Additional file 1 of Identification of the causal relationship between sleep quality, insomnia, and oral ulcers

Supplementary Figure 1. Forest plot showing results from the genetic correlation analysis. Supplementary Figure 2. MR analysis results for sleep duration on risk of oral cavity cancer. Supplementary Figure 3. MR analysis results for sleep duration on risk of periodontal disease. Supplementary Figure 4. MR analysis results for insomnia on risk of mouth ulcer. Supplementary Figure 5. MR analysis results for insomnia on risk of oral cavity cancer. Supplementary Figure 6. MR analysis results for insomnia on risk of periodontal disease. Supplementary Table 1. Summary data from all GWAS used in current study. Supplementary Table 2. Heterogeneity and horizontal pleiotropy analyses between insomnia, sleep duration and oral manifestations. Supplementary Table 3. Effect sizes can be detected with the power of 0.8 given the sample size, proportion of cases and variance explained by the instrumental variables

Fluoroalkylsulfonyl Chlorides Promoted Vicinal Chloro-fluoroalkylthiolation of Alkenes and Alkynes

The unprecedented use of CF₃SO₂Cl for direct bifunctional chloro-trifluoro­methyl­thiolation of alkenes and alkynes is reported. CF₃SCl, which is generated by the reduction of PPh₃, undergoes electrophilic addition and then chlorination to give the bifunctionalized products without using an additional chlorine source. The method is also applicable for chloro-difluoro­methyl­thiolation using CF₂HSO₂Cl

Transcriptome Analysis of Nodes and Buds from High and Low Tillering Switchgrass Inbred Lines

<div><p>In the last two decades switchgrass has received increasing attention as a promising bioenergy feedstock. Biomass is the principal trait for improvement in switchgrass breeding programs and tillering is an important component of biomass yield. Switchgrass inbred lines derived from a single parent showing vast variation in tiller number trait was used in this study. Axillary buds, which can develop into tillers, and node tissues, which give rise to axillary buds, were collected from high and low tillering inbred lines growing in field conditions. RNA from buds and nodes from the contrasting inbred lines were used for transcriptome profiling with switchgrass Affymetrix genechips. Nearly 7% of the probesets on the genechip exhibited significant differential expression in these lines. Real-time PCR analysis of 30 genes confirmed the differential expression patterns observed with genechips. Cluster analysis aided in identifying probesets unique to high or low tillering lines as well as those specific to buds or nodes of high tillering lines. Rice orthologs of the switchgrass genes were used for gene ontology (GO) analysis with AgriGO. Enrichment of genes associated with amino acid biosynthesis, lipid transport and vesicular transport were observed in low tillering lines. Enrichment of GOs for translation, RNA binding and gene expression in high tillering lines were indicative of active metabolism associated with rapid growth and development. Identification of different classes of transcription factor genes suggests that regulation of many genes determines the complex process of axillary bud initiation and development. Genes identified in this study will complement the current ongoing efforts in quantitative trait loci mapping of tillering in switchgrass.</p></div

Comparing qPCR and affymetrix genechip based fold-changes of gene expression in switchgrass.

<p>Quantitative PCR of select genes identified in the microarray analysis of high and low tillering switchgrass lines. HB:LB represents genes differentially expressed in high tillering buds compared to low tillering buds. HN:LN represents genes differentially expressed in high tillering nodes compared to low tillering nodes. Annotations of genes labeled 1–30 on the x-axis and the primers used for qPCR analysis are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083772#pone.0083772.s009" target="_blank">File S9</a>.</p

Summary of K-means clustering and AgriGO analysis.

<p>^a Clusters numbers are related to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083772#pone-0083772-g002" target="_blank">figure 2</a>.</p><p>^b The total number of probesets showing similar expression patterns based on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083772#pone-0083772-g003" target="_blank">figure 3</a>.</p><p>^c Number of unique rice gene identifiers associated with switchgrass probesets.</p><p>^d Rice identifiers for which GOs were retrieved from the MSU rice genome annotation project (<a href="http://rice.plantbiology.msu.edu/downloads_gad.shtml" target="_blank">http://rice.plantbiology.msu.edu/downloads_gad.shtml</a>).</p><p>^e Number of enriched GO terms associated with sub clusters based on singular enrichment analysis in AgriGO (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083772#pone.0083772.s006" target="_blank">Files S6</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083772#pone.0083772.s008" target="_blank">S8</a>).</p

Cluster analysis using signal intensities from Affymetrix genechip hybridizations.

<p>K-means cluster analysis using the normalized average log 2 signal intensities from buds and nodes of high and low tillering lines was conducted using the GENESIS program. HN: High tillering nodes; HB: High tillering buds; LN: Low tillering nodes; LB: Low tillering buds. K = 16 clusters and 100 iterations.</p

Cell Internalizable and Intracellularly Degradable Cationic Polyurethane Micelles as a Potential Platform for Efficient Imaging and Drug Delivery

A cell internalizable and intracellularly degradable micellar system, assembled from multiblock polyurethanes bearing cell-penetrating gemini quaternary ammonium pendent groups in the side chain and redox-responsive disulfide linkages throughout the backbone, was developed for potential magnetic resonance imaging (MRI) and drug delivery. The nanocarrier is featured as a typical “cleavable core–internalizable shell–protective corona” architecture, which exhibits small size, positive surface charge, high loading capacity, and reduction-triggered destabilization. Furthermore, it can rapidly enter tumor cells and release its cargo in response to an intracellular level of glutathione, resulting in enhanced drug efficacy <i>in vitro</i>. The magnetic micelles loaded with superparamagnetic iron oxide (SPIO) nanoparticles demonstrate excellent MRI contrast enhancement, with <i>T</i>₂ relaxivity found to be affected by the morphology of SPIO-clustering inside the micelle core. The multifunctional carrier with good cytocompatibility and nontoxic degradation products can serve as a promising theranostic candidate for efficient intracellular delivery of anticancer drugs and real-time monitoring of therapeutic effect

Parametric analysis of gene expression and gene ontologies in switchgrass inbred lines.

<p>Only significant GO terms associated with the comparisons of high and low tillering lines were selected for display. CM refers to colorful model. Box colors indicates levels of statistical significance: yellow = 0.05; orange = e-05; and red = e-09. Different shades of blue color indicate the extent of down regulation. Onto refers to the ontology category: C- Cellular component; F- Molecular function; P – Biological process. Numbers refer to the number of genes associated with the GO term. FDR refers to false discovery rates.</p

Additional file 1 of Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection

Supplementary materials. The file that contains all supplementary notes, figures and tables. (PDF 1330 kb

Enriched gene ontologies in differentially expressed genes of high tillering switchgrass inbred line.

<p>Singular enrichment analysis was performed in AgriGO to identify enriched gene ontologies associated with high tillering lines. Each box shows the GO term number, the p-value in parenthesis, and GO term. First pair of numerals represents number of genes in input list associated with that GO term and number of genes in input list. Second pair of numerals represents number of genes associated with a particular GO term in the rice database and total number of rice genes with GO annotations in the rice database. Box colors indicates levels of statistical significance: yellow = 0.05; orange = e-05; and red = e-09.</p