Additional file 1 of Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues

Additional file 1. Supplementary Texts and Supplementary Figures S1-S8

Table_1_Alcohol-induced brain deficit in alcohol dependence.docx

Although numerous adverse effects of alcohol addiction on health, behavior, and brain function were widely reported, the neurobiological mechanism of alcohol dependence remains largely unknown. In this study, a total of twenty-nine patients with alcohol dependence and twenty-nine status-matched normal controls (NCs) were recruited. Percent amplitude of fluctuation (PerAF) was applied to identify alcohol-related brain activity deficits. We found that alcohol dependence was associated with widespread differences in the left orbitofrontal cortex, right higher visual cortex, right supramarginal gyrus, right postcentral gyrus, and bilateral cerebellum posterior lobe with decreased PerAF, but no brain areas with increased PerAF differences were found. ROC curve showed that decreased PerAF revealed extremely high discriminatory power with a high AUC value of 0.953, as well as a high degree of sensitivity (96.6%) and specificity (86.2%), in distinguishing patients with alcohol dependence from NCs. In the alcohol dependence group, the amount of daily alcohol consumption showed significant negative correlations with the right cerebellum posterior lobe and right higher visual cortex. These findings suggest that the cerebellar-visual-orbitofrontal circuit was disturbed by alcohol dependence. The proposed new method of PerAF may be served as a potential biomarker to identify the regional brain activity deficits of alcohol dependence.</p

Additional file 4 of Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues

Additional file 4: Table S3. The list of RBPs and the number of dNMD-QTLs or pNMD-QTLs in their binding sites in the K562 or the HepG2 cell lines

Additional file 5 of Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues

Additional file 5: Table S4. The list of cassette exons considered in splicing-QTL mapping

Supplementary document for Novel electromagnetic characteristics of antisymmetric toroidal dipole array of plasmonic metasurfaces - 6582242.pdf

supplemental

Additional file 2 of Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues

Additional file 2: Table S1. The 43 diseases with significant NMD-QTLs enrichment

Additional file 6 of Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues

Additional file 6. Review history

Additional file 3 of Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues

Additional file 3: Table S2. The list of miRNAs and the number of dNMD-QTLs or pNMD-QTLs in their target regions

Table1_Identification of functional TF-miRNA-hub gene regulatory network associated with ovarian endometriosis.XLSX

Endometriosis (EMs), one of the most common gynecological diseases, seriously affects the health and wellness of women; however, the underlying pathogenesis remains unclear. This study focused on dysregulated genes and their predicted transcription factors (TFs) and miRNAs, which may provide ideas for further mechanistic research. The microarray expression dataset GSE58178, which included six ovarian endometriosis (OE) samples and six control samples, was downloaded from the Gene Expression Omnibus (GEO) to identify differentially expressed genes (DEGs). Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to study the cellular and organism-level functions of DEGs. The protein-protein interaction (PPI) network was built and visualized using Cytoscape, and modules and hub genes were explored using various algorithms. Furthermore, we predicted miRNAs and TFs of hub genes using online databases, and constructed the TF-miRNA-hub gene network. There were 124 upregulated genes and 66 downregulated genes in EMs tissues. GO enrichment analysis showed that DEGs were concentrated in reproductive structure development and collagen-containing extracellular matrix, while KEGG pathway analysis showed that glycolysis/gluconeogenesis and central carbon metabolism in cancer require further exploration. Subsequently, HIF1A, LDHA, PGK1, TFRC, and CD9 were identified as hub genes, 22 miRNAs and 34 TFs were predicted to be upstream regulators of hub genes, and these molecules were pooled together. In addition, we found three key feedback loops in the network, MYC-miR-34a-5p-LDHA, YY1-miR-155-5p-HIF1A, and RELA-miR-93-5p-HIF1A, which may be closely related to OE development. Taken together, our study structured a TF-miRNA-hub gene network to decipher the molecular mechanism of OE, which may provide novel insights for clinical diagnosis and treatment.</p

Encoding Optoelectrical Sub-Components in an Al₂O₃ Nanowire for Rewritable High-Resolution Nanopatterning

Nanoscale encoding denotes the creation of distinct electric and photonic properties within small, artificially defined regions by physical or chemical means. An encoded single nanostructure includes independent subcomponents as functional units that can also work as functional integrated nanosystems. These can be applied in high-resolution displays, detection systems, and even more complex devices. However, there is still no agreed-upon best platform satisfying all requirements. This paper demonstrates a competitive candidate based on defect engineering, that is, low energy focused e-beam-induced oxygen ion migration in a carbon-doped Al2O3 nanowire. The electronic and photonic properties of these singular units are examined to be significantly modified. Their application in a nanoscale steganography strategy was also evaluated in detail. Complex patterns composed of points, lines, and planes were printed on a single nanowire using a focused e-beam and were subsequently erasable via a simple thermal process in air