SharpContour: A Contour-based Boundary Refinement Approach for Efficient and Accurate Instance Segmentation

Excellent performance has been achieved on instance segmentation but the quality on the boundary area remains unsatisfactory, which leads to a rising attention on boundary refinement. For practical use, an ideal post-processing refinement scheme are required to be accurate, generic and efficient. However, most of existing approaches propose pixel-wise refinement, which either introduce a massive computation cost or design specifically for different backbone models. Contour-based models are efficient and generic to be incorporated with any existing segmentation methods, but they often generate over-smoothed contour and tend to fail on corner areas. In this paper, we propose an efficient contour-based boundary refinement approach, named SharpContour, to tackle the segmentation of boundary area. We design a novel contour evolution process together with an Instance-aware Point Classifier. Our method deforms the contour iteratively by updating offsets in a discrete manner. Differing from existing contour evolution methods, SharpContour estimates each offset more independently so that it predicts much sharper and accurate contours. Notably, our method is generic to seamlessly work with diverse existing models with a small computational cost. Experiments show that SharpContour achieves competitive gains whilst preserving high efficiencyComment: 10pages, 5 figures, accepted by CVPR 2022, project page: see this https://xyzhang17.github.io/SharpContour

The Single-Cell Immunogenomic Landscape of B and Plasma Cells in Early-Stage Lung Adenocarcinoma

Tumor-infiltrating B and plasma cells (TIB) are prevalent in lung adenocarcinoma (LUAD); however, they are poorly characterized. We performed paired single-cell RNA and B-cell receptor (BCR) sequencing of 16 early-stage LUADs and 47 matching multiregion normal tissues. By integrative analysis of ∼50,000 TIBs, we define 12 TIB subsets in the LUAD and adjacent normal ecosystems and demonstrate extensive remodeling of TIBs in LUADs. Memory B cells and plasma cells (PC) were highly enriched in tumor tissues with more differentiated states and increased frequencies of somatic hypermutation. Smokers exhibited markedly elevated PCs and PCs with distinct differentiation trajectories. BCR clonotype diversity increased but clonality decreased in LUADs, smokers, and with increasing pathologic stage. TIBs were mostly localized within CXCL13+ lymphoid aggregates, and immune cell sources of CXCL13 production evolved with LUAD progression and included elevated fractions of CD4 regulatory T cells. This study provides a spatial landscape of TIBs in early-stage LUAD

An Atlas of Epithelial Cell States and Plasticity in Lung Adenocarcinoma

Understanding the cellular processes that underlie early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies1. Here we studied 246,102 single epithelial cells from 16 early-stage LUADs and 47 matched normal lung samples. Epithelial cells comprised diverse normal and cancer cell states, and diversity among cancer cells was strongly linked to LUAD-specific oncogenic drivers. KRAS mutant cancer cells showed distinct transcriptional features, reduced differentiation and low levels of aneuploidy. Non-malignant areas surrounding human LUAD samples were enriched with alveolar intermediate cells that displayed elevated KRT8 expression (termed KRT8+ alveolar intermediate cells (KACs) here), reduced differentiation, increased plasticity and driver KRAS mutations. Expression profiles of KACs were enriched in lung precancer cells and in LUAD cells and signified poor survival. In mice exposed to tobacco carcinogen, KACs emerged before lung tumours and persisted for months after cessation of carcinogen exposure. Moreover, they acquired Kras mutations and conveyed sensitivity to targeted KRAS inhibition in KAC-enriched organoids derived from alveolar type 2 (AT2) cells. Last, lineage-labelling of AT2 cells or KRT8+ cells following carcinogen exposure showed that KACs are possible intermediates in AT2-to-tumour cell transformation. This study provides new insights into epithelial cell states at the root of LUAD development, and such states could harbour potential targets for prevention or intervention

Prevalence and factors associated with job burnout among nurses in China: A cross‐sectional study

Abstract Aim Many people see nursing as a high‐pressure, high‐risk profession. Therefore, job burnout among nursing staff has become an important topic of study and has received widespread attention worldwide. This research intended to evaluate the frequency of and variables related with work burnout among nurses in public hospitals in China. Design Using a multistage random sample procedure, a cross‐sectional survey was carried out in the eastern, central and western areas of China. Methods The Maslach Inventory‐Human Service Survey and demographic information made up the two sections of the questionnaire. Of the 5250 questionnaires sent, 4865 were deemed legitimate, yielding an effective response rate of 92.67%. A linear regression analysis was performed to investigate the variables linked to nursing work burnout. Results Among the 4865 nurses, women accounted for 97.4% of the survey respondents, most of whom were aged 26–35 years. Results showed that the total scores of emotional exhaustion (EE), depersonalization (DP) and reduced personal accomplishment (PA) were 20.02 ± 12.04, 4.78 ± 5.54 and 34.42 ± 10.32 respectively. 50.7% of subjects obtained high or moderated scores on EE, 32.8% of subjects obtained high or moderated scores on DP and 80.4% of subjects obtained low or moderated scores on PA. Age, department, position, post‐establishment, work shift type in recent months, overtime times in recent months and night shift frequency in recent months were negatively correlated with EE, and child status, monthly income, working days per week and sleep quality in recent 1 month were positively correlated with it (F = 141.827, P < 0.01, R2 = 0.243). Age, gender, department, post‐establishment, overtime hours in recent months and night shift frequency in recent months were negatively correlated with DP, and child status and sleep quality in the last 1 month were positively correlated with it (F = 78.794, p < 0.01, R2 = 0.115). Child status, years of nursing work and sleep quality in the last 1 month were negatively correlated with PA, whereas age, position, work shift type in recent months and night shift frequency in recent months were positively correlated with it (F = 67.981, p < 0.01, R2 = 0.089)

CIC de novo loss of function variants contribute to cerebral folate deficiency by downregulating FOLR1 expression

Background Cerebral folate deficiency (CFD) syndrome is characterised by a low concentration of 5-methyltetrahydrofolate in cerebrospinal fluid, while folate levels in plasma and red blood cells are in the low normal range. Mutations in several folate pathway genes, including FOLR1 (folate receptor alpha, FRα), DHFR (dihydrofolate reductase) and PCFT (proton coupled folate transporter) have been previously identified in patients with CFD.Methods In an effort to identify causal mutations for CFD, we performed whole exome sequencing analysis on eight CFD trios and identified eight de novo mutations in seven trios.Results Notably, we found a de novo stop gain mutation in the capicua (CIC) gene. Using 48 sporadic CFD samples as a validation cohort, we identified three additional rare variants in CIC that are putatively deleterious mutations. Functional analysis indicates that CIC binds to an octameric sequence in the promoter regions of folate transport genes: FOLR1, PCFT and reduced folate carrier (Slc19A1; RFC1). The CIC nonsense variant (p.R353X) downregulated FOLR1 expression in HeLa cells as well as in the induced pluripotent stem cell (iPSCs) derived from the original CFD proband. Folate binding assay demonstrated that the p.R353X variant decreased cellular binding of folic acid in cells.Conclusion This study indicates that CIC loss of function variants can contribute to the genetic aetiology of CFD through regulating FOLR1 expression. Our study described the first mutations in a non-folate pathway gene that can contribute to the aetiology of CFD

Identifying the personal characteristics of decent work perception for nursing students in China using latent profile analysis

Abstract Background Given the importance of perceptions of decent work for nursing students' future career choices, we attempted to determine potential classifications and characteristics of nursing students' perceptions of decent work so that targeted interventions could be developed. Methods A convenience sample of 1004 s- to fourth-year nursing students completed the General Information Questionnaire, Self-Regulatory Fatigue Scale, Occupational Identity Questionnaire, and Decent Work Perceptions Scale in a cross-sectional survey in Heilongjiang Province, China, resulting in 630 valid questionnaires with a valid return rate of 62.75%. Nursing students' perceptions of decent work were defined using descriptive and regression analysis. Results Latent profile analysis (LPA) identified three subgroups: low perceived decent work group, medium perceived decent work group, and high perceived decent work group, accounting for 4.76%, 69.37%, and 25.87% of the sample, respectively. The results of unordered multiclass logistic regression show that nursing students with relatively low levels of perceived decent work are more likely to have a low professional identity, a lack of respect for nursing seniors, an involuntary choice of nursing major, and a low family income. Conclusion Different types of nursing students have different perceptions of decent work, and these universities and related departments can use different educational guidance strategies

<i>KDM6B</i> Variants May Contribute to the Pathophysiology of Human Cerebral Folate Deficiency

(1) Background: The genetic etiology of most patients with cerebral folate deficiency (CFD) remains poorly understood. KDM6B variants were reported to cause neurodevelopmental diseases; however, the association between KDM6B and CFD is unknown; (2) Methods: Exome sequencing (ES) was performed on 48 isolated CFD cases. The effect of KDM6B variants on KDM6B protein expression, Histone H3 lysine 27 epigenetic modification and FOLR1 expression were examined in vitro. For each patient, serum FOLR1 autoantibodies were measured; (3) Results: Six KDM6B variants were identified in five CFD patients, which accounts for 10% of our CFD cohort cases. Functional experiments indicated that these KDM6B variants decreased the amount of KDM6B protein, which resulted in elevated H3K27me2, lower H3K27Ac and decreased FOLR1 protein concentrations. In addition, FOLR1 autoantibodies have been identified in serum; (4) Conclusion: Our study raises the possibility that KDM6B may be a novel CFD candidate gene in humans. Variants in KDM6B could downregulate FOLR1 gene expression, and might also predispose carriers to the development of FOLR1 autoantibodies

The Neurotranscriptome of <i>Monochamus alternatus</i>

The Japanese pine sawyer Monochamus alternatus serves as the primary vector for pine wilt disease, a devastating pine disease that poses a significant threat to the sustainable development of forestry in the Eurasian region. Currently, trap devices based on informational compounds have played a crucial role in monitoring and controlling the M. alternatus population. However, the specific proteins within M. alternatus involved in recognizing the aforementioned informational compounds remain largely unclear. To elucidate the spatiotemporal distribution of M. alternatus chemosensory-related genes, this study conducted neural transcriptome analyses to investigate gene expression patterns in different body parts during the feeding and mating stages of both male and female beetles. The results revealed that 15 genes in the gustatory receptor (GR) gene family exhibited high expression in the mouthparts, most genes in the odorant binding protein (OBP) gene family exhibited high expression across all body parts, 22 genes in the odorant receptor (OR) gene family exhibited high expression in the antennae, a significant number of genes in the chemosensory protein (CSP) and sensory neuron membrane protein (SNMP) gene families exhibited high expression in both the mouthparts and antennae, and 30 genes in the ionotropic receptors (IR) gene family were expressed in the antennae. Through co-expression analyses, it was observed that 34 genes in the IR gene family were co-expressed across the four developmental stages. The Antenna IR subfamily and IR8a/Ir25a subfamily exhibited relatively high expression levels in the antennae, while the Kainate subfamily, NMDA subfamily, and Divergent subfamily exhibited predominantly high expression in the facial region. MalIR33 is expressed only during the feeding stage of M. alternatus, the MalIR37 gene exhibits specific expression in male beetles, the MalIR34 gene exhibits specific expression during the feeding stage in male beetles, the MalIR8 and MalIR39 genes exhibit specific expression during the feeding stage in female beetles, and MalIR8 is expressed only during two developmental stages in male beetles and during the mating stage in female beetles. The IR gene family exhibits gene-specific expression in different spatiotemporal contexts, laying the foundation for the subsequent selection of functional genes and facilitating the full utilization of host plant volatiles and insect sex pheromones, thereby enabling the development of more efficient attractants

Hypermethylation of PI3K-AKT signalling pathway genes is associated with human neural tube defects

Neural tube defects (NTDs) are a group of common and severe congenital malformations. The PI3K-AKT signalling pathway plays a crucial role in the neural tube development. There is limited evidence concerning any possible association between aberrant methylation in PI3K-AKT signalling pathway genes and NTDs. Therefore, we aimed to investigate potential associations between aberrant methylation of PI3K-AKT pathway genes and NTDs. Methylation studies of PI3K-AKT pathway genes utilizing microarray genome-methylation data derived from neural tissues of ten NTD cases and eight non-malformed controls were performed. Targeted DNA methylation analysis was subsequently performed in an independent cohort of 73 NTD cases and 32 controls to validate the methylation levels of identified genes. siRNAs were used to pull-down the target genes in human embryonic stem cells (hESCs) to examine the effects of the aberrant expression of target genes on neural cells. As a result, 321 differentially hypermethylated CpG sites in the promoter regions of 30 PI3K-AKT pathway genes were identified in the microarray data. In target methylation analysis, CHRM1, FGF19, and ITGA7 were confirmed to be significantly hypermethylated in NTD cases and were associated with increased risk for NTDs. The down-regulation of FGF19, CHRM1, and ITGA7 impaired the formation of rosette-like cell aggregates. The down-regulation of those three genes affected the expression of PAX6, SOX2 and MAP2, implying their influence on the differentiation of neural cells. This study for the first time reported that hypermethylation of PI3K-AKT pathway genes such as CHRM1, FGF19, and ITGA7 is associated with human NTDs