Regular SE(3) Group Convolutions for Volumetric Medical Image Analysis

Regular group convolutional neural networks (G-CNNs) have been shown to increase model performance and improve equivariance to different geometrical symmetries. This work addresses the problem of SE(3), i.e., roto-translation equivariance, on volumetric data. Volumetric image data is prevalent in many medical settings. Motivated by the recent work on separable group convolutions, we devise a SE(3) group convolution kernel separated into a continuous SO(3) (rotation) kernel and a spatial kernel. We approximate equivariance to the continuous setting by sampling uniform SO(3) grids. Our continuous SO(3) kernel is parameterized via RBF interpolation on similarly uniform grids. We demonstrate the advantages of our approach in volumetric medical image analysis. Our SE(3) equivariant models consistently outperform CNNs and regular discrete G-CNNs on challenging medical classification tasks and show significantly improved generalization capabilities. Our approach achieves up to a 16.5% gain in accuracy over regular CNNs.Comment: 10 pages, 1 figure, 2 tables, accepted at MICCAI 2023. Updated version to camera ready version

Role of the rdxA and frxA genes in oxygen-dependent metronidazole resistance of Helicobacter pylori

Almost 50 % of all Helicobacter pylori isolates are resistant to metronidazole, which reduces the efficacy of metronidazole-containing regimens, but does not make them completely ineffective. This discrepancy between in vitro metronidazole resistance and treatment outcome may partially be explained by changes in oxygen pressure in the gastric environment, as metronidazole-resistant (MtzR) H. pylori isolates become metronidazole-susceptible (MtzS) under low oxygen conditions in vitro. In H. pylori the rdxA and frxA genes encode reductases which are required for the activation of metronidazole, and inactivation of these genes results in metronidazole resistance. Here the role of inactivating mutations in these genes on the reversibility of metronidazole resistance under low oxygen conditions is established. Clinical H. pylori isolates containing mutations resulting in a truncated RdxA and/or FrxA protein were selected and incubated under anaerobic conditions, and the effect of these conditions on the MICs of metronidazole, amoxycillin, clarithromycin and tetracycline, and cell viability were determined. While anaerobiosis had no effect on amoxycillin, clarithromycin and tetracycline resistance, all isolates lost their metronidazole resistance when cultured under anaerobic conditions. This loss of metronidazole resistance also occurred in the presence of the protein synthesis inhibitor chloramphenicol. Thus, factor(s) that activate metronidazole under low oxygen tension are not specifically induced by low oxygen conditions, but are already present under microaerophilic conditions. As there were no significant differences in cell viability between the clinical isolates, it is likely that neither the rdxA nor the frxA gene participates in the reversibility of metronidazole resistance

Efficacy of serology driven “test and treat strategy” for eradication of H. pylori in patients with rheumatic disease in the Netherlands

The treatment of choice of H. pylori infections is a 7-day triple-therapy with a proton pump inhibitor (PPI) plus amoxicillin and either clarithromycin or metronidazole, depending on local antibiotic resistance rates. The data on efficacy of eradication therapy in a group of rheumatology patients on long-term NSAID therapy are reported here. This study was part of a nationwide, multicenter RCT that took place in 2000–2002 in the Netherlands. Patients who tested positive for H. pylori IgG antibodies were included and randomly assigned to either eradication PPI-triple therapy or placebo. After completion, follow-up at 3 months was done by endoscopy and biopsies were sent for culture and histology. In the eradication group 13% (20/152, 95% CI 9–20%) and in the placebo group 79% (123/155, 95% CI 72–85%) of the patients were H. pylori positive by histology or culture. H. pylori was successfully eradicated in 91% of the patients who were fully compliant to therapy, compared to 50% of those who were not (difference of 41%; 95% CI 18–63%). Resistance percentages found in isolates of the placebo group were: 4% to clarithromycin, 19% to metronidazole, 1% to amoxicillin and 2% to tetracycline

Systematic review: Clinical effectiveness of interventions for the treatment of nocturnal gastroesophageal reflux

Background: Nocturnal gastroesophageal reflux symptoms have a major impact on sleep quality and are associated with complicated gastroesophageal reflux disease (GERD). We performed a systematic review to assess the data on the effectiveness of the currently available interventions for the treatment of nocturnal reflux symptoms. Methods: We searched PubMed, EMBASE, and the Cochrane Library. All prospective, controlled, and uncontrolled clinical trials in adult patients describing interventions (lifestyle modifications, surgical and pharmacological) for nocturnal gastroesophageal reflux symptoms were assessed for eligibility. A narrative descriptive summary of findings is presented together with summary tables for study characteristics and quality assessment. Key Results: The initial reference search yielded 3067 citations; 66 citations were screened in full text, of which 31 articles were included. Studies on lifestyle modifications include head of bed elevation (n = 5), prolonging dinner-to-bed time (n = 2), and promoting left lateral decubitus position (n = 2). Placebo-controlled clinical trials investigating proton pump inhibitors (PPIs) (n = 11) show success rates ranging from 34.4% to 80.8% in the PPI group versus 10.4%–51.7% in the placebo group. Laparoscopic fundoplication is reserved for severe disease only. There is insufficient evidence for a recommendation on the use of nasal continuous positive airway pressure (nCPAP), hypnotics, baclofen and adding bedtime H2 receptor antagonists for reducing nocturnal reflux. Conclusion Inferences: A sequential treatment strategy, including head of bed elevation, prolonging dinner-to-bed time, promoting left lateral decubitus position and treatment with acid-suppressive medication is recommended for nocturnal gastroesophageal reflux symptoms. Currently, there is insufficient evidence for the use of nCPAP, hypnotics, baclofen and adding bedtime H2 receptor antagonists