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Research Question: How do carriers of pathogenic mitochondrial DNA (mtDNA) respond to ovarian stimulation?, Design: A single-centre, retrospective study conducted between January 2006 and July 2021 in France. Ovarian reserve markers and ovarian stimulation cycle outcomes were compared for couples undergoing preimplantation genetic testing (PGT) for maternally inherited mtDNA disease (n = 18) (mtDNA-PGT group) with a matched-control group of patients undergoing PGT for male indications (n = 96). The PGT outcomes for the mtDNA-PGT group and the follow-up of these patients in case of unsuccessful PGT was also reported., Results: For carriers of pathogenic mtDNA, parameters of ovarian response to FSH and ovarian stimulation cycle outcomes were not different from those of matched-control ovarian stimulation cycles. The carriers of pathogenic mtDNA needed a longer ovarian stimulation and higher dose of gonadotrophins. Three patients (16.7%) obtained a live birth after the PGT process, and eight patients (44.4%) achieved parenthood through alternative methods: oocyte donation (n = 4), natural conception with prenatal diagnosis (n = 2) and adoption (n = 2)., Conclusion: To the best of our knowledge, this is the first study of women carrying a mtDNA variant who have undergone a PGT for monogenic (single gene defects) procedure. It is one of the possible options to obtain a healthy baby without observing an impairment in ovarian response to stimulation., (Copyright © 2023 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.)

Purpose: Preimplantation genetic testing (PGT-M) and prenatal diagnosis (PND) followed by medical termination of pregnancy when the fetus is affected are two procedures developed to avoid the transmission of a severe hereditary disease which can be proposed to females that carried BRCA pathogenic variants. These females can also be offered fertility preservation (FP) when diagnosed with cancer or even before a malignancy occurs. The aim of the study was to evaluate the acceptability and personal attitude of women carrying a BRCA mutation toward techniques that can prevent BRCA transmission to their progeny., Methods: Female mutated for BRCA1 or BRCA2 were invited to complete an online survey of 49 queries anonymously between June and August 2022., Results: A total of 87 participants responded to the online survey. Overall, 86.2% of women considered that PGT-M should be proposed to all BRCA mutation carriers regardless of the severity of the family history, and 47.1% considered or would consider PGT-M for themselves. For PND, these percentages were lower reaching 66.7% and 29.9%, respectively. Females with personal history of breast cancer or FP achievement were more prone to undergo PND for themselves despite the overall acceptability of this procedure. Among the subgroup who had undergone FP (n = 58), there was no significant difference in acceptance of principle and personal attitude toward PGT-M and PND compared to the group without FP., Conclusion: BRCA pathogenic variants female carriers do need information about reproductive issues, even if they are not prone to undergo PGT-M nor PND for themselves., Trial Registration Number: N/A., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

In human health research, metabolic signatures extracted from metabolomics data have a strong added value for stratifying patients and identifying biomarkers. Nevertheless, one of the main challenges is to interpret and relate these lists of discriminant metabolites to pathological mechanisms. This task requires experts to combine their knowledge with information extracted from databases and the scientific literature. However, we show that most compounds (>99%) in the PubChem database lack annotated literature. This dearth of available information can have a direct impact on the interpretation of metabolic signatures, which is often restricted to a subset of significant metabolites. To suggest potential pathological phenotypes related to overlooked metabolites that lack annotated literature, we extend the "guilt-by-association" principle to literature information by using a Bayesian framework. The underlying assumption is that the literature associated with the metabolic neighbors of a compound can provide valuable insights, or an a priori, into its biomedical context. The metabolic neighborhood of a compound can be defined from a metabolic network and correspond to metabolites to which it is connected through biochemical reactions. With the proposed approach, we suggest more than 35,000 associations between 1,047 overlooked metabolites and 3,288 diseases (or disease families). All these newly inferred associations are freely available on the FORUM ftp server (see information at https://github.com/eMetaboHUB/Forum-LiteraturePropagation)., (© The Author(s) 2023. Published by Oxford University Press GigaScience.)

Introduction: Accuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However, the annotation process is often hampered by the lack of spectral reference data in experimental conditions, as well as logistical difficulties in the spectral data management and exchange of annotations between laboratories., Objectives: To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with an ergonomic Web interface and Web services to support metabolite annotation and laboratory data management., Methods: We developed the PeakForest infrastructure, an open-source Java tool with automatic programming interfaces that can be deployed locally to organize spectral data for metabolome annotation in laboratories. Standardized operating procedures and formats were included to ensure data quality and interoperability, in line with international recommendations and FAIR principles., Results: PeakForest is able to capture and store experimental spectral MS and NMR metadata as well as collect and display signal annotations. This modular system provides a structured database with inbuilt tools to curate information, browse and reuse spectral information in data treatment. PeakForest offers data formalization and centralization at the laboratory level, facilitating shared spectral data across laboratories and integration into public databases., Conclusion: PeakForest is a comprehensive resource which addresses a technical bottleneck, namely large-scale spectral data annotation and metabolite identification for metabolomics laboratories with multiple instruments. PeakForest databases can be used in conjunction with bespoke data analysis pipelines in the Galaxy environment, offering the opportunity to meet the evolving needs of metabolomics research. Developed and tested by the French metabolomics community, PeakForest is freely-available at https://github.com/peakforest ., (© 2022. The Author(s).)

Motivation: Metabolomics studies aim at reporting a metabolic signature (list of metabolites) related to a particular experimental condition. These signatures are instrumental in the identification of biomarkers or classification of individuals, however their biological and physiological interpretation remains a challenge. To support this task, we introduce FORUM: a Knowledge Graph (KG) providing a semantic representation of relations between chemicals and biomedical concepts, built from a federation of life science databases and scientific literature repositories., Results: The use of a Semantic Web framework on biological data allows us to apply ontological-based reasoning to infer new relations between entities. We show that these new relations provide different levels of abstraction and could open the path to new hypotheses. We estimate the statistical relevance of each extracted relation, explicit or inferred, using an enrichment analysis, and instantiate them as new knowledge in the KG to support results interpretation/further inquiries., Availability and Implementation: A web interface to browse and download the extracted relations, as well as a SPARQL endpoint to directly probe the whole FORUM KG, are available at https://forum-webapp.semantic-metabolomics.fr. The code needed to reproduce the triplestore is available at https://github.com/eMetaboHUB/Forum-DiseasesChem., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2021. Published by Oxford University Press.)

Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the multiplicity of bioinformatics tools, providing experimenters with a simple and efficient resource to conduct comprehensive and rigorous analysis of their data is of utmost importance. In 2014, we launched the Workflow4Metabolomics (W4M; http://workflow4metabolomics.org) online infrastructure for metabolomics built on the Galaxy environment, which offers user-friendly features to build and run data analysis workflows including preprocessing, statistical analysis, and annotation steps. Here we present the new W4M 3.0 release, which contains twice as many tools as the first version, and provides two features which are, to our knowledge, unique among online resources. First, data from the four major metabolomics technologies (i.e., LC-MS, FIA-MS, GC-MS, and NMR) can be analyzed on a single platform. By using three studies in human physiology, alga evolution, and animal toxicology, we demonstrate how the 40 available tools can be easily combined to address biological issues. Second, the full analysis (including the workflow, the parameter values, the input data and output results) can be referenced with a permanent digital object identifier (DOI). Publication of data analyses is of major importance for robust and reproducible science. Furthermore, the publicly shared workflows are of high-value for e-learning and training. The Workflow4Metabolomics 3.0 e-infrastructure thus not only offers a unique online environment for analysis of data from the main metabolomics technologies, but it is also the first reference repository for metabolomics workflows., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Summary: The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation., Availability and Implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB)., Contact: contact@workflow4metabolomics.org., (© The Author 2014. Published by Oxford University Press.)

Responses to [Mpr14]-ADM(14-50), a novel analog of adrenomedullin, were investigated in the hindlimb vascular bed of the cat under conditions of controlled blood flow. Intraarterial injections of [Mpr14]-rADM(14-50) in doses of 0.003-1 nmol caused dose-related decreases in hindlimb perfusion pressure. In terms of relative vasodilator activity, [Mpr14]-rADM(14-50) was more potent than human synthetic adrenomedullin (hADM) in doses of 0.003-0.1 nmol. The recovery half-times (T 1/2) for the vasodilator response to [Mpr14]-rADM(14-50) were significantly greater than the recovery half-times for hADM in all doses studied. Decreases in hindlimb perfusion pressure in response to [Mpr14]-rADM(14-50) were not altered by the calcitonin gene-related peptide receptor antagonist rCGRP(8-37) at the same time vasodilator responses to calcitonin gene-related peptide were significantly reduced. The present data demonstrate that [Mpr14]-(14-50) has potent and long-lasting vasodilator activity when compared to hADM, and that vasodilator responses to [Mpr14]-rADM(14-50) are not dependent on the activation of CGRP receptors in the hindlimb vascular bed of the cat.

Thallium 201 is rapidly fixed by the healthy myocardium and its radiation detectable by a scintillation camera. It may be used to reveal and localise ischaemic zones after intravenous injection. In 74 patients undergoing an exercise test, the results of so-called effort scintigraphy were compared with effort electrocardiograms, coronary arteriography and scintigraphy after the injection of Thallium 201 at rest (rest scintigraphy). The results of effort scintigraphy show a high degree of agreement with those of the effort electrocardiogram and of coronary arteriography. It would appear to be of great value in the determination of the permeability of aorto-coronary by-passes.