Association of genetic variants of membrane receptors related to recognition and induction of immune response with Helicobacter pylori infection in Ecuadorian individuals

Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells

In this work, an unsupervised volumetric semantic instance segmentation of the plasma membrane of HeLa cells as observed with serial block face scanning electron microscopy is described. The resin background of the images was segmented at different slices of a 3D stack of 518 slices with 8192 × 8192 pixels each. The background was used to create a distance map, which helped identify and rank the cells by their size at each slice. The centroids of the cells detected at different slices were linked to identify them as a single cell that spanned a number of slices. A subset of these cells, i.e., the largest ones and those not close to the edges were selected for further processing. The selected cells were then automatically cropped to smaller regions of interest of 2000 × 2000 × 300 voxels that were treated as cell instances. Then, for each of these volumes, the nucleus was segmented, and the cell was separated from any neighbouring cells through a series of traditional image processing steps that followed the plasma membrane. The segmentation process was repeated for all the regions of interest previously selected. For one cell for which the ground truth was available, the algorithm provided excellent results in Accuracy (AC) and the Jaccard similarity Index (JI): nucleus: JI =0.9665, AC =0.9975, cell including nucleus JI =0.8711, AC =0.9655, cell excluding nucleus JI =0.8094, AC =0.9629. A limitation of the algorithm for the plasma membrane segmentation was the presence of background. In samples with tightly packed cells, this may not be available. When tested for these conditions, the segmentation of the nuclear envelope was still possible. All the code and data were released openly through GitHub, Zenodo and EMPIAR.

Risk factors for recurrence of Helicobacter pylori infection after successful eradication in Chinese children: A prospective, nested case-control study

BACKGROUND

Limited research has been published on the recurrence of Helicobacter pylori infection and risk factors in Chinese children. Our study aimed to identify risk factors for Helicobacter pylori infection recurrence after successful eradication in children.

MATERIALS AND METHODS

A prospective, nested case-control study was performed. A cohort of 230 children with successful eradication of Helicobacter pylori in Baoding (China) was selected from January 2018 to February 2019. A standardized questionnaire was used to obtain socioeconomic details. Eradication regimens and Helicobacter pylori antibiotic susceptibility testing results were also recorded. Interleukin-1β level, interferon-γ level, and genetic susceptibility (IFNGR1 and PTPRZ1 gene polymorphisms) were analyzed. All children were followed for 1 year.

RESULTS

Among 218 (94.8%) children who were successfully followed, 41 children (18.8%) had a Helicobacter pylori infection recurrence. The recurrence rate was higher in children ≤10 years old than >10 years old (22.8% vs 7.1%, P = .01). There was no significant difference between the recurrence group and the non-recurrence group in terms of types of therapy and antibiotic sensitivity (P > .05). Multivariable regression results indicated that residence in urban areas, higher household income, and having lunch at home were significantly protective against recurrence (OR 0.155, 0.408, and 0.351 respectively), whereas Helicobacter pylori infection in family members increased the risk of recurrence (OR 2.283). The levels of IL-1β and IFN-γ exhibited no significant difference between the recurrence group and the non-recurrence group. The allele frequency of G in the IFNGR1-56 site, A in the IFNGR1-600 site, and T in the IFNGR1-565 site was significantly higher in the recurrence group when compared to the non-recurrence group (P < .05).

CONCLUSIONS

The Helicobacter pylori infection recurrence rate is high in children in Baoding region and is closely correlated to socioeconomic factors. The IFNGR1 gene polymorphism may be an independent risk factor for Helicobacter pylori infection recurrence.