, including supplementary Figs S1-S10

Additional file 1 of MIR22HG acts as a tumor suppressor via TGFβ/SMAD signaling and facilitates immunotherapy in colorectal cancer

Additional file 1. Supporting Materials and Methods

Table_1_A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome.DOCX

LincRNAs enriched with high H3K4me1 and low H3K4me3 signals often have the enhancer-like features which are named as enhancer-associated lincRNAs (elincRNAs). ElincRNAs are considered to be indispensable for target gene transcription, which play important roles in development, signaling events, and even diseases. In this study, we developed a regularized regression model to identify elincRNAs by integrating the genomic, epigenomic, and regulatory data. Application of the proposed method to mouse ESCs reveals that besides the basic well-known epigenetic features H3K4me1 and H3K4me3, more specific epigenetic features, such as high DNA methylation, high H3K122ac, and H3K36me3 were contributed to mark elincRNAs with the best accuracy and precision. Finally, 3729 elincRNAs were identified in mouse ESCs. Furthermore, the elincRNAs and canonical lincRNAs exhibit distinct genomic features, and elincRNAs have the higher CGI enrichment and lower sequence conservation. Through the analysis of transcription regulation, we found that elincRNAs were significantly regulated by NANOG, POU5F1, SOX2 and ESRRB, and were involved in the core transcriptional regulatory circuitry controlling ES cell state Function enrichment analysis further discovered that elincRNAs tended to regulate specific embryonic development biological processes. These results indicated that these two types of lincRNAs had both specific epigenetic and transcriptional regulation mechanism and display distinct functional characters. In conclusion, we presented a credible computational model to prioritize novel elincRNAs, and depicted the atlas of elincRNAs in mouse ESCs, which would help dissect the function roles of lncRNAs during the mammalian development and diseases.</p