SW-UNet: a U-Net fusing sliding window transformer block with CNN for segmentation of lung nodules

Medical images are information carriers that visually reflect and record the anatomical structure of the human body, and play an important role in clinical diagnosis, teaching and research, etc. Modern medicine has become increasingly inseparable from the intelligent processing of medical images. In recent years, there have been more and more attempts to apply deep learning theory to medical image segmentation tasks, and it is imperative to explore a simple and efficient deep learning algorithm for medical image segmentation. In this paper, we investigate the segmentation of lung nodule images. We address the above-mentioned problems of medical image segmentation algorithms and conduct research on medical image fusion algorithms based on a hybrid channel-space attention mechanism and medical image segmentation algorithms with a hybrid architecture of Convolutional Neural Networks (CNN) and Visual Transformer. To the problem that medical image segmentation algorithms are difficult to capture long-range feature dependencies, this paper proposes a medical image segmentation model SW-UNet based on a hybrid CNN and Vision Transformer (ViT) framework. Self-attention mechanism and sliding window design of Visual Transformer are used to capture global feature associations and break the perceptual field limitation of convolutional operations due to inductive bias. At the same time, a widened self-attentive vector is used to streamline the number of modules and compress the model size so as to fit the characteristics of a small amount of medical data, which makes the model easy to be overfitted. Experiments on the LUNA16 lung nodule image dataset validate the algorithm and show that the proposed network can achieve efficient medical image segmentation on a lightweight scale. In addition, to validate the migratability of the model, we performed additional validation on other tumor datasets with desirable results. Our research addresses the crucial need for improved medical image segmentation algorithms. By introducing the SW-UNet model, which combines CNN and ViT, we successfully capture long-range feature dependencies and break the perceptual field limitations of traditional convolutional operations. This approach not only enhances the efficiency of medical image segmentation but also maintains model scalability and adaptability to small medical datasets. The positive outcomes on various tumor datasets emphasize the potential migratability and broad applicability of our proposed model in the field of medical image analysis.

Comparison of overfeeding effects on gut physiology and microbiota in two goose breeds

To have a better understanding of how the “gut–liver axis” mediates the lipid deposition in the liver, a comparison of overfeeding influence on intestine physiology and microbiota between Gang Goose and Tianfu Meat Goose was performed in this study. After force-feeding, compared with Gang Goose, Tianfu Meat Goose had better fat storage capacity in liver (397.94 vs. 166.54 for foie gras weight (g), P < 0.05; 6.37 vs. 2.92% for the ratio of liver to body, P < 0.05; 60.01 vs. 46.64% for fat content, P < 0.05) and the less subcutaneous adipose tissue weight (1240.96 g vs. 1440.46 g, P < 0.05). After force-feeding, the digestion–absorption capacity of Tianfu Meat Goose was higher than that of Gang Goose (5.56 vs. 3.64 and 4.63 vs. 3.68 for the ratio of villus height to crypt depth in duodenum and ileum, respectively, P < 0.05; 1394.96 vs. 782.59 and 1314.76 vs. 766.17 for the invertase activity (U/mg-prot), in duodenum and ileum, respectively, P < 0.05; 6038.36 vs. 3088.29 and 4645.29 vs. 3927.61 for the activity of maltase (U/mg-prot), in duodenum and ileum, respectively, P < 0.05). Force-feeding decreased the gene expression of Escherichia coli in the ileum of Tianfu Meat Goose; force-feeding increased the number of gut microbiota Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction band in Tianfu Meat Goose and decreased the number in Gang Goose. In conclusion, compared with Gang Goose, the lipid deposition in the liver and the intestine digestion–absorption capacity and stability were higher in Tianfu Meat Goose. Thereby, Tianfu Meat Goose is the better breed for foie gras production for prolonged force-feeding; Gang Goose possesses better fat storage capacity in subcutaneous adipose tissue. However, Gang Goose has lower gut stability responding to force-feeding, so Gang Goose is suited to force-feeding in a short time to gain the body weight and subcutaneous fat as an overfed duck for roast duck.

An extensive study of the mechanism of prostate cancer metastasis

The study aimed to identify the pivotal genes and pathways involved in prostate cancer metastasis. Using the expression profile dataset GSE7930, downloaded from the Gene Expression Omnibus (GEO) database, differentially expressed genes (DEGs) between primary and highly metastatic prostate cell samples were screened, followed by functional analysis and tumor associated genes (TAG) screening. Protein-protein interaction (PPI) network of DEGs was constructed and module analysis was performed. The expression of DEGs and pathway related genes were evaluated by PCR analysis and the migra- tion ability of prostate tumor cells was observed after FABP4-siRNA blocking. Upregulated FABP4 and GK were signifi- cantly enriched in the PPAR signaling pathway, whereas downregulated IGFBP3 and THBS1 were involved in p53 signaling pathway. Among the identified DEGs, 4 downregulated genes (IGFBP3, NPP4B, THBS1, and PCDH1) and 2 upregulated genes (GJA1 and TUSC3) were TAGs. The module was associated with focal adhesion, ECM-receptor interaction, p53 signaling, and gap junction pathways with the hub node GJA1. After FABP4 silencing by siRNAs in LNcap and metastatic DU-145 cells, the numbers of migrated cells were all significantly declined. The expressions of IGFBP3, TP53 and PPAR were significantly lower in DU-145 cells than in LNcap cells. In conclusion, FABP4, IGFBP3, THBS1, and GJA1 were determined to be potential markers of prostate cancer cell metastasis, and P53, PPAR and gap junction pathways were found to play important roles in prostate cancer cell metastasis. This study may provide helpful guidelines for clinical management.

Treatment effect of CDKN1A on rheumatoid arthritis by mediating proliferation and invasion of fibroblast-like synoviocytes cells

The objective of the present study was to evaluate the role of CDKN1A in rheumatoid arthritis (RA). Related gene expression data screened from Gene Expression Omnibus (GEO) were processed with network analysis. Protein-protein interaction was analysed through string database. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to measure mRNA and microRNA expression. Cell proliferation and cell cycle were tested by MTT assay and flow cytometry, respectively. Transwell migration and invasion assay was used to test cell migration and invasion. CDKN1A screened by bioinformatics methods showed differential expression in RA cells compared with healthy controls (HC), and was at an important position in the protein-protein interaction network of RA. Compared with the HC group, CDKN1A was down-regulated in human RA synovium tissues and human fibroblast-like synoviocytes (HFLS). Contrary to CDKN1A silencing, CDKN1A over-expression significantly inhibited the proliferation and invasion of HFLS-RA, arrested HFLS-RA in G0/G1 phase and down-regulated the expressions of tumour necrosis factor (TNF)-α and interleukin (IL)-6, while it up-regulated the expression of IL-10. CDKN1A over-expression could also suppress phosphorylated signal transducers and activators of transcription 1 (pSTAT-1) expression. MiR-146a, highly expressed in RA tissues, could regulate CDKN1A negatively. Anti-146a suppressed cell proliferation and invasion, and at the same time enhanced IL-10 expression but inhibited IL-6, TNF-α and pSTAT-1 expression. The results indicated that CDKN1A over-expression, which could be enhanced by miR-146a suppression, inhibited the proliferation of invasion in HFLS-RA. This was probably a result of suppressed pSTAT-1, IL-6 and TNF-α expression and enhanced IL-10 expression.

Obesity, hypertension and diabetes mellitus affect complication rate of different nephrectomy techniques

INTRODUCTION

To investigate whether obesity, hypertension, and diabetes mellitus (DM) would increase post-nephrectomy complication rates using standardized classification method.

METHODS

We retrospectively included 843 patients from March 2006 to November 2012, of whom 613 underwent radical nephrectomy (RN) and 229 had partial nephrectomy (PN). Modified Clavien classification system was applied to quantify complication severity of nephrectomy. Fisher's exact or chi-square test was used to assess the relationship between complication rates and obesity, hypertension, as well as DM.

RESULTS

The prevalence of obesity, hypertension, and DM was 11.51%, 30.84%, 8.78%, respectively. The overall complication rate was 19.31%, 30.04%, 35.71% and 36.36% for laparoscopic radical nephrectomy (LRN), open-RN, LPN and open-PN respectively. An increasing trend of low grade complication rate as BMI increased was observed in LRN (P=.027) and open-RN (P<.001). Obese patients had greater chance to have low grade complications in LRN (OR=4.471; 95% CI: 1.290-17.422; P=0.031) and open-RN (OR=2.448; 95% CI: 1.703-3.518; P<.001). Patients with hypertension were more likely to have low grade complications, especially grade ii complications in open-RN (OR=1.526; 95% CI: 1.055-2.206; P=.026) and open PN (OR=2.032; 95% CI: 1.199-3.443; P=.009). DM was also associated with higher grade i complication rate in open-RN (OR=2.490; 95% CI: 331-4.657; P=.016) and open-PN (OR=4.425; 95% CI: 1.815-10.791; P=.013). High grade complication rates were similar in comparison.

CONCLUSIONS

Obesity, hypertension, and DM were closely associated with increased post-nephrectomy complication rates, mainly low grade complications.

CPEB1, a histone-modified hypomethylated gene, is regulated by miR-101 and involved in cell senescence in glioma

Epigenetic mechanisms have important roles in carcinogenesis. We certified that the mRNA translation-related gene cytoplasmic polyadenylation element-binding protein 1 (CPEB1) is hypomethylated and overexpressed in glioma cells and tissues. The knockdown of CPEB1 reduced cell senescence by regulating the expression or distribution of p53 in glioma cells. CPEB1 is also regulated directly by the tumor suppressor miR-101, a potential marker of glioma. It is known that the histone methyltransferase enhancer of zeste homolog 2 (EZH2) and embryonic ectoderm development (EED) are direct targets of miR-101. We demonstrated that miR-101 downregulated the expression of CPEB1 through reversing the methylation status of the CPEB1 promoter by regulating the presence on the promoter of the methylation-related histones H3K4me2, H3K27me3, H3K9me3 and H4K20me3. The epigenetic regulation of H3K27me3 on CPEB1 promoter is mediated by EZH2 and EED. EZH2 has a role in the regulation of H3K4me2. Furthermore, the downregulation of CPEB1 induced senescence in a p53-dependent manner.

Biotechnological implications from abscisic acid (ABA) roles in cold stress and leaf senescence as an important signal for improving plant sustainable survival under abiotic-stressed conditions

In the past few years, the signal transduction of the plant hormone abscisic acid (ABA) has been studied extensively and has revealed an unanticipated complex. ABA, characterized as an intracellular messenger, has been proven to act a critical function at the heart of a signaling network operation. It has been found that ABA plays an important role in improving plant tolerance to cold, as well as triggering leaf senescence for years. In addition, there have been many reports suggesting that the signaling pathways for leaf senescence and plant defense responses may overlap. Therefore, the objective was to review what is known about the involvement of ABA signaling in plant responses to cold stress and regulation of leaf senescence. An overview about how ABA is integrated into sugars and reactive oxygen species signaling pathways, to regulate plant cold tolerance and leaf senescence, is provided. These roles can provide important implications for biotechnologically improving plant cold tolerance.

Reduced urinary excretion of intact osteopontin in patients with IgA nephropathy

Osteopontin (OPN) is a phosphoprotein secreted by many cells of epithelial, mesenchymal, and hematopoietic origin. In the kidney, OPN is expressed in the renal tubules and collecting ducts and is excreted into the urine. A pathophysiologic role for urinary OPN has not been established. In this study, urinary excretion of OPN was analyzed in patients with primary glomerular diseases, including immunoglobulin A nephropathy (IgAN; n = 32), minimal change nephrotic syndrome (MCNS; n = 16), and membranous nephropathy (MN; n = 18). Compared with normal controls (n = 20), mean +/- SD of urinary OPN in IgAN patients was decreased significantly (21.4 +/- 6.2 versus 11.6 +/- 9.6 mg/g creatinine, P: < 0.001). In contrast, the levels of urinary OPN in patients with MCNS or MN did not differ significantly from normal values. Immunoblot analysis showed that OPN is present as a 55- to 60-kd molecule in normal urine. A 34-kd fragment of OPN was the major immunoreactive band in samples from IgAN patients. This fragment also was detectable in the urine from some patients with MCNS or MN but was absent in normal subjects. OPN has a thrombin-cleavage site near its central portion. Thrombin treatment of the urine from normal controls could result in 34-kd OPN fragments. Although the underlying mechanisms remain to be determined, these data provide evidence that secretion or processing (or both) of urinary OPN is altered in patients with IgAN.