Media 1: Principle and characteristics of 3D display based on random source constructive interference

Originally published in Optics Express on 14 July 2014 (oe-22-14-16863

Data_Sheet_2_The LINC00452/miR-204/CHST4 Axis Regulating Thymic Tregs Might Be Involved in the Progression of Thymoma-Associated Myasthenia Gravis.XLSX

BackgroundMyasthenia gravis (MG) is an autoimmune disease that mainly affects neuromuscular junctions and is usually associated with immune disorders in the thymoma. The competitive endogenous RNA (ceRNA) hypothesis has been demonstrated to be an intrinsic mechanism regulating the development of several autoimmune diseases; however, the mechanism where the ceRNA network regulates immune cells in patients with thymoma-associated MG (TAMG) has rarely been explored.MethodsRNA-seq data and clinical information of 124 patients with thymoma were obtained from The Cancer Genome Atlas (TCGA) database. The patients were divided into two groups according to whether they were diagnosed with MG. We applied the propensity score matching method to reduce the incidence of baseline confounders. We then constructed a ceRNA network with differentially expressed RNAs between the groups based on four public databases. The expression of genes of interest was validated by qPCR. Moreover, we predicted the immune cells that infiltrated the thymoma and then analyzed the association between immune cells and RNA in the ceRNA network. To further determine the function of the mRNAs associated with immune cells in patients with TAMG, we performed gene set enrichment analysis in thymoma patients with MG.ResultsAfter matching, 94 patients were included in the following analysis. A total of 847 mRNAs, 409 lncRNAs, and 45 miRNAs were differentially expressed between the groups. The ceRNA network, including 18 lncRNAs, four miRNAs, and 13 mRNAs, was then constructed. We then confirmed that CHST4 and LINC00452, miR-204-3p and miR-204-5p were differentially expressed between patients with TAMG and thymoma patients without MG (NMG) by qPCR. Moreover, we found that the percentage of predicted regulatory T (Treg) cells was significantly decreased in patients with TAMG. Further analysis indicated that the LINC00452/miR-204/CHST4 axis might regulate thymic regulatory T cells (Tregs) in the progression of MG.ConclusionsIn this research, we constructed a ceRNA network involved in the progression of TAMG, discovered that thymic Tregs were significantly decreased in patients with TAMG, and assumed that the LINC00452/miR-204/CHST4 axis may regulate thymic Tregs in the development of TAMG. These findings may deepen our understanding of the roles of the ceRNA network in regulating TAMG and highlight the function of CHST4 in recruiting peripheral T cells in the progression of TAMG.</p

Data_Sheet_1_The LINC00452/miR-204/CHST4 Axis Regulating Thymic Tregs Might Be Involved in the Progression of Thymoma-Associated Myasthenia Gravis.XLSX

BackgroundMyasthenia gravis (MG) is an autoimmune disease that mainly affects neuromuscular junctions and is usually associated with immune disorders in the thymoma. The competitive endogenous RNA (ceRNA) hypothesis has been demonstrated to be an intrinsic mechanism regulating the development of several autoimmune diseases; however, the mechanism where the ceRNA network regulates immune cells in patients with thymoma-associated MG (TAMG) has rarely been explored.MethodsRNA-seq data and clinical information of 124 patients with thymoma were obtained from The Cancer Genome Atlas (TCGA) database. The patients were divided into two groups according to whether they were diagnosed with MG. We applied the propensity score matching method to reduce the incidence of baseline confounders. We then constructed a ceRNA network with differentially expressed RNAs between the groups based on four public databases. The expression of genes of interest was validated by qPCR. Moreover, we predicted the immune cells that infiltrated the thymoma and then analyzed the association between immune cells and RNA in the ceRNA network. To further determine the function of the mRNAs associated with immune cells in patients with TAMG, we performed gene set enrichment analysis in thymoma patients with MG.ResultsAfter matching, 94 patients were included in the following analysis. A total of 847 mRNAs, 409 lncRNAs, and 45 miRNAs were differentially expressed between the groups. The ceRNA network, including 18 lncRNAs, four miRNAs, and 13 mRNAs, was then constructed. We then confirmed that CHST4 and LINC00452, miR-204-3p and miR-204-5p were differentially expressed between patients with TAMG and thymoma patients without MG (NMG) by qPCR. Moreover, we found that the percentage of predicted regulatory T (Treg) cells was significantly decreased in patients with TAMG. Further analysis indicated that the LINC00452/miR-204/CHST4 axis might regulate thymic regulatory T cells (Tregs) in the progression of MG.ConclusionsIn this research, we constructed a ceRNA network involved in the progression of TAMG, discovered that thymic Tregs were significantly decreased in patients with TAMG, and assumed that the LINC00452/miR-204/CHST4 axis may regulate thymic Tregs in the development of TAMG. These findings may deepen our understanding of the roles of the ceRNA network in regulating TAMG and highlight the function of CHST4 in recruiting peripheral T cells in the progression of TAMG.</p

Chemiluminescent Labels Released from Long Spacer Arm-Functionalized Magnetic Particles: A Novel Strategy for Ultrasensitive and Highly Selective Detection of Pathogen Infections

Previously, the unique advantages provided by chemiluminescence (CL) and magnetic particles (MPs) have resulted in the development of many useful nucleic acid detection methods. CL is highly sensitive, but when applied to MPs, its intensity is limited by the inner filter-like effect arising from excess dark MPs. Herein, we describe a modified strategy whereby CL labels are released from MPs to eliminate this negative effect. This approach relies on (1) the magnetic capture of target molecules on long spacer arm-functionalized magnetic particles (LSA-MPs), (2) the conjugation of streptavidin-alkaline phosphatase (SA-AP) to biotinylated amplicons of target pathogens, (3) the release of CL labels (specifically, AP tags), and (4) the detection of the released labels. CL labels were released from LSA-MPs through LSA ultrasonication or DNA enzymolysis, which proved to be the superior method. In contrast to conventional MPs, LSA-MPs exhibited significantly improved CL detection, because of the introduction of LSA, which was made of water-soluble carboxymethylated β-1,3-glucan. Detection of hepatitis B virus with this technique revealed a low detection limit of 50 fM, high selectivity, and excellent reproducibility. Thus, this approach may hold great potential for early stage clinical diagnosis of infectious diseases

Table_2_Correlation analysis on physicochemical and structural properties of sorghum starch.DOCX

This manuscript analyzed physicochemical and structural properties of 30 different types of sorghum starches based on their apparent amylose content (AAC). Current results confirmed that sorghum starch exhibited irregular spherical or polygonal granule shape with 14.5 μm average particle size. The AAC of sorghum starch ranged from 7.42 to 36.44% corresponding to relative crystallinities of 20.5 to 32.4%. The properties of enthalpy of gelatinization (ΔH), peak viscosity (PV), relative crystallinity (RC), degree of double helix (DD), degree of order (DO), and swelling power (SP) were negatively correlated with AAC, while the cool paste viscosity (CPV) and setback (SB) were positively correlated with AAC. Correlations analyzed was conducted on various physicochemical parameters. Using principal component analysis (PCA) with 20 variables, the difference between 30 different types of sorghum starch was displayed. Results of current study can be used to guide the selection and breeding of sorghum varieties and its application in food and non-food industries.</p

Access to Amides and Lactams via Pyridotriazole as a Transformable Directing Group

Amide and lactam frameworks were synthesized via an efficient two-step strategy. In this protocol, pyridotriazoles were first treated with isocyanates to form the corresponding amides, which were found to be sufficiently reactive to undergo subsequent intramolecular N–H insertion in the absence of any additional reagents or catalysts

Table_1_Identification of a basement membrane-related gene signature for predicting prognosis and estimating the tumor immune microenvironment in breast cancer.xls

IntroductionBreast cancer (BC) is the most common malignancy in the world and has a high cancer-related mortality rate. Basement membranes (BMs) guide cell polarity, differentiation, migration and survival, and their functions are closely related to tumor diseases. However, few studies have focused on the association of basement membrane-related genes (BMRGs) with BC. This study aimed to explore the prognostic features of BMRGs in BC and provide new directions for the prevention and treatment of BC.MethodsWe collected transcriptomic and clinical data of BC patients from TCGA and GEO datasets and constructed a predictive signature for BMRGs by using univariate, least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis. The reliability of the model was further evaluated and validated by Kaplan-Meier survival curves and receiver operating characteristic curves (ROC). Column line plots and corresponding calibration curves were constructed. Possible biological pathways were investigated by enrichment analysis. Afterward, we assessed the mutation status by tumor mutational burden (TMB) analysis and compared different subtypes using cluster analysis. Finally, we examined drug treatment sensitivity and immunological correlation to lay the groundwork for more in-depth studies in this area.ResultsThe prognostic risk model consisted of 7 genes (FBLN5, ITGB2, LAMC3, MMP1, EVA1B, SDC1, UNC5A). After validation, we found that the model was highly reliable and could accurately predict the prognosis of BC patients. Cluster analysis showed that patients with cluster 1 had more sensitive drugs and had better chances of better clinical outcomes. In addition, TMB, immune checkpoint, immune status, and semi-inhibitory concentrations were significantly different between high and low-risk groups, with lower-risk patients having the better anti-cancer ability.DiscussionThe basement membrane-related gene signature that we established can be applied as an independent prognostic factor for BC and can provide a reference for individualized treatment of BC patients.</p

Catalytic Enantioselective Nucleophilic α‑Chlorination of Ketones with NaCl

Catalytic enantioselective α-chlorination of ketones is a highly desirable process. Different from the conventional approaches that employ corrosive electrophilic chlorination reagents, the process disclosed here employs nucleophilic chloride, aqueous NaCl solution, and even seawater, as green inexpensive chlorine sources. This mechanistically distinct and electronically opposite approach provides facile access to diverse highly enantioenriched acyclic α-chloro ketones that are less straightforward by conventional approaches. With a chiral thiourea catalyst, a range of racemic α-keto sulfonium salts underwent enantioconvergent carbon–chlorine bond formation with high efficiency and excellent enantioselectivity under mild conditions. The sulfonium motif plays a crucial triple role by permitting smooth dynamic kinetic resolution to take place via a chiral anion binding mechanism in a well-designed phase-transfer system. This protocol represents a new general platform for the asymmetric nucleophilic α-functionalization of carbonyl compounds

Additional file 1 of DNMT3A mutation promotes leukemia development through NAM-NAD metabolic reprogramming

Additional file 1: Table S1. Primer sequences used in Q-RT-PCR