GladiaTOX: GLobal Assessment of Dose-IndicAtor in TOXicology.

SUMMARY: GladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the 'tcpl' core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate PDF reports for quality control and data processing. AVAILABILITY AND IMPLEMENTATION: GladiaTOX R package (bioconductor). Also available via: git clone https://github.com/philipmorrisintl/GladiaTOX.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Spontaneous and Masticatory Post-endodontic Pain After Using Endomethasone N vs SP Root Canal Sealers: A Randomised Controlled Clinical Trial.

OBJECTIVE: Post-endodontic pain (PEP) after endodontic treatment (ET) might be reduced by adding cortisone to the composition of root canal sealer (RCS). This study aimed to test this hypothesis using grade A methodology. METHODS: A multicentric prospective randomised controlled clinical trial was performed in general practice. Adult patients with an indication of ET in a molar or premolar performed in one session were included be-tween 2021 and 2022 in 15 centres. The main objective was to demonstrate the superiority of Endomethasone N RCS (EndoN), compared to its hydrocortisone-free equivalent Endomethasone SP RCS (EndoSP), regarding the reduction of the maximum spontaneous PEP pain during the 7 days following the ET, self-estimated on a 0���100 mm Visual Analogic Scale (VAS). The secondary objectives were to assess 1) spontaneous PEP, 2) pro-voked (masticatory) PEP, 3) intake of analgesics, 4) quality of life and anxiety before and after ET, and 5) safety. RESULTS: The final sample consisted of 286 patients with a mean age of 47.7 years, including 51% men and 49% women. Before ET, 49.7% of the teeth were asymptomatic; provoked pain occurred in 29.4% and sponta-neous pain in 21.0%. The study evidenced a lower maximum spontaneous PEP intensity during the 7 days fol-lowing ET in EndoN compared to the EndoSP group (13.5+-17.9 vs 23.9+-26.6, IC 95% 10.5 [5.2���15.8], p=0.0001 Wilcoxon test). Maximal masticatory PEP was also lower in the EndoN group (12.3+-19.1 vs 24.0+-27.8, IC 95% 11.7 [5.8���17.6], p<0.0001 Wilcoxon test). At every evaluation time, the masticatory PEP in the EndoSP group was higher than in the EndoN group. In addition, no serious adverse events occurred during the study. CONCLUSION: This RCT demonstrated EndoN's superiority over EndoSP in reducing spontaneous and mastica-tory PEP during the 7 days following ET. This study was funded by the Septodont company (Saint Maur des Foss��s, France) and registered at ClinicalTrials.gov # NCT04885686.

Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.

BACKGROUND: High-throughput omics technologies such as microarrays and next-generation sequencing (NGS) have become indispensable tools in biological research. Computational analysis and biological interpretation of omics data can pose significant challenges due to a number of factors, in particular the systems integration required to fully exploit and compare data from different studies and/or technology platforms. In transcriptomics, the identification of differentially expressed genes when studying effect(s) or contrast(s) of interest constitutes the starting point for further downstream computational analysis (e.g. gene over-representation/enrichment analysis, reverse engineering) leading to mechanistic insights. Therefore, it is important to systematically store the full list of genes with their associated statistical analysis results (differential expression, t-statistics, p-value) corresponding to one or more effect(s) or contrast(s) of interest (shortly termed as " contrast data") in a comparable manner and extract gene sets in order to efficiently support downstream analyses and further leverage data on a long-term basis. Filling this gap would open new research perspectives for biologists to discover disease-related biomarkers and to support the understanding of molecular mechanisms underlying specific biological perturbation effects (e.g. disease, genetic, environmental, etc.). RESULTS: To address these challenges, we developed Confero, a contrast data and gene set platform for downstream analysis and biological interpretation of omics data. The Confero software platform provides storage of contrast data in a simple and standard format, data transformation to enable cross-study and platform data comparison, and automatic extraction and storage of gene sets to build new a priori knowledge which is leveraged by integrated and extensible downstream computational analysis tools. Gene Set Enrichment Analysis (GSEA) and Over-Representation Analysis (ORA) are currently integrated as an analysis module as well as additional tools to support biological interpretation. Confero is a standalone system that also integrates with Galaxy, an open-source workflow management and data integration system. To illustrate Confero platform functionality we walk through major aspects of the Confero workflow and results using the Bioconductor estrogen package dataset. CONCLUSION: Confero provides a unique and flexible platform to support downstream computational analysis facilitating biological interpretation. The system has been designed in order to provide the researcher with a simple, innovative, and extensible solution to store and exploit analyzed data in a sustainable and reproducible manner thereby accelerating knowledge-driven research. Confero source code is freely available from http://sourceforge.net/projects/confero/.

Multi-omics systems toxicology study of mouse lung assessing the effects of aerosols from two heat-not-burn tobacco products and cigarette smoke.

Cigarette smoke (CS) causes adverse health effects and, for smoker who do not quit, modified risk tobacco products (MRTPs) can be an alternative to reduce the risk of developing smoking-related diseases. Standard toxicological endpoints can lack sensitivity, with systems toxicology approaches yielding broader insights into toxicological mechanisms. In a 6-month systems toxicology study on ApoE-/- mice, we conducted an integrative multi-omics analysis to assess the effects of aerosols from the Carbon Heated Tobacco Product (CHTP) 1.2 and Tobacco Heating System (THS) 2.2-a potential and a candidate MRTP based on the heat-not-burn (HnB) principle-compared with CS at matched nicotine concentrations. Molecular exposure effects in the lungs were measured by mRNA/microRNA transcriptomics, proteomics, metabolomics, and lipidomics. Integrative data analysis included Multi-Omics Factor Analysis and multi-modality functional network interpretation. Across all five data modalities, CS exposure was associated with an increased inflammatory and oxidative stress response, and lipid/surfactant alterations. Upon HnB aerosol exposure these effects were much more limited or absent, with reversal of CS-induced effects upon cessation and switching to CHTP 1.2. Functional network analysis revealed CS-induced complex immunoregulatory interactions across the investigated molecular layers (e.g., itaconate, quinolinate, and miR-146) and highlighted the engagement of the heme-Hmox-bilirubin oxidative stress axis by CS. This work exemplifies how multi-omics approaches can be leveraged within systems toxicology studies and the generated multi-omics data set can facilitate the development of analysis methods and can yield further insights into the effects of toxicological exposures on the lung of mice.