An objective reduction technique of proteomic mass spectra based on multi-scale fuzzy thresholding

A proteomic approach offers a powerful and complementary tool to genomics. It allows to index and characterize proteins, and, for example, to compare their levels of expression between healthy and pathological states. Proteomic analyses are mainly based on the separation of proteins by two-dimensional gel electrophoresis and their subsequent identification by comparing the data from Mass Spectrometry (SM) analyses to the theoretical ones contained in databases. In mass spectrometry, the detector noise, the electronic and chemical noise, sometimes the small amount of peptides that has to be treated and finally the spectrum reduction noise (due to bad filtering and/or thresholding), can induce Parasitic Mass Peaks (PMP) and/or hide some Useful Mass Peaks (UMP) of low intensities. The immediate consequence is that the presence of the PMP and the absence of the UMP will be detrimental to the protein identification quality. In this article, we propose an original algorithm eliminating the PMP, detecting and amplifying those which are useful. The preprocessing principle uses a multi-scale analysis technique coupled to a fuzzy thresholding (multi-scale fuzzy thresholding), a local amplification of the UMP, and finally an adaptive Base Line Correction. The associated frequencies with the PMP are distributed on all the spectrum pass bandwidth. This leads us to a dyadic tree structure subband decomposition. The algorithm principle consists of dividing the frequential pass bandwidth of each masses spectrum into two subbands, a Low and High Frequency (LF,HF) subband, then each subband is in turn divided into two subbands etc. The HF subbands are then thresholded according to the minimization criterion of the Shannon fuzzy entropy, and then amplified locally; the base line is calculated in an adaptive way and subtracted from reconstructed spectrum. To evaluate the quality of this algorithm, we present a comparison of the results obtained by our algorithm, and those obtained by the DataExplorer software. The latter is a reduction software provided within the MALDI-TOF spectrometer software package.La protéomique offre une approche puissante et complémentaire à la génomique. Elle permet de répertorier et caractériser les protéines, de comparer leur niveau d’expression entre un état physiologique sain et malade par exemple. L’analyse protéomique se fait essentiellement par l’utilisation de la technique d’électrophorèse bidimensionnelle couplée à la technique d’analyse par Spectrométrie de Masse (SM). La première, aidée par l’imagerie protéomique, conduit à la localisation des protéines candidates à une analyse par SM. La comparaison des spectres de masses obtenus à des bases de données protéiques, conduit à l’identification des protéines d’intérêt en terme de peptides. Le problème qui se pose souvent est que les spectres sont bruités et pauvres en masses. En effet, le bruit du détecteur, le bruit électronique et chimique, la présence de peu de matériel protéique et enfin le bruit de la réduction des spectres (mauvais filtrage et/ou seuillage), tous ces bruits peuvent induire des Pics de Masses Parasites (PMP) et/ou supprimer des Pics de Masses Utiles (PMU) de faible intensité. La conséquence immédiate est que la présence des PMP et l’absence des PMU seront utilisées au dépens de la qualité d’identification de la protéine. Dans cet article, nous proposons un algorithme original éliminant les PMP, détectant et amplifiant ceux utiles. Le principe du pré-traitement utilise une Analyse Multirésolution (AM) couplée à un seuillage basé sur la logique floue (seuillage flou multi-échelle), une amplification locale des PMU, et enfin une correction adaptative de la Ligne de Base (LB). Les fréquences associées aux PMP sont réparties sur toute la bande passante du spectre, ce qui nous conduit à une AM dite en arbre. Le principe consiste à découper la bande passante fréquentielle de chaque spectre de masses en deux sous-bandes, une Basse Fréquence (BF), l’autre Haute Fréquence (HF), ensuite chaque sous-bande est à son tour découpée en deux sous-bandes etc. Les sous-bandes HF sont seuillées selon le critère de minimisation de l’entropie floue de Shannon et amplifiées localement, la ligne de base est calculée automatiquement et soustraite du spectre reconstruit. Pour évaluer la qualité de cet algorithme, nous présentons une comparaison des résultats obtenus par notre algorithme, et ceux fournis par le spectromètre MALDI-TOF (Matrix Assisted Laser Desorption/Ionisation-Time Of Flight), qui utilise le logiciel « DataExplorer » comme logiciel de réduction

Analyse statistique de données radiomiques et métabolomiques : prédiction des lésions mammaires triple-négatives

International audienceLa caractérisation de l’hétérogénéité tumorale à partir des images médicales (appeléeaussi radiomique) et de l’extraction de données omiques est un enjeu majeur en cancérologie,notamment dans la mise en place de la médecine de précision. Or actuellement, le lien entre lesvariables radiomiques (VR) et les caractéristiques biologiques des lésions est encore mal connu.L’objectif de ce travail est d’étudier la corrélation entre les VR et les variables métabolomiques (VM)dans le cancer du sein, et d’analyser leur capacité à prédire le sous-type immunohistochimique deslésions

JDM treatment with rituximab Personal non-commercial use only

ABSTRACT. Objective. To evaluate the safety and efficacy of rituximab (RTX) in juvenile dermatomyositis (JDM) in off-trial patients. Methods. We conducted a multicenter prospective study of patients with JDM included in the French Autoimmunity and Rituximab (AIR) registry. Results. Nine patients with severe JDM were studied. The main indication for RTX treatment was severe and/or refractory muscle involvement (7 patients), severe calcinosis (1 patient), or severe chronic abdominal pain associated with abdominal lipomatosis (1 patient). RTX was associated with corticosteroids, immunosuppressive drugs, and plasma exchange therapy in 9/9, 5/9, and 2/9 patients, respectively. Mild infections of the calcinosis sites occurred in 2 patients and an infusion-related event in 1. Complete clinical response was achieved in 3/6 patients treated with RTX for muscle involvement. In these responders steroid therapy was stopped or tapered to < 15% of the baseline dosage, with no relapse, with a followup ranging from 1.3 to 3 years. Calcinosis did not improve in the 6 affected patients. Conclusion. This small series suggests that rituximab may be effective for treating muscle and skin involvement in a small subset of children with severe JDM, and that its safety profile was satisfactory. Further studies are needed to identify predictive factors of response to RTX in patients with sever

Social Deprivation Is Associated With Lower Access to Pre-emptive Kidney Transplantation and More Urgent-Start Dialysis in the Pediatric Population

Introduction Socioeconomic status (SES) is recognized as an important determinant of kidney health. We aimed to evaluate the association of social deprivation with different indicators at kidney replacement therapy (KRT) initiation in the French pediatric metropolitan population. Methods All patients with end-stage kidney disease (ESKD) who started KRT before 20 years old in France between 2002 and 2015 were included. We investigated different indicators at KRT initiation, which are as follows: KRT modality (dialysis vs. pre-emptive transplantation), late referral to a nephrologist, and dialysis modality (hemodialysis [HD] vs. peritoneal dialysis [PD], urgent vs. planned start of dialysis, use of catheter vs. use of fistula for HD vascular access). An ecological index (European Deprivation Index [EDI]) was used as a proxy for social deprivation. Results A total of 1115 patients were included (males 59%, median age at dialysis 14.4 years, glomerular/vascular diseases 36.8%). The most deprived group represented 38.7% of the patients, suggesting pediatric patients with ESKD come from a more socially deprived background. The most deprived group was more likely to initiate KRT with dialysis versus kidney transplantation. Among patients on HD, the odds of starting treatment in emergency with a catheter was >2-fold higher for the most deprived compared with the least deprived children (adjusted odds ratio [aOR] 2.35, 95% CI 1.16–4.78). Conclusion Children from the most deprived area have lower access to pre-emptive transplantation, have lower access to PD, tend to be late referred to a nephrologist, and have more urgent initiation of HD with a catheter

BMJ Open

Introduction Guidelines for the treatment of steroid-dependent nephrotic syndrome (SDNS) and frequently relapsing nephrotic syndrome (FRNS) are lacking. Given the substantial impact of SDNS/FRNS on quality of life, strategies aiming to provide long-term remission while minimising treatment side effects are needed. Several studies confirm that rituximab is effective in preventing early relapses in SDNS/FRNS; however, the long-term relapse rate remains high (~70% at 2 years). This trial will assess the association of intravenous immunoglobulins (IVIgs) to rituximab in patients with SDNS/FRNS and inform clinicians on whether IVIg’s immunomodulatory properties can alter the course of the disease and reduce the use of immunosuppressive drugs and their side effects. Methods and analysis We conduct an open-label multicentre, randomised, parallel group in a 1:1 ratio, controlled, superiority trial to assess the safety and efficacy of a single infusion of rituximab followed by IVIg compared with rituximab alone in childhood-onset FRNS/SDNS. The primary outcome is the occurrence of first relapse within 24 months. Patients are allocated to receive either rituximab alone (375 mg/m²) or rituximab followed by IVIg, which includes an initial Ig dose of 2 g/kg, followed by 1.5 g/kg injections once a month for the following 5 months (maximum dose: 100 g). Ethics and dissemination The study has been approved by the ethics committee (Comité de Protection des Personnes) of Ouest I and authorised by the French drug regulatory agency (Agence Nationale de Sécurité du Médicament et des Produits de Santé). Results of the primary study and the secondary aims will be disseminated through peer-reviewed publications

Guidelines for diagnosis and management of the cobalamin-related remethylation disorders cblC, cblD, cblE, cblF, cblG, cblJ and MTHFR deficiency

BACKGROUND: Remethylation defects are rare inherited disorders in which impaired remethylation of homocysteine to methionine leads to accumulation of homocysteine and perturbation of numerous methylation reactions. OBJECTIVE: To summarise clinical and biochemical characteristics of these severe disorders and to provide guidelines on diagnosis and management. DATA SOURCES: Review, evaluation and discussion of the medical literature (Medline, Cochrane databases) by a panel of experts on these rare diseases following the GRADE approach. KEY RECOMMENDATIONS: We strongly recommend measuring plasma total homocysteine in any patient presenting with the combination of neurological and/or visual and/or haematological symptoms, subacute spinal cord degeneration, atypical haemolytic uraemic syndrome or unexplained vascular thrombosis. We strongly recommend to initiate treatment with parenteral hydroxocobalamin without delay in any suspected remethylation disorder; it significantly improves survival and incidence of severe complications. We strongly recommend betaine treatment in individuals with MTHFR deficiency; it improves the outcome and prevents disease when given early

Variability of diagnostic criteria and treatment of idiopathic nephrotic syndrome across European countries

The aim of the surveys conducted by the Idiopathic Nephrotic Syndrome Working Group of the ESPN was to study the possible variability of treatment in Europe at different stages of the disease by means of questionnaires sent to members of the Working Group. Four surveys have been completed: treatment of the first flare, treatment of the first relapse and the issue of steroid dependency, use of rituximab, and the management of steroid-resistant patients. A uniform treatment of the first flare was applied in only three countries, and ten additional centers have adopted one of the three main protocols. Reported treatment of the first relapse was relatively uniform, whereas the use of additional immunosuppressants in steroid dependency was widely variable. Rituximab had already been used in hundreds of patients, although the formal evidence of efficiency in steroid dependency was relatively recent at the time of the survey. The definition of steroid resistance was variable in the European centers, but strikingly, the first-line treatment was uniform throughout the centers and included the combination of prednisone plus calcineurin antagonists. Conclusion: The variability in the approach of idiopathic nephrotic syndrome is unexpectedly large and affects treatment of the first flare, strategies in the case of steroid dependency, as well as the definitions of steroid resistance.What is Known:• Steroids and immunosuppressants are the universal treatment of idiopathic nephrotic syndrome.What is New:• The variability of treatments and strategy of treatment in European centers of pediatric nephrology

[New treatments for Idiopathic Nephrotic Syndrome]

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