Additional file 2: Table S2. Primer sequences for quantitative real-time PCR and real-time PCR analyses.

Abstract Background Endoplasmic reticulum (ER) stress and autophagy are implicated in the pathophysiology of intestinal inflammation; however, their roles in intrauterine growth retardation (IUGR)-induced colon inflammation are unclear. This study explored the protective effects of natural stilbene pterostilbene on colon inflammation using the IUGR piglets and the tumor necrosis factor alpha (TNF-α)-treated human colonic epithelial cells (Caco-2) by targeting ER stress and autophagy. Results Both the IUGR colon and the TNF-α-treated Caco-2 cells exhibited inflammatory...

Abstract Background Endoplasmic reticulum (ER) stress and autophagy are implicated in the pathophysiology of intestinal inflammation; however, their roles in intrauterine growth retardation (IUGR)-induced colon inflammation are unclear. This study explored the protective effects of natural stilbene pterostilbene on colon inflammation using the IUGR piglets and the tumor necrosis factor alpha (TNF-α)-treated human colonic epithelial cells (Caco-2) by targeting ER stress and autophagy. Results Both the IUGR colon and the TNF-α-treated Caco-2 cells exhibited inflammatory...

Abstract Background Homeothermic marine animals in Polar Regions face an energetic bottleneck in winter. The challenges of short days and cold temperatures are exacerbated for flying seabirds with small body size and limited fat stores. We use biologging approaches to examine how habitat, weather, and moon illumination influence behaviour and energetics of a marine bird species, thick-billed murres (Uria lomvia). Methods We used temperature-depth-light recorders to examine strategies murres use to survive winter in the...

Simulations with light sources, such as squares, circles, ellipses, octagons, and peaks, are presented.

The space-variant wavefront reconstruction problem inherently exists in deep tissue imaging. In this paper, we propose a framework of Shack-Hartmann wavefront space-variant sensing with extended source illumination. The space-variant wavefront is modeled as a four-dimensional function where two dimensions are in the spatial domain and two in the Fourier domain with priors that both gently vary. Here, the affine transformation is used to characterize the wavefront space-variant function. Correspondingly, the zonal and modal methods are...

The space-variant wavefront reconstruction problem inherently exists in deep tissue imaging. In this paper, we propose a framework of Shack-Hartmann wavefront space-variant sensing with extended source illumination. The space-variant wavefront is modeled as a four-dimensional function where two dimensions are in the spatial domain and two in the Fourier domain with priors that both gently vary. Here, the affine transformation is used to characterize the wavefront space-variant function. Correspondingly, the zonal and modal methods are...

Abstract Metastasis and chemical resistance are the most serious problems in the treatment of highly aggressive uveal melanoma (UM). The newly identified lncRNA OUM1 is overexpressed in UM, functions as a catalyst and regulates protein tyrosine phosphatase (PTP) activity by binding to PTP receptor type Z1 (PTPRZ1), which plays an important role in cell proliferation, metastasis and chemotherapy resistance in the UM microenvironment. Hence, siRNAs that selectively knocking down the lncRNA OUM1 (siOUM1) and its...

Additional file 3. Average Nutrient Content Per Serving* with Standard Deviations from 13 Food and Drink Categories. Supplemental analysis on average nutrient content per serving from 13 food and drink categories used in this study analysis.

Additional file 10: Table S5. The list of DMRs and annotation.

Temporomandibular disorders (TMDs) are common and cause persistent pain. Comorbidities are associated with TMDs and can affect the effectiveness of their treatments. The literature is lacking enough evidence on the difference between acute and chronic pain, particularly in TMDs. Investigating this difference could highlight potential risk factors for the transition from acute to chronic pain–related TMDs. To compare the likelihood of back and neck pain (BP, NP) between acute and chronic pain–related TMDs (AP-TMD, CP-TMD)...

Additional file 1: Fig. S1 The distributions of variant allele frequencies (VAFs) of ARID1A, ARID1B, ARID2, PBRM1, SMARCA4, and SMARCB1. The median VAFs of the above genes were 16.1%, 13.4%, 13.3%, 17.2%, 15.2%, and 16.7%, respectively. Red solid line, median; black dotted line, quartiles.

Additional file 3: Fig. S3 The signaling pathway enrichment of the variated genes in the SWI/SNF-mutant tumors by GO analysis. The GO analysis was performed on all the mutated genes in 1001 SWI/SNF-mutant samples.

Additional file 4: Table S1. Synthetic lethal interactive pairs and chemical inhibitors involving SWI/SNF members.

Supplementary Material 1

Supplementary Material 1

Additional file 9: Table S4. The number of DMCs (CpG, CHG and CHH) in different genetic regions.

Additional file 9: Table S4. The number of DMCs (CpG, CHG and CHH) in different genetic regions.

Abstract Background Mastitis caused by different pathogens including Streptococcus uberis (S. uberis) is responsible for huge economic losses to the dairy industry. In order to investigate the potential genetic and epigenetic regulatory mechanisms of subclinical mastitis due to S. uberis, the DNA methylome (whole genome DNA methylation sequencing) and transcriptome (RNA sequencing) of milk somatic cells from cows with naturally occurring S. uberis subclinical mastitis and healthy control cows (n = 3/group) were studied. Results...

Abstract Background Mastitis caused by different pathogens including Streptococcus uberis (S. uberis) is responsible for huge economic losses to the dairy industry. In order to investigate the potential genetic and epigenetic regulatory mechanisms of subclinical mastitis due to S. uberis, the DNA methylome (whole genome DNA methylation sequencing) and transcriptome (RNA sequencing) of milk somatic cells from cows with naturally occurring S. uberis subclinical mastitis and healthy control cows (n = 3/group) were studied. Results...

Additional file 15: Table S10. The genome-wide correlation between DNA methylation and gene expression and list of MetGDE genes.

Additional file 15: Table S10. The genome-wide correlation between DNA methylation and gene expression and list of MetGDE genes.

Additional file 16: Table S11. The results of functional enrichment differentially methylated and expressed genes (MetGDE genes).

Additional file 5: Fig. S5. Association between DNA methylation and gene expression levels. (A-B) Scatter plots showing correlation between gene expression level and promoter methylation level (A) and first exon (B). (C) Box plot showing promoter methylation level of genes grouped by expression levels. (D-F) Scatterplots and fitting curves of DNA methylation and relative gene expression of gene body methylation (D), exon methylation (E) and intron methylation (F). (G-I) MetGDE genes selected based on the...

Additional file 2. Recommendations review survey.