Evaluation of the competence of an artificial intelligence-assisted colonoscopy system in clinical practice: A post hoc analysis

BackgroundArtificial intelligence-assisted colonoscopy (AIAC) has been proposed and validated in recent years, but the effectiveness of clinic application remains unclear since it was only validated in some clinical trials rather than normal conditions. In addition, previous clinical trials were mostly concerned with colorectal polyp identification, while fewer studies are focusing on adenoma identification and polyps size measurement. In this study, we validated the effectiveness of AIAC in the clinical environment and further investigated its capacity for adenoma identification and polyps size measurement.MethodsThe information of 174 continued patients who went for coloscopy in Chongqing Rongchang District People’s hospital with detected colon polyps was retrospectively collected, and their coloscopy images were divided into three validation datasets, polyps dataset, polyps/adenomas dataset (all containing narrow band image, NBI images), and polyp size measurement dataset (images with biopsy forceps and polyps) to assess the competence of the artificial intelligence system, and compare its diagnostic ability with endoscopists with different experiences.ResultsA total of 174 patients were included, and the sensitivity of the colorectal polyp recognition model was 99.40%, the accuracy of the colorectal adenoma diagnostic model was 93.06%, which was higher than that of endoscopists, and the mean absolute error of the polyp size measurement model was 0.62 mm and the mean relative error was 10.89%, which was lower than that of endoscopists.ConclusionArtificial intelligence-assisted model demonstrated higher competence compared with endoscopists and stable diagnosis ability in clinical use

High-quality de novo assembly of the Eucommia ulmoides haploid genome provides new insights into evolution and rubber biosynthesis

We report the acquisition of a high-quality haploid chromosome-scale genome assembly for the first time in a tree species, Eucommia ulmoides, which is known for its rubber biosynthesis and medicinal applications. The assembly was obtained by applying PacBio and Hi–C technologies to a haploid that we specifically generated. Compared to the initial genome release, this one has significantly improved assembly quality. The scaffold N50 (53.15 MB) increased 28-fold, and the repetitive sequence content (520 Mb) increased by 158.24 Mb, whereas the number of gaps decreased from 104,772 to 128. A total of 92.87% of the 26,001 predicted protein-coding genes identified with multiple strategies were anchored to the 17 chromosomes. A new whole-genome duplication event was superimposed on the earlier γ paleohexaploidization event, and the expansion of long terminal repeats contributed greatly to the evolution of the genome. The more primitive rubber biosynthesis of this species, as opposed to that in Hevea brasiliensis, relies on the methylerythritol-phosphate pathway rather than the mevalonate pathway to synthesize isoprenyl diphosphate, as the MEP pathway operates predominantly in trans-polyisoprene-containing leaves and central peels. Chlorogenic acid biosynthesis pathway enzymes were preferentially expressed in leaves rather than in bark. This assembly with higher sequence contiguity can foster not only studies on genome structure and evolution, gene mapping, epigenetic analysis and functional genomics but also efforts to improve E. ulmoides for industrial and medical uses through genetic engineering

Study on Gene Differential Expression in Tetraploid Populus Leaves

Polyploids exhibit different phenotypes compared to those of diploids in plants, and the important role of polyploids in tree breeding has been widely recognized. The transcriptomes detected by RNA-seq in the Populus triploid by doubling the chromosomes of the female gamete, in the triploid by doubling the chromosomes of somatic cells and the diploid with the parent were compared to reveal the patterns of gene expression of tetraploid leaves and their influence on growth. The results showed that the high expression of GATA and PORA in tetraploid leaves was the reason for the higher chlorophyll content in the leaves than in diploid and triploid leaves. The 11-day-old tetraploid leaves began to enter the aging stage. Compared with that in the diploid, GRF was significantly upregulated, while the amylase genes were downregulated. Compared with those in the triploid, 3 STN7 genes that regulate photosynthetic genes and PGSIP genes which are related to starch synthesis, were significantly downregulated in the tetraploid, and the auxin receptor protein TIR1 was also significantly downregulated. In the tetraploid, auxin-regulating genes such as GH3 and AUX/IAA as well as genes involved in the regulation of leaf senescence, SAG genes and SRG genes were significantly up-regulated, resulting in a decrease in the auxin content. In senescent leaves, CHLD, CHLI1, and CHLM in the early stage of chlorophyll synthesis all began to downregulate their expressions, leading to the downregulation of LHC genes and a decrease in their photosynthetic efficiency, which led to the downregulation of carbon fixation-related genes such as SS genes, thus affecting carbon synthesis and fixation. This finally led to the slow growth of tetraploid plants. These data represent the transcriptome characteristics of tetraploid, and they can be used as a resource for further research on polyploids and provide a reference for further understanding of the function of polyploid vegetative growth-related genes.</jats:p

Clinicopathological Characteristics and Survival Outcomes for Pneumonectomy: a Population-Based Study

Abstract Background: Prognostic factors in pneumonectomy (PN) are not yet fully defined. This study is to analyze and evaluate long-term survival after PN for non-small cell lung cancer (NSCLC). Methods: We obtained data from the Surveillance, Epidemiology, and End Results (SEER) database for patients who underwent PN between 2004 and 2015. In order to reduce bias and imbalance, propensity score matching (PSM) analysis was performed. We used Kaplan-Meier curves to estimate overall survival (OS), performed univariate and multivariate Cox proportional hazards regression analyses to identify independent prognostic factors for OS, and applied the Cox proportional hazards model to create a forest plot. Results: A total of 1557 PN patients from the SEER database were included. The patients were grouped according to the side of PN. Before matching, OS was worse after right PN (hazard ratio [HR]: 1.303; 95% confidence interval [CI] 1.133-1.498; P&lt;0.001), but survival difference between groups was not significant after matching (HR: 1.061; 95% CI 0.912-1.235; P=0.443). Regression analysis revealed that age, grade, N-stage, radiotherapy, and chemotherapy were independent predictors of OS (P&lt;0.05). Chemotherapy was associated with improved OS (HR: 0.709; 95% CI 0.609-0.825; P&lt;0.001), but radiotherapy was associated with increased risk of death in OS (HR: 1.268; 95% CI 1.061-1.561; P=0.009). On the forest plot, patients with primary overlapping lesions had better OS (HR: 0.684; 95% CI 0.497-0.941; P=0.020) in left, vs right, PN; patients diagnosis during 2004 to 2007 had lower OS (HR: 0.576; 95% CI 0.346-0.960; P=0.034) for left PN vs right PN.Conclusions: Laterality was not a significant prognostic factor for long-term survival after PN for NSCLC. Chemotherapy was a significant independent predictor of improved OS, while radiotherapy appeared to be a negative prognostic factor with increased risk of death in OS.</jats:p

Morphological, Transcriptome, and Hormone Analysis of Dwarfism in Tetraploids of Populus alba &times; P. glandulosa

Breeding for dwarfism is an important approach to improve lodging resistance. Here, we performed comparative analysis of the phenotype, transcriptome, and hormone contents between diploids and tetraploids of poplar 84K (Populus alba &times; P. glandulosa). Compared with diploids, the indole-3-acetic acid (IAA) and gibberellin (GA3) contents were increased, whereas the jasmonic acid (JA) and abscisic acid (ABA) contents were decreased in tetraploids. RNA-sequencing revealed that differentially expressed genes (DEGs) in leaves of tetraploids were mainly involved in plant hormone pathways. Most DEGs associated with IAA and GA promotion of plant growth and development were downregulated, whereas most DEGs associated with ABA and JA promotion of plant senescence were upregulated. Weighted gene co-expression network analysis indicated that certain transcription factors may be involved in the regulation of genes involved in plant hormone pathways. Thus, the altered expression of some genes in the plant hormone pathways may lead to a reduction in IAA and GA contents, as well as an elevation in ABA and JA contents, resulting in the dwarfing of tetraploids. The results show that polyploidization is a complex biological process affected by multiple plant hormone signals, and it provides a foundation for further exploration of the mechanism of tetraploids dwarfing in forest trees

Morphological, Transcriptome, and Hormone Analysis of Dwarfism in Tetraploids of <i>Populus alba</i> × <i>P. glandulosa</i>

Breeding for dwarfism is an important approach to improve lodging resistance. Here, we performed comparative analysis of the phenotype, transcriptome, and hormone contents between diploids and tetraploids of poplar 84K (Populus alba × P. glandulosa). Compared with diploids, the indole-3-acetic acid (IAA) and gibberellin (GA3) contents were increased, whereas the jasmonic acid (JA) and abscisic acid (ABA) contents were decreased in tetraploids. RNA-sequencing revealed that differentially expressed genes (DEGs) in leaves of tetraploids were mainly involved in plant hormone pathways. Most DEGs associated with IAA and GA promotion of plant growth and development were downregulated, whereas most DEGs associated with ABA and JA promotion of plant senescence were upregulated. Weighted gene co-expression network analysis indicated that certain transcription factors may be involved in the regulation of genes involved in plant hormone pathways. Thus, the altered expression of some genes in the plant hormone pathways may lead to a reduction in IAA and GA contents, as well as an elevation in ABA and JA contents, resulting in the dwarfing of tetraploids. The results show that polyploidization is a complex biological process affected by multiple plant hormone signals, and it provides a foundation for further exploration of the mechanism of tetraploids dwarfing in forest trees