GNPI: Graph normalization to integrate phylogenetic information for metagenomic host phenotype prediction.

Microorganisms play important roles in our lives especially on metabolism and diseases. Determining the probability of human suffering from specific diseases and the severity of the disease based on microbial genes is the crucial research for understanding the relationship between microbes and diseases. Previous could extract the topological information of phylogenetic trees and integrate them to metagenomic datasets, thus enable classifiers to learn more information in limited datasets and thus improve the performance of the models. In this paper, we proposed a GNPI model to better learn the structure of phylogenetic trees. GNPI maintained the original vector format of metagenomic datasets, while previous research had to change the input form to matrices. The vector-like form of the input data can be easily adopted in the baseline machine learning models and is available for deep learning models. The datasets processed with GNPI help enhance the accuracy of machine learning and deep learning models in three different datasets. GNPI is an interpretable data processing method for host phenotype prediction and other bioinformatics tasks.

Hsa_circ_0017639 expression promotes gastric cancer proliferation and metastasis by sponging miR-224-5p and upregulating USP3.

Gastric cancer (GC) is a common malignant tumor having poor prognosis globally. Circular RNA (circRNA) is a circular endogenous RNA generated by special selective splicing that occurs in various traits. Studies show that hsa_circ_0017639 is abnormally expressed and involved in tumorigenesis. Nevertheless, the hsa_circ_0017639 role in GC is unknown. This study detected hsa_circ_0017639 expression in a GC cell line using RT-qPCR. Subcellular localization of hsa_circ_0017639 was verified via FISH. We assessed correlations amongst miRNA, hsa_circ_0017639 and relative protein levels using luciferase reporter assays and RNA pulldown assays. The data illustrated that in hsa_circ_assays, expression was enhanced in GC cell. Downregulation of hsa_circ_0017639 decreased GC cell proliferation and migration in in vitro and in vivo experiments. RNA pulldown and RT-qPCR analysis verified that hsa_circ_0017639 sponged miR-224-5p. Bioinformatic and luciferase reporter assays validated that miR-224-5p and USP3 were downstream targets of hsa_circ_0017639. Upregulation of USP3 or downregulation of miR-224-5p restored proliferation and migration by MKN-28 and MGC-803 cells after hsa_circ_0017639 silencing. Upregulation of USP3 restored MKN-28 and MGC-803 cell proliferation and migration after overexpression of miR-224-5p. Our collective findings advised that hsa_circ_0017639 takes part in GC progression through regulating the miR-224-5p/USP3 axis, highlighting its potential as an effective GC therapeutic target.

Robust biomarker discovery for microbiome-wide association studies.

According to the advances of high-throughput sequencing technology, massive microbiome data accumulated from environmental investigations to human studies. The microbiome-wide association studies are to study the relationship between the microbiome and human health or environment. Recently, Deep Neural Networks (DNNs) are encouraging due to their layer-wise learning ability for representation learning. However, DNNs are considered as black boxes and they require a large amount of training data which makes them impractical to conduct microbiome-wide association studies directly. Meanwhile, the microbiome data is high dimension with many features and noise. A single feature selection method for dealing with the kind of dataset is often unstable. In this work, we introduced a deep learning model named Deep Forest to conduct the microbiome-wide association studies and an ensemble feature selection method is proposed to guide microbial biomarkers' identification. The experiments showed that our ensemble feature method based on Deep Forest had good stability and robustness. The results of feature selection could guide the discovery of microbial biomarkers and help to diagnose microbial-related diseases. The code is available at https://github.com/MicroAVA/MWAS-Biomarkers.git.

Roles of circulating endothelial progenitor cells and endothelial cells in gastric carcinoma.

The present study aimed to investigate the role of endothelial progenitor cells (EPCs) and endothelial cells (ECs) in the peripheral blood of patients with gastric cancer (GC), and to investigate vascular endothelial growth factor (VEGF) expression and microvessel density (MVD) in GC tissues. First, 6 ml peripheral blood with added anticoagulant was collected from each of the 42 patients with GC, followed by determination of the number of EPCs and ECs by flow cytometry using the surface markers cluster of differentiation (CD)34brightCD133+CD31+CD45dim and CD34dimCD133-CD31brightCD45-, respectively. VEGF expression in patients with GC was detected by the streptomycin avidin-peroxidase immunohistochemical method, and MVD was calculated using the marker CD34. EPC and EC levels were positively associated with VEGF expression level, as well as with MVD. VEGF expression was positive in 66.67% GC cases, and its level was significantly associated with tumor-node-metastasis (TNM) stage, invasion depth and lymph-node metastasis (P<0.05). VEGF expression level was also positively associated with MVD. MVD in GC was significantly larger than that in normal tissue (P<0.01), and it was significantly associated with TNM stage (P<0.05), invasion depth (P<0.01) and lymph-node metastasis (P<0.01). EPCs in the peripheral blood have an important role in GC development, and may be a promising indicator of GC diagnosis and prognosis.

Calcifying fibrous tumor of stomach: A case report.

RATIONALE: Calcifying fibrous tumor (CFT) is a rare benign soft tissue mesenchymal neoplasm. Although the gastrointestinal (GI) tract is the most common predilection site of CFT, the clinicians, even including pathologist, generally consider it as GI stromal tumor (GIST) or other submucosal tumors such as schwannoma and leiomyoma. PATIENT CONCERNS: A 55-year-old man presented with complaints of epigastric discomfort and abdominal distention for more than 1 year. DIAGNOSES: On the basis of endoscopic and computed tomography examination, preliminary diagnosis was GIST. INTERVENTIONS: Endoscopic submucosal dissection (ESD) surgery was performed to remove the gastric mass. OUTCOMES: The histopathological examination revealed a gastric CFT. LESSONS: We present a case of gastric CFT, which was misdiagnosed as GIST based on endoscopic and radiologic findings.

Association of endothelial progenitor cells and peptic ulcer treatment in patients with type 2 diabetes mellitus.

The present study aimed to investigate the association between endothelial progenitor cells (EPCs) and peptic ulcers in patients with or without type 2 diabetes mellitus (T2DM), in association with the efficiency of peptic ulcer treatment. The study recruited healthy subjects and peptic ulcer patients with or without T2DM. All the ulcer patients, including those with and without T2DM, were administered omeprazole for 8 weeks. Peptic ulcer patients with T2DM were additionally treated with glipizide and novolin. Blood samples were then obtained from the three groups following ulcer treatment. CD133+ cells were isolated from the blood samples using magnetic bead selection, and cultured in complete medium 199. Morphological and quantity changes in EPCs were observed by light and fluorescence microscopy. In addition, flow cytometric analysis was used to quantify the number of vascular endothelial cells. The treatment was partially effective in 7 of the 32 peptic ulcer patients without T2DM and 12 of the 32 peptic ulcer patients with T2DM. However, this treatment was ineffective in 20 of the 32 peptic ulcer patients with T2DM. Notably, 25 peptic ulcer patients without T2DM were defined as completely recovered following treatment. In addition, the number of circulating EPCs as well as their colony forming ability was significantly reduced (P<0.05) in the peptic ulcer patients with T2DM following ulcer treatment, compared with the other groups. Circulating EPC counts were significantly increased in peptic ulcer patients without T2DM, as compared with the healthy controls. With regards to colony formation, peptic ulcer patients without T2DM did not exhibit improved colony formation ability. In conclusion, the number of circulating EPCs and their colony-forming ability was significantly reduced in peptic ulcer patients with T2DM following ulcer treatment when compared with the other groups. This suggests that the poor curative effect of peptic ulcer treatment in these patients is associated with impairment of EPCs.