Chebifier: automating semantic classification in ChEBI to accelerate data-driven discovery.

Connecting chemical structural representations with meaningful categories and semantic annotations representing existing knowledge enables data-driven digital discovery from chemistry data. Ontologies are semantic annotation resources that provide definitions and a classification hierarchy for a domain. They are widely used throughout the life sciences. ChEBI is a large-scale ontology for the domain of biologically interesting chemistry that connects representations of chemical structures with meaningful chemical and biological categories. Classifying novel molecular structures into ontologies such as ChEBI has been a longstanding objective for data scientific methods, but the approaches that have been developed to date are limited in several ways: they are not able to expand as the ontology expands without manual intervention, and they are not able to learn from continuously expanding data. We have developed an approach for automated classification of chemicals in the ChEBI ontology based on a neuro-symbolic AI technique that harnesses the ontology itself to create the learning system. We provide this system as a publicly available tool, Chebifier, and as an API, ChEB-AI. We here evaluate our approach and show how it constitutes an advance towards a continuously learning semantic system for chemical knowledge discovery.

Discovering Biomarkers for Non-Alcoholic Steatohepatitis Patients with and without Hepatocellular Carcinoma Using Fecal Metaproteomics.

High-calorie diets lead to hepatic steatosis and to the development of non-alcoholic fatty liver disease (NAFLD), which can evolve over many years into the inflammatory form of non-alcoholic steatohepatitis (NASH), posing a risk for the development of hepatocellular carcinoma (HCC). Due to diet and liver alteration, the axis between liver and gut is disturbed, resulting in gut microbiome alterations. Consequently, detecting these gut microbiome alterations represents a promising strategy for early NASH and HCC detection. We analyzed medical parameters and the fecal metaproteome of 19 healthy controls, 32 NASH patients, and 29 HCC patients, targeting the discovery of diagnostic biomarkers. Here, NASH and HCC resulted in increased inflammation status and shifts within the composition of the gut microbiome. An increased abundance of kielin/chordin, E3 ubiquitin ligase, and nucleophosmin 1 represented valuable fecal biomarkers, indicating disease-related changes in the liver. Although a single biomarker failed to separate NASH and HCC, machine learning-based classification algorithms provided an 86% accuracy in distinguishing between controls, NASH, and HCC. Fecal metaproteomics enables early detection of NASH and HCC by providing single biomarkers and machine learning-based metaprotein panels.

Steroid-responsive meningitis-arteritis in dogs in Germany: Are there epidemiological or clinical factors influencing recurrence rate?

OBJECTIVE: Steroid-responsive meningitis arteritis (SRMA) is one of the most common inflammatory diseases of the central nervous system in dogs. The present study examined breed and sex predisposition factors based on the population of dogs in Germany as well as epidemiological and clinical factors regarding the relapse rate of SRMA. MATERIAL AND METHODS: Data of 153 dogs with SRMA (SRMA) were analysed retrospectively in this multicentre study. It was investigated whether some dog breeds that suffer from SRMA were disproportionately more often (n ≥ 5) represented when compared to the total population of dogs in Germany. Furthermore it was examined which sex is affected more often. Data provided by "Verband für das deutsche Hundewesen" (VDH) and "Tasso e. V." was used as reference data of the total population. The following factors were investigated with regard to the occurrence of one or more relapses: signalment; body weight; age at first presentation; time period between last vaccination and onset of clinical signs; clinical signs and timepoint of the first SRMA manifestation; results of cerebrospinal fluid (CSF) analysis at first presentation (nucleated cell count and differentiation, protein concentration); immunglobulin A and C-reactive protein (CRP) concentrations in serum and CSF; immunosuppressive medication; follow-up data including response to therapy, occurrence of relapses and mortality including reasons, i. e. due to the disease, therapy or euthanasia. RESULTS: The breed had a statistically significant influence on the development of SRMA (p < 0.05). Beagles and Boxers were affected more often by SRMA than other breeds in relation to the total population in Germany. Relapses occurred in 29.4 % of the 153 dogs of this study. In contrast to the development of SRMA, in which male dogs have a significantly increased risk of developing SRMA (p < 0.05), female dogs are more likely to relapse (p = 0.02). Patients on prednisolone monotherapy had fewer relapses than those with prednisolone and azathioprine in combination (p < 0.05). Younger age (p = 0.071) und lower CRP concentrations (p = 0.081) at first presentation were tentatively associated with a higher incidence of relapses. CONCLUSION: The determined breed and sex predispositions support the diagnosis of SRMA arteritis and confirm previous observations. This study allows a more accurate explanation to owners about the risk of relapse.

Age at epilepsy onset in patients with focal cortical dysplasias, gangliogliomas and dysembryoplastic neuroepithelial tumours.

PURPOSE: The age at epilepsy onset in patients with inborn or very early acquired brain lesions depends on the epileptogenic potential of the lesion and the patients' individual "susceptibility" to epileptic seizures. To gain insight into these determinants, we analysed the case history of patients with focal cortical dysplasias (FCDs) and neuroglial tumours. METHODS: In a systematic, retrospective analysis comprised of 233 patients who underwent surgery (116 with FCDs and 117 with neuroglial tumours), we evaluated the age at epilepsy onset according to histopathologic subgroups, lesion location and family history. RESULTS: Epilepsy onset was significantly earlier in patients with FCD than for those with neuroglial tumours (FCDs: 8.06 ±â€¯0.74 years, gangliogliomas: 15.86 ±â€¯1.24 years, dysembryoplastic neuroepithelial tumours (DNTs): 19.18 ±â€¯2.47 years; p < 0.00001). FCDs were most frequently located in the frontal, whereas neuroglial tumours most frequently in the temporal lobe. For FCD patients, the age at epilepsy onset was not dependent on lesion location, whereas DNTs in a temporal location were associated with a later epilepsy onset than gangliogliomas and extratemporal DNTs. A positive family history for epilepsy or epileptic seizures was found more frequently among patients with FCDs (FCDs: 20.4%, neuroglial tumours: 8.1%; p = 0.013). CONCLUSION: We postulate that the age difference at epilepsy onset between patients with FCDs and neuroglial tumours can be attributed - at least partially - to unidentified genetic factors underlying the epileptogenic potential of the brain tissue. Additionally, the large variance in the age at epilepsy onset is possibly also genetically determined.