A generalized linear model for decomposing cis-regulatory, parent-of-origin, and maternal effects on allele-specific gene expression

Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis-regulatory mutations. Here we propose a simple method to decompose cis-regulatory (i.e., allelic genotype, AG), genomic imprinting (i.e., parent-of-origin, PO), and maternal (i.e., maternal genotype, MG) effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the efficiency of method using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seq data. Consistent with previous studies, we found little evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified dozens and hundreds of mouse genes with significant PO and MG effects, respectively. Interestingly, a similar number of genes with significant PO effect were detect in mouse TSCs and livers, whereas more genes with significant MG effect were observed in livers. Further application of this method will clarify how these three effects influence gene expression levels in different tissues and developmental stages, and provide novel insight into the evolution of gene expression regulation.Comment: 27 pages, 3 figures, 2 tabl

Diagnostic Value of EUS-Guided Fine-Needle Aspiration Biopsy for Gastric Linitis Plastica with Negative Endoscopic Biopsy

Due to the tendency of gastric linitis plastica (GLP) to cause extensive submucosal infiltration, a superficial endoscopic biopsy sometimes yields no evidence of malignancy, hindering definite diagnosis. The present study was a single-center retrospective analysis of 54 consecutive patients diagnosed with GLP between 2016 and 2020 to evaluate EUS-guided fine-needle aspiration (EUS-FNA) biopsy outcomes in patients with negative endoscopic biopsy findings. A pathological GLP diagnosis was achieved by endoscopic biopsy in 40 patients (74.1%). EUS-FNA biopsy with a 22-gauge needle was performed in 13 of the remaining 14 patients, and GLP diagnosis was confirmed in 10 patients, with a median of three needle passes. The remaining four patients were laparoscopically diagnosed with GLP. The diagnostic ability of EUS-FNA biopsy for GLP was 76.9%, and EUS-FNA biopsy contributed to GLP diagnosis in 18.5% (10/54) of all cases. None of the 13 patients exhibited EUS-FNA biopsy-related adverse events. Univariable and multivariable analyses revealed an absence of superficial ulcerations as a predictor of false-negative endoscopic biopsy findings in patients with GLP. These results suggest EUS-FNA biopsy as a minimally invasive and safe alternative diagnostic modality for GLP in cases where conventional endoscopic biopsy fails to verify malignancy, although prospective studies with larger cohorts are warranted to confirm these findings

Strategy in short-term memory for pictures in childhood : A near-infrared spectroscopy study

In Baddeley\u27s working memory model, verbalizable visual material such as pictures are recoded into a phonological form and then rehearsed, while auditory material is rehearsed directly. The recoding and rehearsal processes are mediated by articulatory control process in the left ventrolateral prefrontal cortex (VLPFC). Developmentally, the phonological strategy for serially-presented visual material emerges around 7. years of age, while that for auditory material is consistently present by 4. years of age. However, the strategy change may actually be correlated with memory ability as this usually increases with age. To investigate the relationship between the strategy for pictures and memory ability, we monitored the left VLPFC activation in 5 to 11. year-old children during free recall of visually- or auditorily-presented familiar objects using event-related near-infrared spectroscopy. We hypothesized that the phonological strategy of rehearsal and recoding for visual material would provoke greater activation than only rehearsal for auditory material in the left VLPFC. Therefore, we presumed that the activation difference for visual material compared with auditory material in the left VLPFC may represent the tendency to use a phonological strategy. We found that the activation difference in the left VLPFC showed a significant positive correlation with memory ability but not with age, suggesting that children with high memory ability make more use of phonological strategy for pictures. The present study provides functional evidence that the strategy in short-term memory for pictures shifts gradually from non-phonological to phonological as memory ability increases in childhood

Strategy in short-term memory for pictures in childhood : A near-infrared spectroscopy study

In Baddeley's working memory model, verbalizable visual material such as pictures are recoded into a phonological form and then rehearsed, while auditory material is rehearsed directly. The recoding and rehearsal processes are mediated by articulatory control process in the left ventrolateral prefrontal cortex (VLPFC). Developmentally, the phonological strategy for serially-presented visual material emerges around 7. years of age, while that for auditory material is consistently present by 4. years of age. However, the strategy change may actually be correlated with memory ability as this usually increases with age. To investigate the relationship between the strategy for pictures and memory ability, we monitored the left VLPFC activation in 5 to 11. year-old children during free recall of visually- or auditorily-presented familiar objects using event-related near-infrared spectroscopy. We hypothesized that the phonological strategy of rehearsal and recoding for visual material would provoke greater activation than only rehearsal for auditory material in the left VLPFC. Therefore, we presumed that the activation difference for visual material compared with auditory material in the left VLPFC may represent the tendency to use a phonological strategy. We found that the activation difference in the left VLPFC showed a significant positive correlation with memory ability but not with age, suggesting that children with high memory ability make more use of phonological strategy for pictures. The present study provides functional evidence that the strategy in short-term memory for pictures shifts gradually from non-phonological to phonological as memory ability increases in childhood