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47 results on '"MESH: Reference Standards"'

1. Selecting reference genes in RT-qPCR based on equivalence tests: a network based approach

Author

Curis, Emmanuel, Nepost, Calypso, Grillault Laroche, Diane, Courtin, Cindie, Laplanche, Jean-Louis, Etain, Bruno, Marie-Claire, Cynthia, Variabilité de réponse aux Psychotropes (VariaPsy - U1144), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biomarqueurs de la rechute et de la réponse aux traitements dans les addictions et les troubles de l'humeur [Paris], Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Biochemistry and Molecular Biology [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Lariboisière-Fernand-Widal [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Mondor de recherche biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Marie-Claire, Cynthia, Optimisation thérapeutique en Neuropsychopharmacologie (OPTeN (UMR_S_1144 / U1144)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Laboratoire de biomathématiques, EA 7537 [Paris] (BioSTM), Université Paris Cité - UFR Pharmacie [Santé] (UPCité UFR Pharmacie), Université Paris Cité (UPCité)-Université Paris Cité (UPCité), Hopital Saint-Louis [AP-HP] (AP-HP), Hôpitaux Universitaire Saint-Louis, Lariboisière, Fernand-Widal, and Fondation FondaMental [Créteil]

Subjects
Adult, Male, Bipolar Disorder, Statistical methods, [SDV.MHEP.PSM] Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health, lcsh:Medicine, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, Real-Time Polymerase Chain Reaction, Article, Cell Line, MESH: Gene Expression Profiling, MESH: Bipolar Disorder, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, lcsh:Science, ComputingMilieux_MISCELLANEOUS, MESH: Humans, MESH: Real-Time Polymerase Chain Reaction, Gene Expression Profiling, lcsh:R, MESH: Adult, Reference Standards, MESH: Male, MESH: Cell Line, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, [SDV.MHEP.PSM]Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health, Reverse transcription polymerase chain reaction, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Female, MESH: Reference Standards, lcsh:Q, MESH: Female
Abstract

International audience; Because quantitative reverse transcription PCR (RT-qPCR) gene expression data are compositional, amounts of quantified RNAs must be normalized using reference genes. However, the two most used methods to select reference genes (NormFinder and geNorm) ignore the compositional nature of RT-qPCR data, and often lead to different results making reliable reference genes selection difficult. We propose a method, based on all pairwise equivalence tests on ratio of gene expressions, to select genes that are stable enough to be used as reference genes among a set a candidate genes. This statistical procedure controls the error of selecting an inappropriate gene. Application to 30 candidate reference genes commonly used in human studies, assessed by RT-qPCR in RNA samples from lymphoblastoid cell lines of 14 control subjects and 26 patients with bipolar disorder, allowed to select 7 reference genes. This selection was consistent with geNorm's ranking, less with NormFinder's ranking. Our results provide an important fundamental basis for reference genes identification using sound statistics taking into account the compositional nature of RT-qPCR data. The method, implemented in the SARP.compo package for R (available on the CRAN), can be used more generally to prove that a set of genes shares a common expression pattern.

Published
2019
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2. Consensus international sur la terminologie à utiliser dans le domaine des échinococcoses

Author

Vuitton Dominique A., McManus Donald P., Rogan Michael T., Romig Thomas, Gottstein Bruno, Naidich Ariel, Tuxun Tuerhongjiang, Wen Hao, Menezes da Silva Antonio, Rogan Michael R., Avcioglu Amza, Boufana Belgees, Budke Christine, Casulli Adriano, Güven Esin, Hillenbrand Andreas, Jalousian Fateme, Jemli Mohamed Habib, Knapp Jenny, Laatamna Abdelkarim, Lahmar Samia, Sadjjadi Seyed Mahmoud, Schmidberger Julian, Amri Manel, Bellanger Anne-Pauline, Benazzouz Sara, Brehm Klaus, Kachani Malika, Labsi Moussa, Masala Giovanna, Soufli Imene, Touil-Boukoffa Chafia, Wang Junhua, Zeyhle Eberhard, Aji Tuerganaili, Akhan Okan, Bresson-Hadni Solange, Dziri Chadli, Gräter Tilmann, Grüner Beate, Haïf Assia, Koch Stéphane, Tamarozzi Francesca, Giraudoux Patrick, Torgerson Paul, Vizcaychipi Katherina, Xiao Ning, Altintas Nazmiye, Lin Renyong, Millon Laurence, Zhang Wenbao, Achour Karima, Fan Haining, Junghanss Thomas, Mantion Georges A., Ege Üniversitesi, Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon, 25030 Besançon, France, Molecular Parasitology Laboratory, and University of Queensland [Brisbane]

Subjects
0301 basic medicine, Standardization, Neotropical Echinococcosis, MESH: Echinococcus, MESH: Echinococcus granulosus, Terminology, Reading (process), MESH: Animals, Alveolar Echinococcosis, 610 Medicine & health, media_common, Neotropical Echinococcosis: Echinococcus spp, biology, Publications, Reference Standards, 030108 mycology & parasitology, 16. Peace & justice, Echinococcosis, Linguistics, Infectious Diseases, MESH: Reference Standards, Research Article, MESH: Terminology as Topic, Consensus, Veterinary (miscellaneous), media_common.quotation_subject, MESH: Publications, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, MESH: Echinococcosis, Terminology as Topic, Echinococcus spp, medicine, Animals, Humans, Cystic Echinococcosis, Formalized consensus, lcsh:RC109-216, MESH: Consensus, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, MESH: Humans, Echinococcus granulosus, medicine.disease, biology.organism_classification, Agreement, Readability, Echinococcus, 030104 developmental biology, Insect Science, 570 Life sciences, Animal Science and Zoology, Parasitology, Adjective
Abstract

Echinococcoses require the involvement of specialists from nearly all disciplines; standardization of the terminology used in the field is thus crucial. To harmonize echinococcosis terminology on sound scientific and linguistic grounds, the World Association of Echinococcosis launched a Formal Consensus process. Under the coordination of a Steering and Writing Group (SWG), a Consultation and Rating Group (CRG) had the main missions of (1) providing input on the list of terms drafted by the SWG, taking into account the available literature and the participants' experience; and (2) providing independent rating on all debated terms submitted to vote. The mission of the Reading and Review Group (RRG) was to give an opinion about the recommendation paper in terms of readability, acceptability and applicability. The main achievements of this process were: (1) an update of the current nomenclature of Echinococcus spp.; (2) an agreement on three names of diseases due to Echinococcus spp.: Cystic Echinococcosis (CE), Alveolar Echinococcosis (AE) and Neotropical Echinococcosis (NE), and the exclusion of all other names; (3) an agreement on the restricted use of the adjective “hydatid” to refer to the cyst and fluid due to E. granulosus sensu lato; and (4) an agreement on a standardized description of the surgical operations for CE, according to the “Approach, cyst Opening, Resection, and Completeness” (AORC) framework. In addition, 95 “approved” and 60 “rejected” terms were listed. The recommendations provided in this paper will be applicable to scientific publications in English and communication with professionals. They will be used for translation into other languages spoken in endemic countries. © D.A. Vuitton et al., published by EDP Sciences, 2020, The Steering and Writing Committee would like to thank in particular Dr. Francesca Tamarozzi for her involvement in the fruitful exchanges between the WAE and the WHO-IWGE, and for her very helpful revision of the final manuscript.

Published
2020
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3. Assessing health-related quality of life in patients with heart failure: a systematic, standardized comparison of available measures

Author

Gemma Vilagut, Jordi Alonso, Luis Rajmil, Jose M Valderas, Dennis A. Revicki, Francis Guillemin, Michael Herdman, Montse Ferrer, Aida Ribera, Olatz Garin, CIBER de Epidemiología y Salud Pública (CIBERESP), IMIM-Hospital del Mar, Generalitat de Catalunya, Universitat Pompeu Fabra [Barcelona], Insight Consulting & Research, Universitat Autònoma de Barcelona [Barcelona] (UAB), Vall d'Hebron University Hospital [Barcelona], Agència d’Informació Avaluació i Qualitat en Salut (AIAQS ), Division Public Health and Primary Health Care [Oxford], University of Oxford [Oxford], Centre d'Epidémiologie Clinique (CIC-EC), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Institut National de la Santé et de la Recherche Médicale (INSERM), Maladies chroniques, santé perçue, et processus d'adaptation (APEMAC), Université Paris Descartes - Paris 5 (UPD5)-Université de Lorraine (UL), United BioSource Corporation, Universitat Pompeu Fabra [Barcelona] (UPF), Universitat Autònoma de Barcelona (UAB), Centre d'investigation clinique - Epidémiologie clinique [Nancy] (CIC-EC), Centre d'investigation clinique [Nancy] (CIC), and Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL)-Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL)

Subjects
medicine.medical_specialty, MEDLINE, Severity of Illness Index, Quality of life, Sickness Impact Profile, Surveys and Questionnaires, MESH: Severity of Illness Index, Severity of illness, Humans, Medicine, Health profile, In patient, MESH: Surveys and Questionnaires, Heart Failure, Health related quality of life, MESH: Humans, business.industry, MESH: Chronic Disease, Reproducibility of Results, MESH: Quality of Life, Health Status Disparities, Reference Standards, medicine.disease, humanities, 3. Good health, MESH: Health Status Disparities, MESH: Reproducibility of Results, MESH: Sickness Impact Profile, Heart failure, Chronic Disease, MESH: Heart Failure, Quality of Life, Physical therapy, MESH: Reference Standards, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Metric (unit), Cardiology and Cardiovascular Medicine, business
Abstract

To systematically evaluate available health-related quality of life (HRQL) instruments for use in patients with heart failure (HF). Seven HF-specific HRQL questionnaires and associated studies of their metric properties were identified by systematic review: the Chronic Heart Failure Assessment Tool, the Cardiac Health Profile congestive heart failure, the Chronic Heart Failure Questionnaire (CHFQ), the Kansas City Cardiomyopathy Questionnaire (KCCQ), the Left Ventricular Disease Questionnaire (LVDQ), the Minnesota Living with Heart Failure Questionnaire (MLHFQ), and the Quality of Life in Severe Heart Failure Questionnaire. Each instrument was assessed by four experts using a standardized tool for evaluating patient-reported outcomes (EMPRO; scores from 0 to 100). Four questionnaires were given adequate scores (median >50) for the attribute "conceptual model." The LVDQ had the highest rated median for "reliability" (72.8). The CHFQ, the KCCQ, and the MLHFQ all got reasonable scores for "validity" (from 54.4 to 76.4). The reviewers rated the KCCQ the highest in terms of "sensitivity to change" (median 94.4). Only the CHFQ (50.0) and the KCCQ (72.2) received adequate scores for the "interpretability" attribute. The most highly rated instruments based on the overall EMPRO score were the KCCQ (64.4) and the MLHFQ (60.7), followed by the CHFQ (59.2). Based on the first systematic and reliable expert-based evaluation of available HF-specific HRQL questionnaires, the evidence seems to support the choice of the KCCQ, the MLHFQ, and the CHFQ over the others, which require further research on metric properties. © 2013 Springer Science+Business Media New York.

Published
2013
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4. Current standards and new innovative approaches for treatment of pancreatic cancer

Author

Jean-Luc Van Laethem, Michel Ducreux, Ahmet Ayav, Florence Huguet, Jean-Baptiste Bachet, Caroline Caramella, Aurélien Lambert, Raphaël Maréchal, Thierry Conroy, Maladies chroniques, santé perçue, et processus d'adaptation (APEMAC), Université Paris Descartes - Paris 5 (UPD5)-Université de Lorraine (UL), Institut de Cancérologie de Lorraine - Alexis Vautrin [Nancy] (UNICANCER/ICL), UNICANCER, Service d'Hépato-Gastro-Entérologie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Chirurgie Digestive Hépatobiliaire et Endocrine [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Service d'oncologie-radiothérapie [CHU Tenon], CHU Tenon [AP-HP], Institut Gustave Roussy (IGR), Service de Gastro-Entérologie, d'Hépato-Pancréatologie et d'Oncologie Digestive - Endoscopie Digestive (hôpital Erasme), Hôpital Erasme [Bruxelles] (ULB), Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB)-Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), Institut de Cancérologie de Lorraine - Alexis Vautrin (ICL), Service d'Hépato-Gastroentérologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Service d’Oncologie-Radiothérapie [CHU Tenon], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Tenon [APHP], and Université Libre de Bruxelles [Bruxelles] (ULB)-Hôpital Erasme (Bruxelles)

Subjects
0301 basic medicine, Oncology, Cancer Research, Palliative care, Staging, FOLFIRINOX, medicine.medical_treatment, MESH: Therapies, Investigational, Targeted therapy, Imaging, 0302 clinical medicine, Antineoplastic Combined Chemotherapy Protocols, MESH: Molecular Targeted Therapy, Molecular Targeted Therapy, Precision Medicine, Neoadjuvant therapy, Therapies, Investigational, Palliative Care, MESH: Neoplasm Staging, Reference Standards, Neoadjuvant Therapy, 3. Good health, MESH: Antineoplastic Combined Chemotherapy Protocols, Chemotherapy, Adjuvant, MESH: Chemotherapy, Adjuvant, 030220 oncology & carcinogenesis, MESH: Palliative Care, MESH: Reference Standards, MESH: Pancreatic Neoplasms, MESH: Neoplasm Recurrence, Local, medicine.drug, Diagnostic Imaging, medicine.medical_specialty, MESH: Neoadjuvant Therapy, Adenocarcinoma, MESH: Precision Medicine, 03 medical and health sciences, Pancreatic cancer, Internal medicine, medicine, Humans, Chemotherapy, Survival rate, Neoplasm Staging, MESH: Humans, Radiotherapy, business.industry, MESH: Diagnostic Imaging, MESH: Adenocarcinoma, medicine.disease, Gemcitabine, Pancreatic Neoplasms, Radiation therapy, 030104 developmental biology, Surgery, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Neoplasm Recurrence, Local, business
Abstract

International audience; Pancreatic adenocarcinoma remains a devastating disease with a 5-year survival rate not exceeding 6%. Treatment of this disease remains a major challenge. This article reviews the state-of-the-art in the management of this disease and the new innovative approaches that may help to accelerate progress in treating its victims. After careful pre-therapeutic evaluation, only 15-20% of patients diagnosed with a pancreatic cancer (PC) are eligible for upfront radical surgery. After R0 or R1 resection in such patients, evidence suggests a significantly positive impact on survival of adjuvant chemotherapy comprising 6 months of gemcitabine or fluorouracil/folinic acid. Delayed adjuvant chemoradiation is considered as an option in cases of positive margins. Borderline resectable pancreatic cancer (BRPC) is defined as a tumour involving the mesenteric vasculature to a limited extend. Resection of these tumours is technically feasible, yet runs the high risk of a R1 resection. Neoadjuvant treatment probably offers the best chance of achieving successful R0 resection and long-term survival, but the best treatment options should be determined in prospective randomised studies. Gemcitabine has for 15 years been the only validated therapy for advanced PC. Following decades of negative phase III studies, increasing evidence now suggests that further significant improvements to overall survival can be achieved via either Folfirinox or gemcitabine + nab-paclitaxel regimens. Progress in systemic therapy may improve the chances of resection in borderline resectable pancreatic cancer (BRPC) or locally advanced PC. This requires first enhancing knowledge of the genetic events driving carcinogenesis, which may then be translated into clinical studies.

Published
2016
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5. Characterization of desoxymethyltestosterone main urinary metabolite produced from cultures of human fresh hepatocytes

Author

Donald Poirier, Julie Gauthier, Christiane Ayotte, Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), Centre de recherche du CHU de Québec-Université Laval (CRCHUQ), CHU de Québec–Université Laval, and Université Laval [Québec] (ULaval)-Université Laval [Québec] (ULaval)

Subjects
Desoxymethyltestosterone, Metabolite, Urinary system, medicine.medical_treatment, Clinical Biochemistry, MESH: Androstenols, Urine, Biology, 01 natural sciences, Biochemistry, Mass Spectrometry, Steroid, MESH: Hepatocytes, Synthesis, chemistry.chemical_compound, Endocrinology, MESH: Doping in Sports, Biosynthesis, Metabolites, medicine, Humans, Molecular Biology, Cells, Cultured, Doping in Sports, MESH: Mass Spectrometry, Pharmacology, Androstenols, MESH: Humans, Chromatography, 010405 organic chemistry, 010401 analytical chemistry, Organic Chemistry, Reference Standards, 3. Good health, 0104 chemical sciences, medicine.anatomical_structure, chemistry, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Hepatocyte, Hepatocytes, MESH: Reference Standards, GC-MS, Gas chromatography–mass spectrometry, MESH: Cells, Cultured
Abstract

International audience; Desoxymethyltestosterone (DMT; 17β-hydroxy-17α-methyl-5α-androst-2-ene) is a designer steroid present in hormonal supplements distributed illegally as such or in combination with other steroids, for self-administration. It figures on the list of substances prohibited in sports and its detection in athlete's urine samples is based upon the presence of the parent compound or the main urinary metabolite, which has not been characterized yet. Following its isolation from cultures of human fresh hepatocytes and S9 fractions of liver homogenates, we were able to identify this metabolite as being 17α-methyl-2β,3α,17β-trihydroxy-5α-androstane. Other minor metabolites were also characterized. The production, isolation, NMR, mass spectral analyses and chemical synthesis are presented.

Published
2012
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6. Quantification of 4-Methylimidazole in Class III and IV Caramel Colors: Validation of a New Method Based on Heart-Cutting Two-Dimensional Liquid Chromatography (LC-LC)

Author

Cédric Moretton, J. L. Rocca, Gérard Crétier, Henri Nigay, Nigay SA, TECHSEP - TECHniques de SEParations (2011-2014), Institut des Sciences Analytiques (ISA), Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

Subjects
4-TETRAHYDROXYBUTYL)IMIDAZOLE, Analytical chemistry, 4(5)-METHYLIMIDAZOLE, Caramel color, 01 natural sciences, ION-PAIR EXTRACTION, CARBON, chemistry.chemical_compound, HARMONIZATION, Tandem Mass Spectrometry, SFSTP PROPOSAL, 4-Methylimidazole, 4-methylimidazole, Coloring Agents, accuracy profile validation, Imidazoles, two-dimensional liquid chromatography, 04 agricultural and veterinary sciences, Reference Standards, 040401 food science, MESH: Reproducibility of Results, MASS-SPECTROMETRIC QUANTIFICATION, SEPARATION, MESH: Reference Standards, General Agricultural and Biological Sciences, QUANTITATIVE ANALYTICAL PROCEDURES, MESH: Coloring Agents, MESH: Imidazoles, food.ingredient, STRATEGIES, Mass spectrometry, 0404 agricultural biotechnology, food, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, caramel colors, Dichloromethane, Chromatography, 010401 analytical chemistry, Extraction (chemistry), Reproducibility of Results, MESH: Tandem Mass Spectrometry, General Chemistry, gas chromatography-mass spectrometry, MESH: Gas Chromatography-Mass Spectrometry, 0104 chemical sciences, chemistry, Two-dimensional chromatography, Gas chromatography, Gas chromatography–mass spectrometry, 2-ACETYL-4-(1, MESH: Chromatography, Liquid, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Chromatography, Liquid
Abstract

International audience; 4-Methylimidazole (4MeI) is a nitrogen compound formed during the manufacture of class III and IV caramel colors. The European Commission has limited its content to 250 ppm. Two methods were compared to perform 4MeI quantification in caramels. The first one, currently used and considered to be the reference method, consists of a hot extraction of caramel color with dichloromethane and an analysis of the acetyl derivative of the extract by gas chromatography coupled to mass spectrometry (GC-MS). The second method is based on the heart-cutting two-dimensional liquid chromatography technique (LC-LC) to directly separate 4MeI from the other components present in caramel color sample (diluted in water) in

Published
2011
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7. Proteome analysis of the culture environment supporting undifferentiated mouse embryonic stem and germ cell growth

Author

Christine Carapito, Nicolas Buhr, Agnès Hovasse, Stéphane Viville, Alain Van Dorsselaer, Christine Schaeffer, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Louis Pasteur - Strasbourg I, Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Proteomics, Clinical Biochemistry, Cell, Bioinformatics, Biochemistry, Analytical Chemistry, Mice, 0302 clinical medicine, MESH: Animals, Electrophoresis, Gel, Two-Dimensional, MESH: Embryonic Stem Cells, Cells, Cultured, reproductive and urinary physiology, 0303 health sciences, Ethical issues, Culture environment, MESH: Proteomics, Reference Standards, Cell biology, medicine.anatomical_structure, embryonic structures, Proteome, MESH: Pluripotent Stem Cells, MESH: Reference Standards, MESH: Gelatin, biological phenomena, cell phenomena, and immunity, Germ cell, MESH: Cells, Cultured, Pluripotent Stem Cells, Biology, Mouse embryonic fibroblast, MESH: Coculture Techniques, 03 medical and health sciences, MESH: Cell Proliferation, medicine, Animals, Fibroblast, MESH: Mice, Embryonic Stem Cells, Cell Proliferation, 030304 developmental biology, urogenital system, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Fibroblasts, MESH: Electrophoresis, Gel, Two-Dimensional, Embryonic stem cell, Coculture Techniques, Culture Media, MESH: Germ Cells, Germ Cells, MESH: Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, MESH: Fibroblasts, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, MESH: Culture Media, Gelatin, 030217 neurology & neurosurgery
Abstract

The therapeutical interest of pluripotent cells and ethical issues related to the establishment of human embryonic stem cell (ESC) or embryonic germ cell (EGC) lines raise the understanding of the mechanism underlying pluripotency to a fundamental issue. Establishing a protein pluripotency signature for these cells can be complicated by the presence of unrelated proteins produced by the culture environment. Here, we have analyzed the environment supporting ESC and EGC growth, and established 2-D reference maps for each constituent present in this culture environment: mouse embryonic fibroblast feeder cells, culture medium (CM) and gelatin. The establishment of these reference maps is essential prior to the study of ESC and EGC specific proteomes. Indeed, these maps can be subtracted from ESC or EGC maps to allow focusing on spots specific for ESCs or EGCs. Our study led to the identification of 110 unique proteins from fibroblast feeder cells and 23 unique proteins from the CM, which represent major contaminants of ESC and EGC proteomes. For gelatin, no collagen-specific proteins were identified, most likely due to difficulties in resolution and low quantities. Furthermore, no differences were observed between naive and conditioned CM. Finally, we compared these reference maps to ESC 2-D gels and isolated 17 ESC specific spots. Among these spots, proteins that had already been identified in previous human and mouse ESC proteomes were identified but no apparent ESC-specific pluripotency marker could be identified. This work represents an essential step in furthering the knowledge of environmental factors supporting ESC and EGC growth.

Published
2007
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8. Lipid composition of membranes ofEscherichia coli by liquid chromatography/tandem mass spectrometry using negative electrospray ionization

Author

Corinne Loutelier-Bourhis, Catherine Lange, Nicole Orange, Victor Norris, Sylvie Chevalier, Delphine Oursel, Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Normandie Université (NU)-Normandie Université (NU), Assemblages moléculaires : modélisation et imagerie SIMS (AMMIS), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), and Spectrométrie de Masse Bio-organique [Rouen]

Subjects
Spectrometry, Mass, Electrospray Ionization, Protein mass spectrometry, Acylation, Electrospray ionization, Mass spectrometry, Tandem mass spectrometry, MESH: Spectrometry, Mass, Electrospray Ionization, MESH: Membranes, 01 natural sciences, Sample preparation in mass spectrometry, Analytical Chemistry, 03 medical and health sciences, Tandem Mass Spectrometry, Liquid chromatography–mass spectrometry, Escherichia coli, Phospholipids, Spectroscopy, 030304 developmental biology, MESH: Phospholipids, MESH: Acylation, 0303 health sciences, Membranes, Chromatography, MESH: Escherichia coli, Chemistry, Fatty Acids, 010401 analytical chemistry, Organic Chemistry, MESH: Indicators and Reagents, MESH: Tandem Mass Spectrometry, Reference Standards, Lipids, MESH: Lipids, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Culture Media, MESH: Fatty Acids, 0104 chemical sciences, MESH: Culture Media, Mass spectrum, Indicators and Reagents, MESH: Reference Standards, lipids (amino acids, peptides, and proteins), MESH: Chromatography, Liquid, Chromatography, Liquid
Abstract

International audience; A liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method using reversed-phase chromatography was developed for the analysis of phospholipids from bacterial extracts of a wild-type strain of Escherichia coli. Product ion mass spectra from [M--H](-) precursor ions allowed an identification of individual phospholipid species that includes both fatty acid composition and fatty acyl location on the glycerol backbone using diagnostic product ions. Thus, complete assignment, including sn-1/sn-2 fatty acyl position, was achieved for this strain of E. coli. In addition, the phospholipids were quantified relative to one another using an internal standard method.

Published
2007
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9. The European competence network on mastocytosis (ECNM)

Author

Luis Escribano, Torsten Zuberbier, Hans-Jörg Bühring, Knut Brockow, Reza Parwaresch, Michel Arock, Margarida Lima, Jürgen Grabbe, Beate M. Henz, Peter Valent, Gianni Marone, Hans-Peter Horny, Klaus Wolff, Alberto Orfao, Hanneke C. Kluin-Nelemans, Wolfgang R. Sperr, Karl Sotlar, Karin Hartmann, Massimo Triggiani, Stephan C. Bischoff, Jaap J van Doormaal, Christian Sillaber, Manuela Födinger, Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Institute of Physics, Universidade de Brasilia [Brasília] (UnB), International Center for Condensed Matter Physics Brasilia, Division of Clinical Immunology and Allergy, Università degli studi di Napoli Federico II, Bioprofiles Ltd, Faculteit Medische Wetenschappen/UMCG, Damage and Repair in Cancer Development and Cancer Treatment - 1, Stem Cell Aging Leukemia and Lymphoma, Valent, P, Arock, M, Bischoff, Sc, Bühring, Hj, Brockow, K, Escribano, L, Födinger, M, Grabbe, J, Hartmann, K, Henz, Bm, Horny, Hp, Kluin Nelemans, Hc, Lima, M, Marone, Gianni, Orfao, A, Parwaresch, Rm, Sillaber, C, Sotlar, K, Sperr, Wr, Triggiani, M, Van Doormaal, Jj, Wolff, K, and Zuberbier, T.

Subjects
Malignant Mastocytosis, Standardization, Consensus Development Conferences as Topic, International Cooperation, mast cells, Disease, 0302 clinical medicine, Multicenter Studies as Topic, MAST-CELL LEUKEMIA, Systemic mastocytosis, Referral and Consultation, Randomized Controlled Trials as Topic, mastocytosis, MESH: Mast Cells, General Medicine, SYSTEMIC MASTOCYTOSIS, Reference Standards, competence network, 3. Good health, Europe, MESH: Research, 030220 oncology & carcinogenesis, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH: Reference Standards, MESH: Clinical Competence, Clinical Competence, c-kit mutations, medicine.medical_specialty, MALIGNANT MASTOCYTOSIS, MESH: Information Services, DIAGNOSIS, CLASSIFICATION, 03 medical and health sciences, MESH: Referral and Consultation, medicine, Humans, Medical physics, Competence (human resources), Information Services, standardization, MESH: Humans, criteria, business.industry, MESH: Consensus Development Conferences as Topic, Network on, Single component, Research, medicine.disease, Clinical trial, MESH: International Cooperation, MESH: Randomized Controlled Trials as Topic, 030228 respiratory system, Immunology, MESH: Mastocytosis, MESH: Multicenter Studies as Topic, MESH: Europe, business
Abstract

The European Competence Network on Mastocytosis (ECNM) is a Europe-wide, multinational cooperative approach attempting to improve recognition, diagnosis, and therapy of mastocytosis. The network is composed of local centers, physicians, and scientists who have dedicated their work to patients with mastocytosis. However, because of the rarity and complexity of the disease, each single component in the network alone would fail to meet important demands and to reach solid conclusions in this field of applied medicine. The ECNM represents an attempt to overcome this restriction as a cooperative multicenter platform that should serve as an important basis for the development of new therapeutic strategies and diagnostic concepts, and for the standardization of techniques used to determine diagnostic and prognostic parameters. Moreover, using future central databases and registries, a suitable infrastructure for the development of co-operative multicenter clinical trials will be established. In addition, the ECNM is dedicated to provide the best available information about the disease to patients and physicians.

Published
2004
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10. Software in pharmacy: functionalities and doers

Author

Brisset, C., Université de Poitiers - Faculté de Médecine et de Pharmacie, Université de Poitiers, Université de Poitiers, Faculté de Médecine et de Pharmacie, Delphine BON, François SEGUIN, and BRISSET, Charles

Subjects
MESH: Informatics, Medical Informatics Computing, MESH: Pharmacovigilance, carte vitale, ACM: K.: Computing Milieux/K.4: COMPUTERS AND SOCIETY/K.4.4: Electronic Commerce, Pharmacy, [INFO] Computer Science [cs], Officine, MESH: Database, Database, Pharmacovigilance, MESH: Software, Système Informatique de santé, groupement, dossier pharmaceutique, ACM: H.: Information Systems/H.2: DATABASE MANAGEMENT/H.2.0: General, group, MESH: Data Collection, [INFO]Computer Science [cs], Pharmacie, Free Software, ACM: K.: Computing Milieux/K.4: COMPUTERS AND SOCIETY/K.4.3: Organizational Impacts, base de données, OpenSource, logiciel métier, software, Linux, MESH: Comparative Study, Informatique, ACM: D.: Software, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, Logiciels Libres, MESH: Medical Informatics Computing, [SDV.SP] Life Sciences [q-bio]/Pharmaceutical sciences, MESH: Pharmacy, coopérative, MESH: Association, MESH: Reference Standards, logiciel de gestion d'officine
Abstract

Companion of the pharmacy since the introduction of the system SESAM-vitale in 1998, management softwares (aka Logiciels de gestion d'Officine) of pharmacy are becoming over the years, a key element of the French informatics tool. This work proposes an exhaustive list of softwares commercialized in France in 2014 and a list of their functionalities classified by order needs: obligatory, essential and optional functions and services given by editors. After that, this work deals with a development of the different doers and institutions that interact with those softwares, especially by describing organization where the pharmacists had an active participation. A brief table comparing editors is proposed. A generalist explanation of free software is given because they are used inside some of this professionalssoftwares. Then, analyses of teletransmission data are undertaken, before a series of tables ranking the various LGO softwares of the market by the functionalities, the operating system, the software of database used. Finally, a discussion concludes this work, Compagnon de l'Officine depuis la mise en place du système SESAM-Vitale en 1998, les logiciels de gestion d'officine (LGO) sont devenus au fil des années, un élément clé de l'outil informatique du pharmacien officinal. Cet ouvrage propose une liste exhaustive des logiciels de gestion d'officine (LGO) présents sur le marché français en 2014, un catalogue des fonctionnalités et services proposés par les éditeurs en les classant par ordre de nécessité: les fonctionnalités obligatoires d'un LGO, celles jugées indispensables, les fonctionnalités optionnelles et les services que proposent les éditeurs de LGO.Il poursuit avec un développement sur les différents acteurs et institutions qui interagissent avec ces logiciels, notamment en décrivant les structures où les pharmaciens ont eu une participation active. Un tableau succinct comparant les éditeurs est proposé.Une explication généraliste sur les logiciels libres est abordée, car ils sont utilisés au sein de certains de ces logiciels métiers. Une analyse des chiffres de la télétransmission est entreprise par la suite, avant une succession de tableaux classant les différents LGO du marché en fonction des fonctionnalités qu'ils proposent, les systèmes d'exploitations sur lesquels ils tournent, les moteurs de bases de données qu'ils utilisent.Enfin une discussion conclue ce travail.

Published
2014

11. Les logiciels de gestion d'officine: fonctionnalités et acteurs

Author

Brisset, C., Université de Poitiers - Faculté de Médecine et de Pharmacie, Université de Poitiers, Université de Poitiers, Faculté de Médecine et de Pharmacie, Delphine BON, and François SEGUIN

Subjects
MESH: Informatics, Medical Informatics Computing, MESH: Pharmacovigilance, carte vitale, ACM: K.: Computing Milieux/K.4: COMPUTERS AND SOCIETY/K.4.4: Electronic Commerce, Pharmacy, Officine, MESH: Database, Database, Pharmacovigilance, MESH: Software, Système Informatique de santé, groupement, dossier pharmaceutique, ACM: H.: Information Systems/H.2: DATABASE MANAGEMENT/H.2.0: General, group, MESH: Data Collection, [INFO]Computer Science [cs], Pharmacie, Free Software, ACM: K.: Computing Milieux/K.4: COMPUTERS AND SOCIETY/K.4.3: Organizational Impacts, base de données, OpenSource, logiciel métier, software, Linux, MESH: Comparative Study, Informatique, ACM: D.: Software, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, Logiciels Libres, MESH: Medical Informatics Computing, MESH: Pharmacy, coopérative, MESH: Association, MESH: Reference Standards, logiciel de gestion d'officine
Abstract

Companion of the pharmacy since the introduction of the system SESAM-vitale in 1998, management softwares (aka Logiciels de gestion d'Officine) of pharmacy are becoming over the years, a key element of the French informatics tool. This work proposes an exhaustive list of softwares commercialized in France in 2014 and a list of their functionalities classified by order needs: obligatory, essential and optional functions and services given by editors. After that, this work deals with a development of the different doers and institutions that interact with those softwares, especially by describing organization where the pharmacists had an active participation. A brief table comparing editors is proposed. A generalist explanation of free software is given because they are used inside some of this professionalssoftwares. Then, analyses of teletransmission data are undertaken, before a series of tables ranking the various LGO softwares of the market by the functionalities, the operating system, the software of database used. Finally, a discussion concludes this work; Compagnon de l'Officine depuis la mise en place du système SESAM-Vitale en 1998, les logiciels de gestion d'officine (LGO) sont devenus au fil des années, un élément clé de l'outil informatique du pharmacien officinal. Cet ouvrage propose une liste exhaustive des logiciels de gestion d'officine (LGO) présents sur le marché français en 2014, un catalogue des fonctionnalités et services proposés par les éditeurs en les classant par ordre de nécessité: les fonctionnalités obligatoires d'un LGO, celles jugées indispensables, les fonctionnalités optionnelles et les services que proposent les éditeurs de LGO.Il poursuit avec un développement sur les différents acteurs et institutions qui interagissent avec ces logiciels, notamment en décrivant les structures où les pharmaciens ont eu une participation active. Un tableau succinct comparant les éditeurs est proposé.Une explication généraliste sur les logiciels libres est abordée, car ils sont utilisés au sein de certains de ces logiciels métiers. Une analyse des chiffres de la télétransmission est entreprise par la suite, avant une succession de tableaux classant les différents LGO du marché en fonction des fonctionnalités qu'ils proposent, les systèmes d'exploitations sur lesquels ils tournent, les moteurs de bases de données qu'ils utilisent.Enfin une discussion conclue ce travail.

Published
2014

12. Characterization and multicentric validation of a common standard for Toxoplasma gondii detection using nucleic acid amplification assays

Author

Yvon Sterkers, Laurence Delhaes, Sophie Cassaing, Hervé Pelloux, Denis Filisetti, Emmanuelle Varlet-Marie, Feriel Touafek, Marie-Pierre Brenier-Pinchart, Hélène Yera, Patrick Bastien, Frédéric Dalle, Laboratoire de Parasitologie-Mycologie (CHU de Montpellier), Pôle Biologie-Pathologie [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Université de Montpellier (UM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Laboratoire de parasitologie-mycologie, CHU Grenoble, Service de Parasitologie et Mycologie, CHU Toulouse [Toulouse]-Institut Fédératif de Biologie (IFB) - Hôpital Purpan, Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse], Laboratoire de parasitologie mycologie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), FLAveur, VIsion et Comportement du consommateur (FLAVIC), Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Université de Bourgogne (UB), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), Service de Parasitologie-Mycologie [CHRU LIlle], Institut de Microbiologie [CHRU Lille], Pôle de Biologie Pathologie Génétique [CHU Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Pôle de Biologie Pathologie Génétique [CHU Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Laboratoire de parasitologie et mycologie médicale [CHU Strasbourg], CHU Strasbourg, Service de parasitologie - mycologie [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de parasitologie-mycologie [CHU Cochin], Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), We acknowledge the financial support of the 'RSI Assurance Maladie Professions Libérales—Provinces, C.A.M.P.L.P.' for buying the LightCycler 480 (Roche) real-time PCR equipment in Montpellier as well as that of the Institut de Veille Sanitaire (InVS)., We thank Florence Robert-Gangneux (CHU of Rennes) and Jean Menotti (Hôpital Saint-Louis, Paris) for fruitful discussions. We are grateful to Sylvie Matern and Rachel Huber (Strasbourg), Filomena Naji and Michèle Wauquier (Lille), Sylvie Douzou, Ghislaine Serres, and Bounleth Sanichanh (Montpellier), Catherine Barois (Grenoble), Anne Lamy, Raphaelle Laurenceau, Sandrine Chalmeton, Elodie Duthu, Séverine Gisquet, and Catherine Paris (Toulouse), and Cédric Rondot and Yacine Garaoun (Paris-Cochin) for technical assistance. We are indebted to Nathalie Van Langendonck (Academic Hospital of Tours) for providing AF samples. We are also grateful to Sebastien Besteiro (UMR CNRS 5235/University Montpellier 2, 'DIMNP') for providing the in vitro cultivated parasites., Pôle biologie Pathologie [CHRU Montpellier], Service de Parasitologie-Mycologie [Toulouse], Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Cochin [AP-HP]

Subjects
Microbiology (medical), MESH: Reference Standards, MESH: Molecular Diagnostic Techniques/methods, MESH: Parasite Load/standards, [SDV]Life Sciences [q-bio], Toxoplasma gondii, diagnostic, Parasitic loads, Parasite Load, MESH: Nucleic Acid Amplification Techniques/standards, MESH: Toxoplasma/isolation & purification, medicine, Molecular diagnostic techniques, Humans, National level, Reference standards, MESH: Parasite Load/methods, standardization, MESH: Humans, biology, MESH: Nucleic Acid Amplification Techniques/methods, Nucleic acid amplification technique, MESH: Toxoplasmosis/diagnosis, MESH: Molecular Diagnostic Techniques/standards, Reference Standards, biology.organism_classification, medicine.disease, Virology, Toxoplasmosis, quantification, 3. Good health, MESH: France, Molecular Diagnostic Techniques, Immunology, Nucleic acid, MESH: Toxoplasma/genetics, Parasitology, France, Nucleic Acid Amplification Techniques, Toxoplasma
Abstract

The molecular diagnosis of toxoplasmosis essentially relies upon laboratory-developed methods and suffers from lack of standardization, hence the large diversity of performances between laboratories. Moreover, quantifications of parasitic loads differ among centers, a fact which prevents the possible prediction of the severity of this disease as a function of parasitic loads. The objectives of this multicentric study performed in eight proficient laboratories of the Molecular Biology Pole of the French National Reference Center for Toxoplasmosis (NRC-T) were (i) to assess the suitability of a lyophilized preparation of Toxoplasma gondii as a common standard for use in this PCR-based molecular diagnosis and (ii) to make this standard available to the community. High-quality written procedures were used for the production and qualification of this standard. Three independent batches of this standard, containing concentrations ranging from 10 4 to 0.01 T. gondii genome equivalents per PCR, were first assessed: the linear dynamic range was ≥6 log, the intra-assay coefficients of variation (CV) from a sample containing 10 T. gondii organisms per PCR were 0.3% to 0.42%, and the interassay CV over a 2-week period was 0.76% to 1.47%. A further assessment in eight diagnostic centers showed that the standard is stable, robust, and reliable. These lyophilized standards can easily be produced at a larger scale when needed and can be made widely available at the national level. To our knowledge, this is the first quality control assessment of a common standard which is usable both for self-evaluation in laboratories and for accurate quantification of parasitic loads in T. gondii prenatal infections.

Published
2014
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13. The characterization and certification of a quantitative reference material for Legionella detection and quantification by qPCR

Author

M. Baume, C. Yardin, L. Garrelly, M. Reyrolle, S. Bouton, S. Jarraud, J.P. Facon, P.O. Fraisse, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Certification, Legionella, [SDV]Life Sciences [q-bio], Real-Time Polymerase Chain Reaction, Bioinformatics, Applied Microbiology and Biotechnology, MESH: Certification, 03 medical and health sciences, Limiting dilution, Reliability (statistics), 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, MESH: Real-Time Polymerase Chain Reaction, General Medicine, Reference Standards, biology.organism_classification, Reliability engineering, Certified reference materials, Primary standard, MESH: Reference Standards, Biotechnology, MESH: Legionella
Abstract

Aims The characterization and certification of a Legionella DNA quantitative reference material as a primary measurement standard for Legionella qPCR. Methods and Results Twelve laboratories participated in a collaborative certification campaign. A candidate reference DNA material was analysed through PCR-based limiting dilution assays (LDAs). The validated data were used to statistically assign both a reference value and an associated uncertainty to the reference material. Conclusions This LDA method allowed for the direct quantification of the amount of Legionella DNA per tube in genomic units (GU) and the determination of the associated uncertainties. This method could be used for the certification of all types of microbiological standards for qPCR. Significance and Impact of the Study The use of this primary standard will improve the accuracy of Legionella qPCR measurements and the overall consistency of these measurements among different laboratories. The extensive use of this certified reference material (CRM) has been integrated in the French standard NF T90-471 (April 2010) and in the ISO Technical Specification 12 869 (Anon 2012 International Standardisation Organisation) for validating qPCR methods and ensuring the reliability of these methods.

Published
2013
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14. Thyroid-stimulating hormone receptor antibody assays: recommendation for correct interpretation of results in Graves disease

Author

Catherine Massart, Michèle d’Herbomez, Unité Laboratoire CIC, Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM)-Pôle biologie, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes]-CHU Pontchaillou [Rennes], Pôle de Biologie Pathologie Génétique [CHU Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM)-Pôle biologie, and Université de Rennes (UR)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes]-CHU Pontchaillou [Rennes]

Subjects
endocrine system, medicine.medical_specialty, endocrine system diseases, Graves' disease, Clinical Biochemistry, 030209 endocrinology & metabolism, Trab, MESH: Graves Disease, Gastroenterology, Thyrotropin receptor, MESH: Calibration, MESH: Receptors, Thyrotropin, 03 medical and health sciences, 0302 clinical medicine, Pharmacotherapy, MESH: Practice Guidelines as Topic, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Internal medicine, medicine, Humans, ComputingMilieux_MISCELLANEOUS, Immunoassay, MESH: Humans, biology, business.industry, Biochemistry (medical), Thyroid, Receptors, Thyrotropin, Reference Standards, medicine.disease, Graves Disease, 3. Good health, medicine.anatomical_structure, Hormone receptor, Calibration, Practice Guidelines as Topic, Immunology, 030221 ophthalmology & optometry, biology.protein, Etiology, MESH: Reference Standards, Antibody, business, MESH: Immunoassay, MESH: Immunoglobulins, Thyroid-Stimulating, Immunoglobulins, Thyroid-Stimulating
Abstract

To the Editor: In Graves disease, the clinical uses of thyrotropin receptor [thyroid-stimulating hormone receptor (TSH-R)1] antibody (TRAb) measurements have been reported in the Thyroid Guidelines of the American Thyroid Association (1). First, TRAb measurements are used to investigate the etiology of hyperthyroidism when the diagnosis is not clinically obvious; second, a declining TRAb concentration during long-term antithyroid drug therapy is suggestive of remission, although TRAb measurements can be misleading in 25% of such patients; third, TRAb is used in the follow-up of pregnant women with a history or recent onset of Graves …

Published
2013
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15. Normal Reference Ranges for Echocardiography: Rationale, study design, and methodology (NORRE Study)

Author

Gerald Maurer, Jose David Rodrigo Carbonero, Andreas Hagendorff, Geneviève Derumeaux, Natela Akhaladze, Martin Penicka, Ralph Stephan von Bardeleben, Seisyou Kou, Krasimira Hristova, Roberto M. Lang, Julien Magne, Nuno Cardim, Teresa López, Dragos Vinereanu, Bogdan A. Popescu, Damien Voilliot, Tolga Rasit, Gilbert Habib, Jens-Uwe Voigt, Maurizio Galderisi, Daniele Barone, Patrizio Lancellotti, Monica Baroni, Gonzalo de la Morena, Alexandra Gonçalves, Alessandro Salustri, Thor Edvardsen, J. Zamorano, Erwan Donal, Raluca Elena Dulgheru, Nico Van de Veire, George Athanassopoulos, Luigi P. Badano, José Juan Gómez de Diego, Lancellotti, Patrizio, Badano, Luigi P., Lang, Roberto M., Akhaladze, Natela, Athanassopoulos, George D., Barone, Daniele, Baroni, Monica, Cardim, Nuno, Gomez De Diego, Jose Juan, Derumeaux, Genevieve, Dulgheru, Raluca, Edvardsen, Thor, Galderisi, Maurizio, Gonçalves, Alexandra, Habib, Gilbert, Hagendorff, Andrea, Hristova, Krasimira, Kou, Seisyou, Lopez, Teresa, Magne, Julien, De La Morena, Gonzalo, Popescu, Bogdan A., Penicka, Martin, Rasit, Tolga, Rodrigo Carbonero, Jose David, Salustri, Alessandro, Van De Veire, Nico, Von Bardeleben, Ralph Stephan, Vinereanu, Drago, Voigt, Jens Uwe, Voilliot, Damien, Zamorano, Jose Loui, Donal, Erwan, Maurer, Gerald, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-Research), Université de Liège, Cardiac Imaging Center, Rush University Medical Center [Chicago], Service de cardiologie, Université de la Méditerranée - Aix-Marseille 2-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Cardiology, University and Emergency Hospital, Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de cardiologie, Université médicale de Vienne, Autriche, Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Male, Radiology, Nuclear Medicine and Imaging, MESH: Echocardiography, Doppler, Left, Sex Factor, 030204 cardiovascular system & hematology, Doppler echocardiography, Doppler imaging, MESH: Stroke Volume, MESH: Ventricular Function, Left, Ventricular Function, Left, 030218 nuclear medicine & medical imaging, Heart Ventricle, Cohort Studies, 0302 clinical medicine, [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, Nuclear Medicine and Imaging, Ventricular Function, Age Factor, Prospective Studies, Prospective cohort study, MESH: Cohort Studies, MESH: Aged, 2D and 3D echocardiography, MESH: Middle Aged, medicine.diagnostic_test, Anthropometry, Age Factors, Doppler, General Medicine, Pulsed, Reference Standards, reference values, Middle Aged, Cardiac mechanic, Echocardiography, Doppler, 3. Good health, Europe, MESH: Echocardiography, Doppler, Pulsed, Cardiac mechanics, Echocardiography, MESH: Reference Standards, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Female, Radiology, Cardiology and Cardiovascular Medicine, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Cohort study, Chamber size and function, M-mode, Adult, Aged, Echocardiography, Doppler, Pulsed, Heart Ventricles, Humans, Sensitivity and Specificity, Sex Factors, Stroke Volume, Human, medicine.medical_specialty, 03 medical and health sciences, MESH: Sex Factors, MESH: Anthropometry, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, medicine, Medical physics, MESH: Age Factors, Reproducibility, MESH: Humans, business.industry, reference value, MESH: Adult, MESH: Male, MESH: Prospective Studies, MESH: Sensitivity and Specificity, Surgery, Clinical trial, Prospective Studie, Sample size determination, Reference Standard, Observational study, MESH: Europe, MESH: Heart Ventricles, Cohort Studie, business, MESH: Female
Abstract

International audience; BACKGROUND: Availability of normative reference values for cardiac chamber dimensions, volumes, mass, and function is a prerequisite for the accurate application of echocardiography for both clinical and research purposes. However, due to the lack of consistency in current echocardiographic 'reference values', their use for clinical decision-making remains questionable. AIMS: The aim of the 'Normal Reference Ranges for Echocardiography Study (NORRE Study)' is to obtain a set of 'normal values' for cardiac chamber geometry and function in a large cohort of healthy Caucasian individuals aged over a wide range of ages (25-75 years) using both conventional and advanced echocardiographic techniques. METHODS: The NORRE Study is a large prospective, observational multicentre study in which transthoracic echocardiographic studies will be acquired in 22 laboratories accredited by the European Association of Cardiovascular Imaging and in one laboratory in the USA accredited by ICAEL. The final sample size has been estimated in 1100 normal subjects in whom M-mode, 2D, and 3D imaging, colour Doppler, pulsed-wave Doppler, pulsed-wave tissue Doppler, and colour tissue Doppler imaging data will be obtained. All studies will be sent to a central echocardiographic core laboratory for quantitative analysis. Multiple studies will be performed for reproducibility analysis. CONCLUSION: After completion of the NORRE Study, uniform reference limits according to age, gender, and anthropometric parameters will be available to standardize the quantitative interpretation of echocardiography.

Published
2013
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16. Quantitative PCR pitfalls: the case of the human placenta

Author

Dave Lanoix, Cathy Vaillancourt, Joey St-Pierre, Maude Ethier-Chiasson, Sean C. Taylor, Julie Lafond, Andrée-Anne Lacasse, Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), BioMed Research Centre [Montréal], Institut National de la Recherche Scientifique [Québec] (INRS)-Université du Québec à Trois-Rivières (UQTR)-Université du Québec à Montréal = University of Québec in Montréal (UQAM), Bio-Rad Laboratories (Canada) Ltd, BIO-RAD, Laboratoire de Physiologie materno-foetale, Department of Biological Sciences, Biomed Research Center, and This study was financially supported by grants from the Natural Sciences and Engineering Research Council of Canada (NSERC # 262011-2009)

Subjects
Male, MESH: Sequence Analysis, DNA, MESH: Pre-Eclampsia, Placenta, MESH: Quality Control, Gene Expression, Bioinformatics, Applied Microbiology and Biotechnology, Biochemistry, DNA Glycosylases, MESH: Pregnancy, Pre-Eclampsia, Pregnancy, MESH: Reverse Transcriptase Polymerase Chain Reaction, Gene expression, MESH: DNA Glycosylases, Gestational diabetes, MESH: Diabetes, Gestational, Reverse Transcriptase Polymerase Chain Reaction, MESH: Real-Time Polymerase Chain Reaction, MESH: Research Design, MESH: Guidelines as Topic, Rna degradation, Reference Standards, MESH: Placenta, Real-time polymerase chain reaction, Research Design, MESH: Young Adult, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Female, MESH: Reference Standards, Biotechnology, RNA integrity, Adult, Quality Control, MESH: Gene Expression, Guidelines as Topic, Bioengineering, Biology, Real-Time Polymerase Chain Reaction, Specimen Handling, Young Adult, MESH: Gene Expression Profiling, MESH: RNA, Humans, Reference gene, MESH: Specimen Handling, Molecular Biology, Reference standards, MESH: Humans, Gene Expression Profiling, Human placenta, MESH: Adult, Sequence Analysis, DNA, Preeclampsia, Human genetics, MESH: Male, Real-time RT-PCR, Gene expression profiling, Diabetes, Gestational, RNA, 8-Oxoguanine DNA glycosylase, MESH: Female
Abstract

International audience; Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is a rapid and high throughput gene expression quantification technology. In order to obtain accurate results, several key experimental design and standardization steps must be rigorously followed as previously described in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. This study investigates the effect of reference gene normalization and the impact of RNA degradation on gene expression of 8-oxoguanine DNA glycosylase in human placenta from pregnancies complicated by preeclampsia and gestational diabetes mellitus and their gestation-matched controls. The data presented here show how RNA quality and appropriate reference gene selection is not only important to obtain accurate and reproducible RT-qPCR data but how different and even opposite results can be reported if the key steps outlined in the MIQE guidelines are not followed. The procedures and associated results presented in this study provide the first practical application of the MIQE guidelines to placental analysis in normal and pathological pregnancies.

Published
2012
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17. Should functional sensitivity of a new thyroid stimulating hormone immunoassay be monitored routinely? The ADVIA Centaur TSH3-UL assay experience

Author

Françoise Gasser, Béatrice Heurtault, Catherine Massart, Nathalie Reix, Arnaud Agin, Laboratoire d'Explorations Fonctionnelles par les Isotopes, Les Hôpitaux Universitaires de Strasbourg (HUS), Société Française de Médecine Nucléaire, Centre Antoine Béclère-Groupe de Biologie Spécialisée, Unité Laboratoire CIC, Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM)-Société Française de Médecine Nucléaire, Centre Antoine Béclère-Groupe de Biologie Spécialisée-Centre Antoine Béclère-Groupe de Biologie Spécialisée-Unité Fonctionnelle d'Hormonologie, Hôpital Pontchaillou, Conception et application de molécules bioactives (CAMB), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM)-Société Française de Médecine Nucléaire

Subjects
Quality Control, medicine.medical_specialty, endocrine system, Third-generation potential, endocrine system diseases, Clinical Biochemistry, MESH: Reagent Kits, Diagnostic, MESH: Quality Control, Thyrotropin, Thyroid-stimulating hormone, Enzyme-Linked Immunosorbent Assay, 030204 cardiovascular system & hematology, Sensitivity and Specificity, QC materials, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, Humans, Functional sensitivity, ADVIA Centaur, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Serum pool, MESH: Humans, medicine.diagnostic_test, business.industry, Reproducibility of Results, MESH: Enzyme-Linked Immunosorbent Assay, General Medicine, Reference Standards, MESH: Sensitivity and Specificity, 3. Good health, MESH: Reproducibility of Results, Endocrinology, 030220 oncology & carcinogenesis, Immunoassay, MESH: Thyrotropin, MESH: Reference Standards, Reagent Kits, Diagnostic, business, hormones, hormone substitutes, and hormone antagonists
Abstract

International audience; OBJECTIVES: We emphasize the importance of routine follow-up of subnormal TSH concentrations with QC materials. DESIGN AND METHODS: The functional sensitivity (FS) of the ADVIA Centaur system TSH assay was assessed. We report the values yielded for QC materials in two clinical laboratories. RESULTS: The FS was

Published
2012
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18. Comparison of serum and lithium-heparinate plasma for the accurate measurements of endogenous and exogenous morphine concentrations

Author

Laux-Biehlmann, Alexis, Gräfe, Nadja, Mouheiche, Jinane, Stuber, Denise, Welters, Ingeborg, Delalande, François, Poisbeau, Pierrick, Garnero, Patrick, Metz-Boutigue, Marie-Hélène, Schneider, Francis, Goumon, Yannick, Institut des Neurosciences Cellulaires et Intégratives (INCI), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Universitatsklinikum Giessen und Marburg [Marburg,Germany], University of Liverpool, Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Cisbio Bioassays [Codolet, France] (Innovation Management / CbB), Biomatériaux et ingénierie tissulaire, Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Réanimation Médicale [Strasbourg], Les Hôpitaux Universitaires de Strasbourg (HUS), and Goumon, Yannick

Subjects
MESH: Heparin, MESH: Humans, MESH: Lithium, MESH: Enzyme-Linked Immunosorbent Assay, MESH: Serum, [SCCO] Cognitive science, MESH: Analgesics, Opioid, Letter to the Editors, MESH: Calibration, MESH: Reproducibility of Results, [SCCO]Cognitive science, MESH: Morphine, MESH: Reference Standards, MESH: Specimen Handling, MESH: Plasma, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; No abstract available

Published
2012
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19. Stability of reference proteins in human placenta: general protein stains are the benchmark

Author

Julie Lafond, Dave Lanoix, Cathy Vaillancourt, Andrée-Anne Lacasse, Joey St-Pierre, M. Viau, Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), BioMed Research Centre [Montréal], Institut National de la Recherche Scientifique [Québec] (INRS)-Université du Québec à Trois-Rivières (UQTR)-Université du Québec à Montréal = University of Québec in Montréal (UQAM), Laboratoire de Physiologie materno-foetale, Department of Biological Sciences, Université du Québec à Montréal = University of Québec in Montréal (UQAM), and This study was financially supported by a grant from the Natural Sciences and Engineering Research Council of Canada (NSERC # 262011-2009) awarded to C Vaillancourt and from the Canadian Institute of Health Research (CIHR NET 2002-2007) awarded to J Lafond. D Lanoix received tudentships from the Fond de la recherche en Santé du Québec (FRSQ), AA Lacasse from the Fonds québécois de la recherche sur la nature et les technologies (FQRNT) and the NSERC and J St-Pierre from the Réseau Québécois en reproduction (RQR)-NSERC-CREATE and the Fondation Armand Frappier scholarship program.

Subjects
Adult, Peptidylprolyl isomerase A, Coefficient of variation, Placenta, Pregnancy Proteins, Young Adult, MESH: Pregnancy, Western blot, Pregnancy, MESH: Protein Stability, medicine, Humans, Diagnostic Techniques, Obstetrical and Gynecological, Glyceraldehyde 3-phosphate dehydrogenase, Serotonin transporter, MESH: Pregnancy Proteins, MESH: Humans, biology, medicine.diagnostic_test, Staining and Labeling, Protein Stability, MESH: Infant, Newborn, Infant, Newborn, Obstetrics and Gynecology, MESH: Adult, Reference Standards, MESH: Placenta, Molecular biology, MESH: Case-Control Studies, Staining, MESH: Diagnostic Techniques, Obstetrical and Gynecological, Pregnancy Complications, MESH: Staining and Labeling, medicine.anatomical_structure, Reproductive Medicine, Biochemistry, MESH: Young Adult, MESH: Pregnancy Complications, Case-Control Studies, [SDV.TOX]Life Sciences [q-bio]/Toxicology, biology.protein, Female, MESH: Reference Standards, Target protein, MESH: Female, Developmental Biology
Abstract

International audience; The stability of reference proteins in semi-quantitative Western blot experiments in normal and diseased placenta has never been studied. This study aims to determine the stability of five reference proteins and two general protein stains in placentas from preeclampsia, gestational diabetes mellitus and matched control pregnancies. The stability of the reference proteins was analysed using indicators of inter-group (P value) and intra-group (coefficient of variation) stability. The effect of different normalization strategies was determined by normalizing serotonin transporter (SERT) expression against the different reference protein markers. Results show significant expression variability of β-actin, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), hypoxanthine phosphoribosyltransferase 1 (HPRT1), peptidylprolyl isomerase A (PPIA) and α-tubulin, and that amido black staining is the most stable reference protein marker. Furthermore, results show that SERT expression significantly differs according to the reference protein markers used for its normalization. The present study demonstrated the importance of using stable reference protein markers and normalization strategy in order to get correct results in semi-quantitative Western blot experiments in placental tissues.

Published
2012
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20. BEaST: brain extraction based on nonlocal segmentation technique

Author

Vladimir Fonov, D. Louis Collins, Brandon Whitcher, Hakon Grydeland, Pierrick Coupe, Yongxia (Sharon) Zhou, Lasse Riis ؘstergaard, Pierre Payoux, Simon Eskildsen, Jeffrey Looi, Eric Jouvent, Jens Pruessner, Harald Hampel, Christian Gaser, Freimut Juengling, Herve Lemaitre, McConnell Brain Imaging Centre (MNI), Montreal Neurological Institute and Hospital, McGill University = Université McGill [Montréal, Canada]-McGill University = Université McGill [Montréal, Canada], Aalborg University [Denmark] (AAU), ITACA, Universitat Politècnica de València (UPV), Dementia Research Centre [London] (DRC), University College of London [London] (UCL), This work has been supported by funding from the Canadian Institutes of Health Research MOP-84360 & MOP-111169 as well as CDA (CECR)-Gevas-OE016. KKL acknowledges support from the MRC, ARUK and the NIHR. The Dementia Research Centre is an Alzheimer's Research UK Co-ordinating Centre and has also received equipment funded by the Alzheimer's Research UK. This work has been partially supported by the Spanish Health Institute Carlos III through the RETICS Combiomed, RD07/0067/2001., The Alzheimer's Disease Neuroimaging Initiative, Coupé, Pierrick, Neurology, ANS - Amsterdam Neuroscience, and AMS - Amsterdam Movement Sciences

Subjects
Male, Databases, Factual, Computer science, MESH: Quality Control, [INFO.INFO-IM] Computer Science [cs]/Medical Imaging, Brain mapping, 030218 nuclear medicine & medical imaging, MESH: Magnetic Resonance Imaging, 0302 clinical medicine, multi-resolution, [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], [STAT.AP] Statistics [stat]/Applications [stat.AP], Alzheimer Centre [DCN PAC - Perception action and control NCEBP 11], Image Processing, Computer-Assisted, skull stripping, Segmentation, Computer vision, False Negative Reactions, MESH: Brain Mapping, MESH: False Negative Reactions, Brain Mapping, [STAT.AP]Statistics [stat]/Applications [stat.AP], Skull stripping, medicine.diagnostic_test, patch-based segmentation, Brain, Reference Standards, Magnetic Resonance Imaging, MESH: Image Processing, Computer-Assisted, 3. Good health, MESH: Reproducibility of Results, medicine.anatomical_structure, Neurology, Patch-based segmentation, MESH: Young Adult, Multi-resolution, Female, MESH: Reference Standards, [SDV.IB]Life Sciences [q-bio]/Bioengineering, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Algorithms, MRI, Adult, Quality Control, Brain development, Adolescent, MESH: Computers, [INFO.INFO-TS] Computer Science [cs]/Signal and Image Processing, Cognitive Neuroscience, Image processing, MESH: Algorithms, Young Adult, 03 medical and health sciences, MESH: Software, MESH: Brain, Neuroimaging, Atlas (anatomy), medicine, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, Humans, False Positive Reactions, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Alzheimer Centre [NCEBP 11], Brain extraction, [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing, MESH: Adolescent, [SDV.IB] Life Sciences [q-bio]/Bioengineering, MESH: Humans, MESH: False Positive Reactions, Computers, business.industry, Brain morphometry, Reproducibility of Results, Magnetic resonance imaging, Pattern recognition, MESH: Adult, Image segmentation, BET, MESH: Databases, Factual, MESH: Male, [STAT.ML] Statistics [stat]/Machine Learning [stat.ML], FISICA APLICADA, Artificial intelligence, business, MESH: Female, Software, 030217 neurology & neurosurgery
Abstract

Brain extraction is an important step in the analysis of brain images. The variability in brain morphology and the difference in intensity characteristics due to imaging sequences make the development of a general purpose brain extraction algorithm challenging. To address this issue, we propose a new robust method (BEaST) dedicated to produce consistent and accurate brain extraction. This method is based on nonlocal segmentation embedded in a multi-resolution framework. A library of 80 priors is semi-automatically constructed from the NIH-sponsored MRI study of normal brain development, the International Consortium for Brain Mapping, and the Alzheimer's Disease Neuroimaging Initiative databases. In testing, a mean Dice similarity coefficient of 0.9834 ± 0.0053 was obtained when performing leave-one-out cross validation selecting only 20 priors from the library. Validation using the online Segmentation Validation Engine resulted in a top ranking position with a mean Dice coefficient of 0.9781 ± 0.0047. Robustness of BEaST is demonstrated on all baseline ADNI data, resulting in a very low failure rate. The segmentation accuracy of the method is better than two widely used publicly available methods and recent state-of-the-art hybrid approaches. BEaST provides results comparable to a recent label fusion approach, while being 40 times faster and requiring a much smaller library of priors., Data collection and sharing for this project was funded by the Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904). ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: Abbott, AstraZeneca AB, Bayer Schering Pharma AG, Bristol-Myers Squibb, Eisai Global Clinical Development, Elan Corporation, Genentech, GE Healthcare, GlaxoSmithKline, Innogenetics, Johnson and Johnson, Eli Lilly and Co., Medpace, Inc., Merck and Co., Inc., Novartis AG, Pfizer Inc, F. Hoffman-La Roche, Schering-Plough, Synarc, Inc., as well as non-profit partners the Alzheimer's Association and Alzheimer's Drug Discovery Foundation, with participation from the U.S. Food and Drug Administration. Private sector contributions to ADNI are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimer's Disease Cooperative Study at the University of California, San Diego. ADNI data are disseminated by the Laboratory for Neuro Imaging at the University of California, Los Angeles. This research was also supported by NIH grants P30AG010129, K01 AG030514, and the Dana Foundation.

Published
2012
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21. Evaluation of Registration Methods on Thoracic CT: The EMPIRE10 Challenge

Author

Julia A. Schnabel, Olivier Commowick, Grégoire Malandain, Kaifang Du, Mattias P. Heinrich, Jamie R. McClelland, M. de Bruijne, Nicholas Ayache, Max A. Viergever, Manuel Werlberger, Nicholas J. Tustison, Sascha E. A. Muenzing, Nassir Navab, Jan Ehrhardt, Dante De Nigris, Kunlin Cao, Marc Modat, Xiang Deng, Martin Urschler, D. L. Collins, James C. Gee, Cristian Lorenz, Gregory C. Sharp, Berend C. Stoel, Joseph M. Reinhardt, Rui Li, Xiao Han, Keelin Murphy, Jef Vandemeulebroucke, Simon Rit, M. Peroni, Tom Vercauteren, Sven Kabus, Stefan Klein, Marius Staring, Nikos Paragios, Gang Song, Dirk Loeckx, Dirk Smeets, David Sarrut, Sebastien Ourselin, Josien P. W. Pluim, B. van Ginneken, Jon Sporring, V. Garcia, Alexander Schmidt-Richberg, Kai Ding, Vladlena Gorbunova, Ben Glocker, Brian B. Avants, René Werner, Tal Arbel, Gary E. Christensen, Mark Jenkinson, Image sciences institute - University of Utrecht (ISI), University Medical Center [Utrecht], Department of Electrical and Computer Engineering [Iowa], University of Iowa [Iowa City], Philips Research [Germany], Philips Research, Siemens [Beijing], China Corporate Technology, State Key Laboratory of Chemical Engineering (Polymerization Division), Zhejiang University, Service DREAM, Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Mauna Kea Technologies, Analysis and Simulation of Biomedical Images (ASCLEPIOS), Vision, Action et Gestion d'informations en Santé (VisAGeS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SIGNAUX ET IMAGES NUMÉRIQUES, ROBOTIQUE (IRISA-D5), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Computer Aided Medical Procedures & Augmented Reality (CAMPAR), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Organ Modeling through Extraction, Representation and Understanding of Medical Image Content (GALEN), Ecole Centrale Paris-Inria Saclay - Ile de France, Mathématiques Appliquées aux Systèmes - EA 4037 (MAS), Ecole Centrale Paris, Department of Computer Science [Copenhagen] (DIKU), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Biomedical Imaging Group [Rotterdam] (BIG), Erasmus University Medical Center [Rotterdam] (Erasmus MC), CMS Software, Elekta Inc. [Maryland Heights], Institute of Biomedical Engineering [Oxford] (IBME), University of Oxford [Oxford], Department of Clinical Neurology [Oxford], University of Oxford [Oxford]-FMRIB Centre- John Radcliffe Hospital [Oxford University Hospital], Centre for Medical Image Computing (CMIC), University College of London [London] (UCL), Centre for Intelligent Machines (CIM), McGill University = Université McGill [Montréal, Canada], Montreal Neurological Institute and Hospital, McConnell Brain Imaging Centre (MNI), McGill University = Université McGill [Montréal, Canada]-McGill University = Université McGill [Montréal, Canada], Massachusetts General Hospital [Boston], Institute of Medical Informatics [Lübeck], Universität zu Lübeck [Lübeck], Medical imaging research center [Leuven], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven)-Faculty of Engineering, Penn Image Computing & Science Lab [Philadelphia] (PICSL), University of Pennsylvania [Philadelphia], Department of radiology and medical imaging [Charlottesville], University of Virginia [Charlottesville], Division of image processing [Leiden], Leiden University Medical Center (LUMC)-Department of Radiology, Institute for Computer Graphics and Vision [Graz] (ICG), Graz University of Technology [Graz] (TU Graz), Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Imagerie Tomographique et Radiothérapie, Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Commowick, Olivier, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Ecole Centrale Paris, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Oxford, University of Oxford-FMRIB Centre- John Radcliffe Hospital [Oxford University Hospital], Universität zu Lübeck = University of Lübeck [Lübeck], University of Pennsylvania, University of Virginia, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Electronics and Informatics, Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden-Department of Radiology, Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Medical Image Analysis, Rehabilitation Medicine, Radiology & Nuclear Medicine, and Neurology

Subjects
Databases, Factual, Computer science, Software Validation, [INFO.INFO-IM] Computer Science [cs]/Medical Imaging, Computed tomography, Aetiology, screening and detection [ONCOL 5], MESH: Observer Variation, 030218 nuclear medicine & medical imaging, Task (project management), 0302 clinical medicine, MESH: Animals, Segmentation, Observer Variation, evaluation, Radiological and Ultrasound Technology, medicine.diagnostic_test, Reference Standards, Thorax, Computer Science Applications, Test (assessment), Radiographic Image Enhancement, MESH: Reproducibility of Results, Chest, Radiographic Image Interpretation, Computer-Assisted, Radiography, Thoracic, MESH: Reference Standards, [SDV.IB]Life Sciences [q-bio]/Bioengineering, MESH: Tomography, X-Ray Computed, Algorithms, medicine.medical_specialty, MESH: Sheep, Image registration, MESH: Algorithms, Sensitivity and Specificity, MESH: Thorax, lung, Set (abstract data type), 03 medical and health sciences, registration, MESH: Radiographic Image Interpretation, Computer-Assisted, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, Medical imaging, medicine, Animals, MESH: Lung, Medical physics, Electrical and Electronic Engineering, [SDV.IB] Life Sciences [q-bio]/Bioengineering, Sheep, MESH: Software Validation, Information retrieval, Poverty-related infectious diseases [N4i 3], computed tomography, Image segmentation, MESH: Radiography, Thoracic, MESH: Databases, Factual, MESH: Sensitivity and Specificity, MESH: Radiographic Image Enhancement, Algorithm design, reproducibility of results, Tomography, X-Ray Computed, 030217 neurology & neurosurgery, Software
Abstract

Contains fulltext : 96888.pdf (Publisher’s version ) (Open Access) EMPIRE10 (Evaluation of Methods for Pulmonary Image REgistration 2010) is a public platform for fair and meaningful comparison of registration algorithms which are applied to a database of intrapatient thoracic CT image pairs. Evaluation of nonrigid registration techniques is a nontrivial task. This is compounded by the fact that researchers typically test only on their own data, which varies widely. For this reason, reliable assessment and comparison of different registration algorithms has been virtually impossible in the past. In this work we present the results of the launch phase of EMPIRE10, which comprised the comprehensive evaluation and comparison of 20 individual algorithms from leading academic and industrial research groups. All algorithms are applied to the same set of 30 thoracic CT pairs. Algorithm settings and parameters are chosen by researchers expert in the configuration of their own method and the evaluation is independent, using the same criteria for all participants. All results are published on the EMPIRE10 website (http://empire10.isi.uu.nl). The challenge remains ongoing and open to new participants. Full results from 24 algorithms have been published at the time of writing. This paper details the organization of the challenge, the data and evaluation methods and the outcome of the initial launch with 20 algorithms. The gain in knowledge and future work are discussed.

Published
2011
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22. Systematic review reveals heterogeneity in definition of a clinically relevant difference in pain

Author

Ruyssen-Witrand, Adeline, Tubach, Florence, Ravaud, Philippe, Modèles et méthodes de l'évaluation thérapeutique des maladies chroniques (U738 / UMR_S738), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7), Département d'épidémiologie, biostatistique et recherche clinique, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)

Subjects
Clinical trials, MESH: Analgesics, MESH: Humans, MESH: Randomized Controlled Trials as Topic, clinically relevant, group or patient perspective, treatment outcome, data interpretation, MESH: Reference Standards, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Pain, MESH: Pain Measurement, pain measurement
Abstract

International audience; OBJECTIVE: To describe the pain decrease considered as clinically relevant when designing a trial and reporting its results. METHODS: A systematic review of the literature in MEDLINE was conducted to select randomized controlled trials (RCTs) with pain as a primary outcome. Data extracted included the definition (terms and values) of a clinically relevant difference in pain, the type of pain studied (acute or chronic), the level of application (group or individual) of the clinically relevant difference, and the reference justifying the choice of value for clinically relevant difference. STUDY DESIGN AND SETTING: Seventy-four trials were included, and only 16 articles justified the choice of a value for clinically relevant difference with a reference citation. The values chosen for the clinically relevant relative decrease in pain varied from 4 to 40 mm or from 15% to 55% at the group level and from 20 to 50 mm at the individual level. In seven articles, the authors confused the application of the reference value at the individual or group level. CONCLUSION: Our review revealed a great heterogeneity in definition, format, and values of what is considered a clinically relevant difference in pain in RCTs of analgesics, and standardizations are advisable.

Published
2011
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23. Toward a standardized urine proteome analysis methodology

Author

Mariette Matondo, Nathalie Selevsek, Jérôme Garin, Yves Allory, Bruno Domon, Christophe Masselon, Magali Court, Laboratoire d'étude de la dynamique des protéomes (LEDyP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute of Molecular Systems Biology [Zurich], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Plateforme de Ressources Biologiques [Henri Mondor AP-HP, Créteil] (PRB), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Henri Mondor [Créteil], Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Luxembourg Clinical Proteomics Center [Luxembourg], Luxembourg Institute of Health (LIH), This work was funded through the EU FP7 program DECanBio (www.decanbio.eu) [grant agreement ♯201333]. The Decon‐2LS and VIPER software used for data processing were provided by the W. R. Wiley Environmental Molecular Science Laboratory, a national scientific user facility sponsored by the US Department of Energy's Office of Biological and Environmental Research, located at PNNL. PNNL is operated by Battelle Memorial Institute for the US Department of Energy under contract DE‐AC05‐76RL0 1830. B.D. acknowledges the Luxembourg FNR (PEARL grant)., Dr. Dimitri Vordos and Edwige Lopes, Hopital Mondor in Paris, are gratefully acknowledged for their assistance in the specimen collection. The authors thank Dr. Christophe Bruley, CEA Grenoble, for his help with AMT tag database compilation, and Madalen LeGorrec, CEA Grenoble, for the protein dosage and the pools constitution. The authors are also grateful to Dr. Markus Fisher and Dr. Monika Litchenauer, Entelechon GmbH, for the QconCAT design and synthesis. The authors thank Dr. Elodie Duriez for her comments and helpful discussion. The authors also express gratitude to all the members of the DECanBio consortium for their help and advice., DECanBio consortium (www.decanbio.eu), France, European Project: 201333,EC:FP7:HEALTH,FP7-HEALTH-2007-A,DECANBIO(2008), CHU Henri Mondor-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Henri Mondor, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10

Subjects
Proteomics, Technology, Proteome, Clinical Biochemistry, MESH: Quality Control, MESH: Amino Acid Sequence, MESH: Peptides / standards, computer.software_genre, Biochemistry, 01 natural sciences, Tandem Mass Spectrometry, Sample preparation, Databases, Protein, 0303 health sciences, Chemistry, Reference Standards, MESH: Proteomics / methods, Proteinuria, MESH: Proteome / standards, Selected reaction monitoring, MESH: Reference Standards, Sample collection, Data mining, Quality Control, MESH: Databases, Protein, MESH: Proteomics / statistics & numerical data, MESH: Tandem Mass Spectrometry / standards, MESH: Peptides / urine, MESH: Tandem Mass Spectrometry / statistics & numerical data, 03 medical and health sciences, Urinary proteomics, MESH: Proteome / analysis, MESH: Chromatography, Liquid / standards, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, MESH: Proteinuria / urine, Molecular Biology, 030304 developmental biology, Protocol (science), Reproducibility, Chromatography, MESH: Humans, MESH: Biomarkers / urine, AMT tag, 010401 analytical chemistry, MESH: Proteomics / standards, Standardization, Biomarker (cell), 0104 chemical sciences, MESH: Peptides / chemistry, Peptides, computer, Biomarkers, Chromatography, Liquid
Abstract

International audience; Urine is an easily accessible bodily fluid particularly suited for the routine clinical analysis of disease biomarkers. Actually, the urinary proteome is more diverse than anticipated a decade ago. Hence, significant analytical and practical issues of urine proteomics such as sample collection and preparation have emerged, in particular for large-scale studies. We have undertaken a systematic study to define standardized and integrated analytical protocols for a biomarker development pipeline, employing two LC-MS analytical platforms, namely accurate mass and time tags and selected reaction monitoring, for the discovery and verification phase, respectively. Urine samples collected from hospital patients were processed using four different protocols, which were evaluated and compared on both analytical platforms. Addition of internal standards at various stages of sample processing allowed the estimation of protein extraction yields and the absolute quantification of selected urinary proteins. Reproducibility of the entire process and dynamic range of quantification were also evaluated. Organic solvent precipitation followed by in-solution digestion provided the best performances and was thus selected as the standard method common to the discovery and verification phases. Finally, we applied this protocol for platforms' cross-validation and obtained excellent consistency between urinary protein concentration estimates by both analytical methods performed in parallel in two laboratories.

Published
2011
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24. Systematic quantification of peptides/proteins in urine using selected reaction monitoring

Author

Mariette Matondo, Bruno Domon, Ruedi Aebersold, Nathalie Selevsek, Marta Sanchez Carbayo, Institute of Molecular Systems Biology [Zurich], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Spanish National Cancer Research Center (CNIO), Universität Zürich [Zürich] = University of Zurich (UZH), Luxembourg Clinical Proteomics Center [Luxembourg], Luxembourg Institute of Health (LIH), This study was supported by the FP7 Program DECanBio (Coordinator: Jérôme Garin). The Fonds National de la Recherche (FNR) of the Grand Duchy of Luxembourg is acknowledged (PEARL grant)., The authors thank Jérôme Garin, Christophe Masselon, Elodie Duriez, and Martin Soste for their comments and helpful discussions. The authors also thank their clinical collaborators, the hospitals in Salamanca, Oviedo, Barcelona, Guadalajara, and Córdoba for providing the clinical samples analyzed in this study., and European Project: 201333,EC:FP7:HEALTH,FP7-HEALTH-2007-A,DECANBIO(2008)

Subjects
Proteomics, MESH: Clusterin / urine, Technology, Clinical Biochemistry, Analytical chemistry, MESH: Quality Control, MESH: Amino Acid Sequence, Urine, MESH: Peptides / standards, Tandem mass spectrometry, Biochemistry, 0302 clinical medicine, Tandem Mass Spectrometry, Multiplex, Sample preparation, 0303 health sciences, Chemistry, 030302 biochemistry & molecular biology, Bladder cancer, Reference Standards, Immunohistochemistry, MESH: Case-Control Studies, MESH: Hyaluronan Receptors / urine, MESH: Proteomics / methods, MESH: Reproducibility of Results, MESH: Urine / chemistry, Proteinuria, Hyaluronan Receptors, 030220 oncology & carcinogenesis, Data Interpretation, Statistical, Selected reaction monitoring, MESH: Reference Standards, Quality Control, MESH: Proteomics / statistics & numerical data, Analyte, MESH: Tandem Mass Spectrometry / standards, Molecular Sequence Data, MESH: Peptides / urine, MESH: Tandem Mass Spectrometry / statistics & numerical data, 03 medical and health sciences, MESH: Analysis of Variance, MESH: Biomarkers, Tumor / urine, Biomarkers, Tumor, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, MESH: Proteinuria / urine, Molecular Biology, 030304 developmental biology, Reproducibility, Analysis of Variance, Chromatography, MESH: Molecular Sequence Data, MESH: Humans, Reproducibility of Results, MESH: Proteomics / standards, MESH: Immunohistochemistry, MESH: Urinary Bladder Neoplasms / urine, Clusterin, Urinary Bladder Neoplasms, Case-Control Studies, MESH: Peptides / chemistry, Peptides, Quantitative analysis (chemistry), MESH: Chromatography, Liquid, MESH: Data Interpretation, Statistical, Biomarkers, Chromatography, Liquid
Abstract

International audience; The evaluation of biomarkers in bodily fluids necessitates the development of robust methods to quantify proteins in a complex background, using large sets of samples. The ability to multiplex numerous analytes in a single assay expedites the process. Liquid chromatography-mass spectrometry (LC-MS) analyses performed in selected reaction monitoring (SRM) in conjunction with stable isotope dilution MS present an effective way to detect and quantify biomarker candidates in bodily fluids. The strategy presented involves an initial qualification of predefined sets of proteins in urine. The technique was applied to detect and quantify peptides in urine samples as surrogates for a few endogenous proteins. Multiplexed assays were developed to analyze proteins associated with bladder cancer; a few exogenous proteins were added as internal standards. The sample preparation and the analytical protocols were optimized to ensure reproducibility, analytical precision, and quantification limits in the low nanogram per milliliter range. Analyses were performed using known amounts of isotopically labeled peptides. Systematic replication of the measurements indicated intra-assay and inter-assay variability, with CVs in the range of 10%. The differences measured for two targeted proteins were correlated with their level of expression in the corresponding tumors using immunohistochemistry.

Published
2011
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25. Systematic review reveals heterogeneity in definition of a clinically relevant difference in pain

Author

Ruyssen-Witrand, Adeline, Tubach, Florence, Ravaud, Philippe, Gillet, Catherine, Modèles et méthodes de l'évaluation thérapeutique des maladies chroniques (U738 / UMR_S738), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département d'épidémiologie, biostatistique et recherche clinique, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)

Subjects
MESH: Analgesics, MESH: Humans, clinically relevant, data interpretation, MESH: Pain Measurement, pain measurement, Clinical trials, MESH: Randomized Controlled Trials as Topic, group or patient perspective, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, treatment outcome, MESH: Reference Standards, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Pain
Abstract

International audience; OBJECTIVE: To describe the pain decrease considered as clinically relevant when designing a trial and reporting its results. METHODS: A systematic review of the literature in MEDLINE was conducted to select randomized controlled trials (RCTs) with pain as a primary outcome. Data extracted included the definition (terms and values) of a clinically relevant difference in pain, the type of pain studied (acute or chronic), the level of application (group or individual) of the clinically relevant difference, and the reference justifying the choice of value for clinically relevant difference. STUDY DESIGN AND SETTING: Seventy-four trials were included, and only 16 articles justified the choice of a value for clinically relevant difference with a reference citation. The values chosen for the clinically relevant relative decrease in pain varied from 4 to 40 mm or from 15% to 55% at the group level and from 20 to 50 mm at the individual level. In seven articles, the authors confused the application of the reference value at the individual or group level. CONCLUSION: Our review revealed a great heterogeneity in definition, format, and values of what is considered a clinically relevant difference in pain in RCTs of analgesics, and standardizations are advisable.

Published
2011
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26. Multicenter collaborative study for standardization of Candida albicans genotyping using a polymorphic microsatellite marker

Author

Stéphane Bretagne, Paula Sampaio, Dea Garcia-Hermoso, Corné H. W. Klaassen, Frédéric Grenouillet, Donna M. MacCallum, Maria-José Buitrago Serna, Timothy J. Lott, Centre National de Référence Mycologie et Antifongiques-Mycologie Moléculaire (CNRMA), Institut Pasteur [Paris], Laboratoire Chrono-environnement - UFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Hôpital Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre National de Référence Mycologie et Antifongiques-Mycologie Moléculaire ( CNRMA ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Biologie moléculaire et immunologie parasitaires et fongiques ( BIPAR ), Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -AFSSA-Ecole Nationale Vétérinaire d'Alfort-Institut National de la Recherche Agronomique ( INRA ), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut Pasteur [Paris] (IP), Laboratoire Chrono-environnement (UMR 6249) (LCE), and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie

Subjects
Interlaboratory reproducibility, MESH : Polymorphism, Genetic, MESH : Genotype, MESH: Molecular Diagnostic Techniques, MESH : Microsatellite Repeats, MESH: Genotype, Genotype, Candida albicans, Polymorphic Microsatellite Marker, [ SDV.MP.MYC ] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Genetics, 0303 health sciences, biology, Reference Standards, Bacterial Typing Techniques, MESH: Reproducibility of Results, Molecular Diagnostic Techniques, MESH: Laboratories, Microsatellite, MESH: Reference Standards, Microbiology (medical), MESH : Candida albicans, Mycology, MESH : Laboratories, MESH: Bacterial Typing Techniques, 03 medical and health sciences, Genetic, MESH: Polymorphism, Genetic, Typing, Polymorphism, Reference standards, Genotyping, Alleles, 030304 developmental biology, Polymorphism, Genetic, 030306 microbiology, MESH : Reproducibility of Results, MESH: Alleles, MESH: Candida albicans, Reproducibility of Results, biology.organism_classification, MESH : Reference Standards, MESH : Bacterial Typing Techniques, MESH: Microsatellite Repeats, Laboratories, MESH : Alleles, MESH : Molecular Diagnostic Techniques, Microsatellite Repeats
Abstract

Microsatellite-based genotyping for Candida albicans can give discrepant results between laboratories when expressed in fragment sizes, because their determination depends on electrophoretic conditions. The interlaboratory reproducibility was assessed in six laboratories provided with an allelic ladder. Despite variations in size determinations, alleles were correctly assigned, making data transportable between laboratories.

Published
2010
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27. Reproducibility of joint swelling assessment by sonography in patients with long-lasting rheumatoid arthritis (SEA-Repro study part II)

Author

Christophe Hudry, Jérémie Sellam, Maxime Dougados, M.A. D'Agostino, F. Etchepare, Cécile Hacquard, Isabelle Chary Valckenaere, Gérard Chalès, Jean David Albert, Sandrine Jousse-Joulin, Laurent Grange, Alain Saraux, Thierry Marhadour, Jacques Bentin, Damien Loeuille, Philippe Gaudin, Immunologie et Pathologie (EA2216), Université de Brest (UBO)-IFR148, Service de Rhumatologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Ambroise Paré [AP-HP], Service de rhumatologie [Rennes] = Rheumatology [Rennes], CHU Pontchaillou [Rennes], Service de Rhumatologie, CHU Brugmann, CHU Brugmann, Belgium, Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de rhumatologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Foie, métabolismes et cancer, Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Physiopathologie, Pharmacologie et Ingénierie articulaires (PPIA), Université Henri Poincaré - Nancy 1 (UHP)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche Saint-Antoine (UMRS893), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de rhumatologie [CHU Pitié Salpêtrière] (GRC-08 EEMOIS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Ambroise Paré, Service de rhumatologie, Hôpital Sud, Service de Rhumatologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], CHU Cochin [AP-HP]-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Centre de Recherche Saint-Antoine (CR Saint-Antoine), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Immunologie et Pathologie ( EA2216 ), Université de Brest ( UBO ) -IFR148, Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Ambroise Paré, Centre Hospitalier Régional Universitaire de Nancy ( CHRU Nancy ), Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Pitié-Salpêtrière [APHP], Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Cochin [AP-HP], Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Physiopathologie, Pharmacologie et Ingénierie articulaires ( PPIA ), Université Henri Poincaré - Nancy 1 ( UHP ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche Saint-Antoine ( CR Saint-Antoine ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité ( CRESS (U1153 / UMR_A 1125) ), Institut National de la Recherche Agronomique ( INRA ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Cochin [AP-HP]

Subjects
Male, Settore MED/16 - REUMATOLOGIA, MESH: Synovitis, MESH : Aged, Severity of Illness Index, Arthritis, Rheumatoid, 0302 clinical medicine, Cohen's kappa, Rheumatoid, Immunology and Allergy, [ SDV.IMM ] Life Sciences [q-bio]/Immunology, MESH : Female, 030212 general & internal medicine, Disease activity, MESH : Joints, Ultrasonography, MESH : Synovitis, MESH: Aged, MESH: Arthritis, Rheumatoid, Synovitis, MESH: Middle Aged, medicine.diagnostic_test, Doppler, Middle Aged, Reference Standards, MESH : Ultrasonography, Doppler, MESH: Reproducibility of Results, MESH: Joints, Rheumatoid arthritis, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH : Severity of Illness Index, Female, MESH: Reference Standards, Long lasting, medicine.medical_specialty, MESH : Male, Immunology, Physical examination, 03 medical and health sciences, Rheumatology, MESH: Severity of Illness Index, Ultrasound, medicine, Humans, In patient, MESH : Middle Aged, Aged, 030203 arthritis & rheumatology, Reproducibility, MESH: Humans, business.industry, MESH : Reproducibility of Results, Arthritis, MESH : Humans, Reproducibility of Results, Ultrasonography, Doppler, medicine.disease, MESH: Male, Surgery, Sonographer, MESH : Arthritis, Rheumatoid, MESH : Reference Standards, MESH: Ultrasonography, Doppler, Joints, Nuclear medicine, business, MESH: Female
Abstract

Objective.To evaluate the intraobserver and interobserver reproducibility of B-mode and power Doppler (PD) sonography in patients with active long-standing rheumatoid arthritis (RA) comparatively with clinical data.Methods.In each of 7 patients being considered for a change in their RA treatment regimen, 7 healthcare professionals examined the 28 joints used in the Disease Activity Score 28-joint count (DAS28). Then 7 sonographers examined each of the 7 patients twice, using previously published B-mode and PD grading systems. The clinical reference standard was presence of synovitis according to at least 4/7 examiners. The sonographic reference standard was at least grade 1 (ALG1) or 2 (ALG2) synovitis according to at least 4/7 sonographers. Interobserver reproducibility of sonography was assessed versus the sonographer having the best intraobserver reproducibility. Agreement was measured by Cohen’s kappa statistic.Results.Intraobserver and interobserver reproducibility of B-mode and PD used separately was fair to good. Agreement between clinicians and sonographers at all sites using B-mode, PD, and both was 0.46, 0.37, and 0.36, respectively, for grade 1 synovitis; and 0.58, 0.19, and 0.19 for grade 2 synovitis. The number of joints with synovitis was smaller by physical examination (36.7%) than by B-mode with ALG1 (58.6%; p < 0.001). The number of joints with synovitis was higher by physical examination than by PD with both ALG1 (17.8%; p < 0.0001) and ALG2 (6.6%; p < 0.0001).Conclusion.PD findings explain most of the difference between clinical and sonographic joint assessments for synovitis in patients with long-standing RA.

Published
2010
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28. Potential of an age adjusted D-dimer cut-off value to improve the exclusion of pulmonary embolism in older patients: a retrospective analysis of three large cohorts

Author

Pieter Willem Kamphuisen, Marieke J. H. A. Kruip, Marc Philip Righini, Pierre-Marie Roy, Grégoire Le Gal, Henri Bounameaux, Renée A. Douma, Maaike Sohne, Harry R. Büller, Arnaud Perrier, Department of Vascular Medicine (DVM - AMC), Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA)-University of Amsterdam [Amsterdam] (UvA), Centre d'Investigation Clinique (CIC - Brest), Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM), Groupe d'Etude de la Thrombose de Bretagne Occidentale (GETBO), Université de Brest (UBO)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO), Service d'angiologie et d'hémostase (MR), Hôpital Universitaire de Genève, Division of Internal General Medicine (DIGM), University of Geneva [Switzerland], Department of Haematology (DH - Rotterdam), Erasmus Medical Centre, Centre de Recherche Clinique (CRC Angers), Université d'Angers (UA)-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Faculteit der Geneeskunde, Hematology, Cardiovascular Centre (CVC), Vascular Ageing Programme (VAP), Vascular Medicine, and ACS - Amsterdam Cardiovascular Sciences

Subjects
Male, MESH: Pulmonary Embolism, validity, Pediatrics, retrospective study, 030204 cardiovascular system & hematology, 0302 clinical medicine, MESH: Aged, 80 and over, Belgium, Older patients, Medicine, 030212 general & internal medicine, Biological Markers/blood, comparative study, Netherlands, General Environmental Science, ddc:616, Aged, 80 and over, MESH: Aged, receiver operating characteristic, MESH: Middle Aged, article, Age Factors, General Engineering, General Medicine, Middle Aged, Reference Standards, cohort analysis, 3. Good health, Pulmonary embolism, priority journal, D dimer, Female, MESH: Reference Standards, diagnostic value, France, lung embolism, Switzerland, Cohort study, Adult, medicine.medical_specialty, Age adjustment, Pulmonary Embolism/*diagnosis, Fibrin Fibrinogen Degradation Products, 03 medical and health sciences, D-dimer, MESH: Fibrin Fibrinogen Degradation Products, false negative result, Humans, controlled study, Fibrin Fibrinogen Degradation Products/*analysis, human, Derivation, Aged, Retrospective Studies, MESH: Age Factors, MESH: Humans, Receiver operating characteristic, business.industry, MESH: Biological Markers, Retrospective cohort study, MESH: Adult, MESH: Retrospective Studies, MESH: ROC Curve, medicine.disease, major clinical study, MESH: Male, ROC Curve, General Earth and Planetary Sciences, Pulmonary Embolism, business, MESH: Female, Biomarkers, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Objectives In older patients, the the D-dimer test for pulmonary embolism has reduced specificity and is therefore less useful. In this study a new, age dependent cut-off value for the test was devised and its usefulness with older patients assessed. Design Retrospective multicentre cohort study. Setting General and teaching hospitals in Belgium, France, the Netherlands, and Switzerland. Patients 5132 consecutive patients with clinically suspected pulmonary embolism. Intervention Development of a new D-dimer cut-off point in patients aged >50 years in a derivation set (data from two multicentre cohort studies), based on receiver operating characteristics (ROC) curves. This cut-off value was then validated with two independent validation datasets. Main outcome measures The proportion of patients in the validation cohorts with a negative D-dimer test, the proportion in whom pulmonary embolism could be excluded, and the false negative rates. Results The new D-dimer cut-off value was defined as (patient's age x 10) mu g/l in patients aged >50. In 1331 patients in the derivation set with an "unlikely" score from clinical probability assessment, pulmonary embolism could be excluded in 42% with the new cut-off value versus 36% with the old cut-off value (70 years, ranging from 13% to 16% in the three datasets. The failure rates (all ages) were 0.2% (95% CI 0% to 1.0%) in the derivation set and 0.6% (0.3% to 1.3%) and 0.3% (0.1% to 1.1%) in the two validation sets. Conclusions The age adjusted D-dimer cut-off point, combined with clinical probability, greatly increased the proportion of older patients in whom pulmonary embolism could be safely excluded.

Published
2010
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29. Reproducibility of joint swelling assessments in long-lasting rheumatoid arthritis: Influence on disease activity score-28 values (SEA-repro study part I)

Author

Laurent Grange, Jean-David Albert, Christophe Hudry, Jérémie Sellam, F. Etchepare, Cécile Hacquard, Sandrine Jousse-Joulin, M.A. D'Agostino, Maxime Dougados, Thierry Marhadour, Alain Saraux, Philippe Gaudin, Gérard Chalès, Isabelle Chary Valckenaere, Jacques Bentin, Damien Loeuille, Immunologie et Pathologie (EA2216), Université de Brest (UBO)-IFR148, Service de rhumatologie [Rennes] = Rheumatology [Rennes], CHU Pontchaillou [Rennes], Foie, métabolismes et cancer, Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Service de Rhumatologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Ambroise Paré [AP-HP], Physiopathologie, Pharmacologie et Ingénierie articulaires (PPIA), Université Henri Poincaré - Nancy 1 (UHP)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche Saint-Antoine (UMRS893), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Rhumatologie, CHU Brugmann, CHU Brugmann, Belgium, CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de rhumatologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de rhumatologie, Hôpital Sud, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Ambroise Paré, Centre de Recherche Saint-Antoine (CR Saint-Antoine), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Service de Rhumatologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], CHU Cochin [AP-HP]-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Service de rhumatologie [CHU Pitié Salpêtrière] (GRC-08 EEMOIS), Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Cochin [AP-HP], Immunologie et Pathologie ( EA2216 ), Université de Brest ( UBO ) -IFR148, Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre Hospitalier Régional Universitaire de Nancy ( CHRU Nancy ), Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Ambroise Paré, Physiopathologie, Pharmacologie et Ingénierie articulaires ( PPIA ), Université Henri Poincaré - Nancy 1 ( UHP ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche Saint-Antoine ( CR Saint-Antoine ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Pitié-Salpêtrière [APHP], Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Cochin [AP-HP], Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité ( CRESS (U1153 / UMR_A 1125) ), and Institut National de la Recherche Agronomique ( INRA ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM )

Subjects
Male, Settore MED/16 - REUMATOLOGIA, MESH: Synovitis, MESH : Aged, Arthritis, Severity of Illness Index, Arthritis, Rheumatoid, 0302 clinical medicine, Cohen's kappa, Rheumatoid, [ SDV.IMM ] Life Sciences [q-bio]/Immunology, Immunology and Allergy, MESH : Female, MESH : Joints, Ultrasonography, MESH : Synovitis, MESH: Aged, MESH: Arthritis, Rheumatoid, MESH: Middle Aged, Synovitis, Disease activity score-28, Technician, Middle Aged, Reference Standards, Reproducibility, MESH: Reproducibility of Results, MESH: Joints, Rheumatoid arthritis, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH : Severity of Illness Index, MESH: Reference Standards, Female, musculoskeletal diseases, medicine.medical_specialty, MESH : Male, Immunology, Rheumatoid Arthritis, Disease activity, 03 medical and health sciences, Rheumatology, MESH: Severity of Illness Index, Severity of illness, medicine, Humans, MESH : Middle Aged, Joint swelling, Aged, 030203 arthritis & rheumatology, MESH: Humans, business.industry, MESH : Reproducibility of Results, MESH : Humans, Reproducibility of Results, medicine.disease, MESH: Male, MESH : Reference Standards, MESH : Arthritis, Rheumatoid, Physical therapy, Joints, business, MESH: Female, 030215 immunology
Abstract

Objectives.To evaluate the reproducibility of clinical synovitis assessments in rheumatoid arthritis and the effect of variability on the Disease Activity Score-28 (DAS28).Methods.Seven healthcare professionals from different cities examined the same patients with active non-early rheumatoid arthritis (RA; duration > 4 yrs), for whom a treatment change was being considered. There was no training session and the examination was to be performed as quickly as possible. The healthcare professionals assessed the 28 joints of the DAS28 in 7 patients (196 joints), then reexamined the same 28 joints in 4 of these 7 patients (112 joints), who had been rendered unrecognizable. Then 7 sonographers examined each of the 7 patients twice, using B-mode and power Doppler ultrasound (PD). The reference standards were presence of synovitis according to at least 50% of clinical examiners and 50% of sonographers. Agreement was assessed by Cohen’s kappa statistic.Results.Intraobserver reliability ranged from 0.31 (least experienced research technician) to 0.77 (most experienced physician). Interobserver reliability ranged from 0.18 to 0.62. The largest difference between the lowest and the highest swollen joint counts in the same patient was 15, and the greatest variation in the DAS28 score was 0.92. Agreement between clinical and sonographic reference standards was 0.46, 0.37, and 0.36 for B-mode, PD, and both, respectively.Conclusion.Clinical inter- and intraobserver reliability is highly dependent on the examiner. Consequences on the DAS28 score can be substantial. Agreement with sonography is poor when both B-mode and PD are used but seems better, although low, when B-mode is used alone.

Published
2010
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30. How surface composition of high milk proteins powders is influenced by spray-drying temperature

Author

Muriel Jacquot, Pierre Schuck, Claire Gaiani, E. Arab Tehrany, M. Morand, C. Sanchez, Joël Scher, Romain Jeantet, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
Protein Denaturation, MESH: Protein Structure, Quaternary, 030309 nutrition & dietetics, Surface concentration, MESH: Powders, MESH: Wettability, chemistry.chemical_compound, Colloid and Surface Chemistry, Casein, Spectroscopy, Fourier Transform Infrared, MESH: Animals, Food science, Lactose, 2. Zero hunger, Principal Component Analysis, 0303 health sciences, Chemistry, Photoelectron Spectroscopy, Temperature, 04 agricultural and veterinary sciences, Surfaces and Interfaces, General Medicine, Reference Standards, Elements, Milk Proteins, 040401 food science, Micellar casein, MESH: Temperature, MESH: Cattle, free-fat content, Spray drying, [SDV.IDA.SMA]Life Sciences [q-bio]/Food engineering/domain_sdv.ida.sma, Composition (visual arts), MESH: Reference Standards, Wetting, Powders, dried whole milk, Biotechnology, MESH: Milk Proteins, Surface Properties, ingredients, MESH: Spectroscopy, Fourier Transform Infrared, lactose, storage, lipids, 03 medical and health sciences, 0404 agricultural biotechnology, X-ray photoelectron spectroscopy, XPS, MESH: Photoelectron Spectroscopy, Animals, MESH: Lactose, MESH: Particle Size, Particle Size, Physical and Theoretical Chemistry, Protein Structure, Quaternary, Drying, MESH: Surface Properties, MESH: Principal Component Analysis, MESH: Elements, surface composition, MESH: Lipids, proteins, Whey Proteins, Wettability, phosphocaseinate, Cattle, native, MESH: Protein Denaturation, stabilized emulsions, Dairy powders
Abstract

High milk proteins powders are common ingredients in many food products. The surface composition of these powders is expected to play an essential role during their storage, handling and/or final application. Therefore, an eventual control of the surface composition by modifying the spray-drying temperature could be very useful in the improvement of powder quality and the development of new applications. For this purpose, the influence of five spray-drying temperatures upon the surface composition of the powders was investigated by X-ray photoelectron spectroscopy. The major milk proteins were studied: native micellar casein and native whey, both more or less enriched in lactose. The results show a surface enrichment in lipids for all the powders and in proteins for many powders. Whatever the drying temperature, lipids and proteins are preferentially located near the surface whereas lactose is found in the core. This surface enrichment is also highly affected by the spray-drying temperature. More lipids, more proteins and less lactose are systematically observed at the surface of powders spray-dried at lower outlet air temperatures. The nature of proteins is also found essential; surface enrichment in lipids being much stronger for whey proteins containing powders than for casein containing powders. Additionally, we found a direct correlation between the lipids surface concentration and the wetting ability for the 25 powders studied.

Published
2010
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31. Systematic review reveals heterogeneity in definition of a clinically relevant difference in pain.: Definition of clinically relevant difference in pain assessment

Author

Florence Tubach, Adeline Ruyssen-Witrand, Philippe Ravaud, Modèles et méthodes de l'évaluation thérapeutique des maladies chroniques (U738 / UMR_S738), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7), Département d'épidémiologie, biostatistique et recherche clinique, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)

Subjects
medicine.medical_specialty, Pathology, MESH: Analgesics, Epidemiology, clinically relevant, MEDLINE, data interpretation, Pain, MESH: Pain Measurement, law.invention, 03 medical and health sciences, 0302 clinical medicine, Primary outcome, Clinical trials, Randomized controlled trial, 030202 anesthesiology, law, medicine, Humans, Group level, Pain Measurement, Randomized Controlled Trials as Topic, Analgesics, MESH: Humans, business.industry, Data interpretation, Reference Standards, Individual level, 3. Good health, Clinical trial, MESH: Randomized Controlled Trials as Topic, group or patient perspective, Physical therapy, treatment outcome, Pain psychology, MESH: Reference Standards, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Pain, business, 030217 neurology & neurosurgery
Abstract

International audience; OBJECTIVE: To describe the pain decrease considered as clinically relevant when designing a trial and reporting its results. METHODS: A systematic review of the literature in MEDLINE was conducted to select randomized controlled trials (RCTs) with pain as a primary outcome. Data extracted included the definition (terms and values) of a clinically relevant difference in pain, the type of pain studied (acute or chronic), the level of application (group or individual) of the clinically relevant difference, and the reference justifying the choice of value for clinically relevant difference. STUDY DESIGN AND SETTING: Seventy-four trials were included, and only 16 articles justified the choice of a value for clinically relevant difference with a reference citation. The values chosen for the clinically relevant relative decrease in pain varied from 4 to 40 mm or from 15% to 55% at the group level and from 20 to 50 mm at the individual level. In seven articles, the authors confused the application of the reference value at the individual or group level. CONCLUSION: Our review revealed a great heterogeneity in definition, format, and values of what is considered a clinically relevant difference in pain in RCTs of analgesics, and standardizations are advisable.

Published
2009
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32. [Considerations for normalisation of RT-qPCR in oncology]

Author

A, Ho-Pun-Cheung, D, Cellier, E, Lopez-Crapez, Merck Santé - Lyon, Merck & Co. Inc, Département d'oncologie Médicale, CRLCC Val d'Aurelle - Paul Lamarque, Immunociblage et radiobiologie en oncologie, Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Le Ster, Yves

Subjects
Electrophoresis, DNA, Complementary, MESH: Gene Expression, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, RT-PCR, Gene Expression, Cell Count, MESH: Electrophoresis, Fluorescence, normalisation, Neoplasms, MESH: Reverse Transcriptase Polymerase Chain Reaction, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, cancer, MESH: Neoplasms, RNA, Messenger, RNA, Neoplasm, MESH: Models, Genetic, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, MESH: RNA, Messenger, housekeeping gene, MESH: Humans, Models, Genetic, Reverse Transcriptase Polymerase Chain Reaction, MESH: Cell Count, MESH: Fluorescence, MESH: DNA, Complementary, Reference Standards, MESH: RNA, Neoplasm, quantification, [SDV.BIO] Life Sciences [q-bio]/Biotechnology, [INFO.INFO-BT] Computer Science [cs]/Biotechnology, RNA, Ribosomal, MESH: RNA, Ribosomal, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Reference Standards
Abstract

International audience; Gene expression analysis has many applications in the management of cancer, including diagnosis, prognosis, and therapeutic care. In this context, the reverse transcription quantitative polymerase chain reaction (RT-qPCR) has become the "gold standard" for mRNA quantification. However, this technique involves several critical steps such as RNA extraction, cDNA synthesis, quantitative PCR, and analysis, which all can be source of variation. To obtain biologically meaningful results, data normalisation is required to correct sample-to-sample variations that may be introduced during this multistage process. Normalisation can be carried out against a housekeeping gene, total RNA mass, or cell number. Careful choice of the normalization method is crucial, as any variation in the reference will introduce errors in the quantification of mRNA transcripts. By reviewing the different methods available and their related problems, the aim of this article is to provide recommendations for the set up of an appropriate normalisation strategy for RT-qPCR data in oncology.

Published
2009
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33. Standardization of flow cytometry in myelodysplastic syndromes: report from the first European LeukemiaNet working conference on flow cytometry in myelodysplastic syndromes

Author

Gerrit Jan Schuurhuis, Theo de Witte, Theresia M. Westers, Anna Porwit, Matteo G. Della Porta, Alberto Orfao, Robin M. Ireland, Peter Valent, Michael R. Loken, Vincent H.J. van der Velden, Kiyoyuki Ogata, Detlef Haase, Jeroen G. te Marvelde, Patricia Font, Wolfgang Kern, Luca Malcovati, Jean Feuillard, Ulrich Germing, Angelika M. Dräger, A.H. Westra, Frank Preijers, Christa Homburg, Canan Alhan, Marie C. Béné, Arjan A. van de Loosdrecht, Ghulam J. Mufti, Dolores Subirá, Paresh Vyas, Stephen J. Richards, Gert J. Ossenkoppele, Denise A. Wells, Joop H. Jansen, Hematology, Immunology, Physiologie Moléculaire de la Réponse Immune et des Lymphoproliférations (PMRIL), Université de Limoges (UNILIM)-Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST FR CNRS 3503)-Centre National de la Recherche Scientifique (CNRS), Hematology laboratory, and CCA - Disease profiling

Subjects
Oncology, medicine.medical_specialty, MESH: Immunophenotyping, Decision Making and Problem Solving, CD34, MESH: Flow Cytometry, 03 medical and health sciences, European LeukemiaNet, 0302 clinical medicine, Immunophenotyping, Immune Regulation [NCMLS 2], Translational research [ONCOL 3], Internal medicine, Medicine, MESH: Antigens, CD, Cytopenia, MESH: Humans, business.industry, Myelodysplastic syndromes, Myeloid leukemia, Hematology, medicine.disease, 3. Good health, medicine.anatomical_structure, Dysplasia, 030220 oncology & carcinogenesis, Immunology, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH: Reference Standards, Bone marrow, business, myelodysplastic syndromes, flow cytometry, standardization, ELN, consensus, MESH: Myelodysplastic Syndromes, 030215 immunology
Abstract

Contains fulltext : 81483.pdf (Publisher’s version ) (Open Access) The myelodysplastic syndromes are a group of clonal hematopoietic stem cell diseases characterized by cytopenia(s), dysplasia in one or more cell lineages and increased risk of evolution to acute myeloid leukemia (AML). Recent advances in immunophenotyping of hematopoietic progenitor and maturing cells in dysplastic bone marrow point to a useful role for multiparameter flow cytometry (FCM) in the diagnosis and prognostication of myelodysplastic syndromes. In March 2008, representatives from 18 European institutes participated in a European LeukemiaNet (ELN) workshop held in Amsterdam as a first step towards standardization of FCM in myelodysplastic syndromes. Consensus was reached regarding standard methods for cell sampling, handling and processing. The group also defined minimal combinations of antibodies to analyze aberrant immunophenotypes and thus dysplasia. Examples are altered numbers of CD34(+) precursors, aberrant expression of markers on myeloblasts, maturing myeloid cells, monocytes or erythroid precursors and the expression of lineage infidelity markers. When applied in practice, aberrant FCM patterns correlate well with morphology, the subclassification of myelodysplastic syndromes, and prognostic scoring systems. However, the group also concluded that despite strong evidence for an impact of FCM in myelodysplastic syndromes, further (prospective) validation of markers and immunophenotypic patterns are required against control patient groups as well as further standardization in multi-center studies. Standardization of FCM in myelodysplastic syndromes may thus contribute to improved diagnosis and prognostication of myelodysplastic syndromes in the future.

Published
2009
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34. [Diagnostic strategy for chronic inflammatory demyelinating polyradiculoneuropathy. Recommendations of the French working group]

Author

Magy, Laurent, Service de Neurologie [CHU Limoges], CHU Limoges, Biomolécules Thérapies anti-tumorales (EA4021), and Université de Limoges (UNILIM)-Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST FR CNRS 3503)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, Electrodiagnosis, MESH: Immunologic Factors, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: Electrodiagnosis, Reference Standards, MESH: Polyradiculoneuropathy, Chronic Inflammatory Demyelinating, Polyradiculoneuropathy, Chronic Inflammatory Demyelinating, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, Immunologic Factors, MESH: Reference Standards, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; The diagnosis of chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) requires a careful clinical and neurophysiological evaluation, often completed by CSF analysis. In numerous cases, this diagnosis is straightforward and leads to rapid initiation of an immunomodulatory treatment. However, some patients are not diagnosed because of atypical clinical and/or neurophysiological features, and do not benefit from a potentially effective treatment. In this context, a working group was composed with the task of establishing recommendations on diagnostic strategies for CIDP in the main clinical situations where this diagnosis may be suspected. We have summarized these recommendations and tried to present them in the form of a decision-making algorithm.

Published
2008
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35. A liquid chromatography-mass spectrometry assay for simultaneous determination of two antimalarial thiazolium compounds in human and rat matrices

Author

Françoise Bressolle, Delphine Margout, Michèle Calas, Nicolas Taudon, Henri Vial, T. Kezutyte, Laboratoire de Chimie des Biomolécules et de l'Environnement (LCBE), Université de Perpignan Via Domitia (UPVD)-Université Montpellier 1 (UM1), Dynamique des interactions membranaires normales et pathologiques (DIMNP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), DMF, Ministère de la Culture et de la Communication (MCC), Laboratoire des Amino-acides Peptides et Protéines (LAPP), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Dynamique moléculaire des interactions membranaires (DMIM), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2), Département de Pharmacocinétique clinique, Université Montpellier 1 (UM1), and Clinical Pharmacokinetic Laboratory (CLINICAL PHARMACOKINETIC LABORATORY)

Subjects
Electrospray, Erythrocytes, Clinical Biochemistry, Pharmaceutical Science, MESH: Rats, Sprague-Dawley, Mass Spectrometry, Analytical Chemistry, MESH: Dose-Response Relationship, Drug, Rats, Sprague-Dawley, Plasma, Drug Stability, MESH: Practice Guidelines as Topic, Liquid chromatography–mass spectrometry, Drug Discovery, MESH: Animals, Solid phase extraction, Quadrupole mass analyzer, Spectroscopy, Whole blood, 0303 health sciences, Molecular Structure, Chemistry, MESH: Erythrocytes, Reference Standards, 3. Good health, MESH: Reproducibility of Results, Area Under Curve, Calibration, Practice Guidelines as Topic, MESH: Reference Standards, Half-Life, MESH: Half-Life, Spectrometry, Mass, Electrospray Ionization, MESH: Rats, Metabolic Clearance Rate, Electrospray ionization, MESH: Molecular Structure, MESH: Thiazoles, Mass spectrometry, Sensitivity and Specificity, MESH: Spectrometry, Mass, Electrospray Ionization, MESH: Calibration, 03 medical and health sciences, Antimalarials, MESH: Drug Stability, Protein precipitation, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Plasma, 030304 developmental biology, MESH: Mass Spectrometry, MESH: Metabolic Clearance Rate, Chromatography, MESH: Humans, Dose-Response Relationship, Drug, 030306 microbiology, Reproducibility of Results, MESH: Antimalarials, MESH: Sensitivity and Specificity, Rats, Thiazoles, MESH: Area Under Curve, MESH: Chromatography, Liquid, Chromatography, Liquid
Abstract

International audience; A new class of antimalarial drugs targeting phospholipid metabolism of the malarial parasite is now in development. In the strategy of this development, two mono-thiazolium salts, T1 and T2, need to be monitored. A liquid chromatography-mass spectrometry (LC-MS) method has been developed and validated according to FDA guidelines for simultaneous determination of T1 and T2 in plasma, whole blood and red blood cells (RBCs) from human and rat. The sample-pre-treatment procedure involved solid phase extraction after protein precipitation. Chromatography was carried out on a Zorbax eclipse XDB C8 column and mass spectrometric analysis was performed using an Agilent 1,100 quadrupole mass spectrometer working with an electrospray ionization source. LC-MS data were acquired in single ion monitoring mode at m/z 312, 326 and 227 for T1, T2 and the internal standard (T3), respectively. The drug/internal standard peak area ratios were linked via a quadratic relationship to concentrations (human and rat plasma: 2.25-900 microg/l; human blood and rat RBCs: 4.5-900 microg/kg). Precision was below 14.5% for T1 and below 13% for T2. Accuracy was 92.6-111% for T1 and 95.6-108% for T2. Extraction recoveries were >or=85% in plasma and >or=53% in blood and RBCs. For T1 and T2, the lower limits of quantitation were 2.25 microg/l in plasma, and 4.5 microg/kg in whole blood and RBCs. Stability tests under various conditions were also investigated. This highly specific and sensitive method was useful to analyse samples from pharmacokinetic studies carried out in rat and would also be useful in clinical trials at a later stage.

Published
2008
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36. Analysis of drug transporter expression in human intestinal Caco-2 cells by real-time PCR

Author

Nathalie Maubon, Marc Le Vee, Lina Fossati, Mathilde Audry, Sébastien Bolze, Eric Le Ferrec, Olivier Fardel, Signalisation et Réponses aux Agents Infectieux et Chimiques (SeRAIC), Université de Rennes (UR), Service d'Hématologie, Immunologie et de Thérapie Cellulaire (HITC), Université de Rennes (UR)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes]

Subjects
ATP Binding Cassette Transporter, Subfamily B, MESH: P-Glycoprotein, Cell, Organic Anion Transporters, ATP-binding cassette transporter, Biology, 030226 pharmacology & pharmacy, MESH: Membrane Transport Proteins, 03 medical and health sciences, 0302 clinical medicine, MESH: Reverse Transcriptase Polymerase Chain Reaction, medicine, Humans, Pharmacology (medical), ATP Binding Cassette Transporter, Subfamily B, Member 1, RNA, Messenger, Intestinal Mucosa, Caco-2 cells, intestine, 030304 developmental biology, MESH: RNA, Messenger, Pharmacology, MESH: Organic Anion Transporters, 0303 health sciences, Messenger RNA, MESH: Humans, Reverse Transcriptase Polymerase Chain Reaction, Multidrug resistance-associated protein 2, Membrane Transport Proteins, Transporter, Reference Standards, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, Multidrug Resistance-Associated Protein 2, 3. Good health, medicine.anatomical_structure, Real-time polymerase chain reaction, Biochemistry, Caco-2, transporter, MESH: Reference Standards, Efflux, MESH: Caco-2 Cells, Multidrug Resistance-Associated Proteins, real-time PCR, absorption, MESH: Multidrug Resistance-Associated Proteins, MESH: Intestines
Abstract

International audience; Expression of drug transporters corresponds to a crucial parameter in intestinal Caco-2 cells widely used for investigating drug absorption. In order to characterize it in an accurate, reproducible and comparative manner, we analyzed mRNA levels of 19 influx and efflux drug transporters through real-time quantitative polymerase chain reaction assays combined with the use of a total RNA reference standard. Profiles of transporter expression were found to be significantly correlated in two independent Caco-2 cell clones and in human small intestine, which may support the use of Caco-2 cells for investigating intestinal drug transport. Several transporters were nevertheless quantitatively expressed at higher (MRP2, MRP3, MRP4, MRP5, MRP6, OATP-A, OATP-B, OCT1 and MCT1) or lower (BCRP) levels in Caco-2 cells comparatively to small intestine. Moreover, MDR1, MRP2, OATP-A and PEPT1 mRNA relative expression were found to differ in the two analyzed Caco-2 cell clones by at least a twofold factor, highlighting that some variations in transporter expression may occur in Caco-2 cells depending on cell origin, and therefore underlining the interest of carefully characterizing transporter levels in any Caco-2 cell clone before its use for drug transport assays.

Published
2007
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37. Cloning and use of a coral 36B4 gene to study the differential expression of coral genes between light and dark conditions

Author

Sylvie Tambutté, Guillaume E. Beranger, Béatrice Gaume, Jean-Claude Scimeca, Denis Allemand, Didier Zoccola, Aurelie Moya, Centre Scientifique de Monaco (CSM), Centre Scientifique de Monaco, Génétique, physiopathologie et ingénierie du tissu osseux (GéPITOS), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Biologie des organismes marins et écosystèmes (BOME), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Cognition, Langues, Langage, Ergonomie (CLLE-ERSS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Toulouse - Jean Jaurès (UT2J)-Université Bordeaux Montaigne-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Valrose (IBV), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), SCIMECA, Jean-Claude, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), and Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)

Subjects
0106 biological sciences, Light, Coral, Stylophora pistillata, [SDV.BC.IC] Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], MESH: Base Sequence, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: Ribulose-Bisphosphate Carboxylase, 01 natural sciences, Applied Microbiology and Biotechnology, Reference genes, Gene expression, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], MESH: Animals, Cloning, Molecular, MESH: Phylogeny, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Phylogeny, Genetics, Regulation of gene expression, 0303 health sciences, [SDV.MHEP.RSOA] Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, biology, MESH: Photosystem II Protein Complex, MESH: Darkness, Darkness, Reference Standards, MESH: Ribosomal Proteins, Anthozoa, MESH: Gene Expression Regulation, Acidic ribosomal phosphoprotein P0, [SDV.MHEP.RSOA]Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, 36B4, MESH: Calcium Channels, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Reference Standards, Ribosomal Proteins, Ribulose-Bisphosphate Carboxylase, Molecular Sequence Data, [SDV.CAN]Life Sciences [q-bio]/Cancer, Calcium-Transporting ATPases, MESH: Actins, 010603 evolutionary biology, MESH: Calcium-Transporting ATPases, Coral calcification, 03 medical and health sciences, Aposymbiotic, [SDV.CAN] Life Sciences [q-bio]/Cancer, MESH: RNA, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Animals, MESH: Cloning, Molecular, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, Gene, 030304 developmental biology, MESH: Molecular Sequence Data, Base Sequence, RuBisCO, Photosystem II Protein Complex, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, MESH: Light, Actins, [SDV.IB.BIO] Life Sciences [q-bio]/Bioengineering/Biomaterials, Gene Expression Regulation, MESH: Anthozoa, biology.protein, RNA, Calcium Channels, Real-time PCR
Abstract

International audience; This paper aims to validate reference genes for gene expression studies between light and dark conditions in the scleractinian coral Stylophora pistillata for future gene expression studies of the "light-enhanced calcification" phenomenon. For this purpose, we cloned, sequenced, and characterized a candidate reference gene, the 36B4 gene from the coral S. pistillata, and validated 36B4 and beta-actin as reference genes. To illustrate the future applications of these reference genes, we tested the dark and light expression of two photosynthetic genes (Rubisco and D1 protein of the photosystem II) and two genes encoding proteins involved in calcium transport for coral calcification (a calcium ATPase and a calcium channel). Results show that both photosynthetic genes are enhanced during the light when standardized against 36B4 and beta-actin, whereas the two genes encoding proteins involved in calcium transport are not differentially expressed between light and dark conditions. The characterization of a coral 36B4 and the establishment of such valid reference genes will be useful for future gene expression studies between diverse conditions (aposymbiotic/symbiotic, stress/control, light/dark conditions) in scleractinian corals.

Published
2007
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38. MRS quality assessment in a multicentre study on MRS-based classification of brain tumours

Author

Arend Heerschap, Àngel Moreno-Torres, Yvonne M. van der Meulen, Kirstie S. Opstad, Anne Ziegler, Carles Majós, Mark Rijpkema, Marinette van der Graaf, Margarida Julià-Sapé, Carles Arús, Dionisio Acosta, Franklyn A. Howe, Department of Radiology, Radboud University Medical Center [Nijmegen], Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona (UAB), Department of Basic Medical Sciences, Queen Mary University of London (QMUL), Neuroimagerie Fonctionnelle et Metabolique, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Diagnòstic per la Imatge, CSU de Bellvitge, Centre Diagnòstic Pedralbes, European Union, Grant Number: IST 1999-10310, and Dojat, Michel

Subjects
Magnetic Resonance Spectroscopy, Databases, Factual, Computer science, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, MESH: Quality Control, MESH: Equipment Failure Analysis, computer.software_genre, 030218 nuclear medicine & medical imaging, Pattern Recognition, Automated, MESH: Clinical Protocols, 0302 clinical medicine, Data acquisition, Clinical Protocols, Voxel, MESH: Pattern Recognition, Automated, Multicenter Studies as Topic, Spectroscopy, media_common, MESH: Program Evaluation, medicine.diagnostic_test, Quality assessment, Brain Neoplasms, Phantoms, Imaging, phantom, Nutrition and Health [UMCN 5.5], Reference Standards, multicentre study, Visual inspection, MESH: Reproducibility of Results, MESH: Brain Neoplasms, Molecular Medicine, MESH: Reference Standards, MR spectra, Protons, Quality Control, system quality assurance, quality assessment, [SDV.CAN]Life Sciences [q-bio]/Cancer, Expert Systems, Imaging phantom, 03 medical and health sciences, MESH: Software, [SDV.CAN] Life Sciences [q-bio]/Cancer, medicine, MESH: Water, MESH: European Union, media_common.cataloged_instance, Humans, Radiology, Nuclear Medicine and imaging, European Union, European union, MESH: Humans, business.industry, MESH: Expert Systems, MESH: Magnetic Resonance Spectroscopy, Reproducibility of Results, Water, Magnetic resonance imaging, MESH: Databases, Factual, Equipment Failure Analysis, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, System quality, MESH: Phantoms, Imaging, MESH: Multicenter Studies as Topic, H MRS, MESH: Protons, Functional Imaging [UMCN 1.1], Nuclear medicine, business, computer, 030217 neurology & neurosurgery, Software, Program Evaluation
Abstract

Contains fulltext : 69096.pdf (Publisher’s version ) (Closed access) This paper reports on quality assessment of MRS in the European Union-funded multicentre project INTERPRET (International Network for Pattern Recognition of Tumours Using Magnetic Resonance; http://azizu.uab.es/INTERPRET), which has developed brain tumour classification software using in vivo proton MR spectra. The quality assessment consisted of both MR system quality assurance (SQA) and quality control (QC) of spectral data acquired from patients and healthy volunteers. The system performance of the MR spectrometers at all participating centres was checked bimonthly by a short measurement protocol using a specially designed INTERPRET phantom. In addition, a more extended SQA protocol was performed yearly and after each hardware or software upgrade. To compare the system performance for in vivo measurements, each centre acquired MR spectra from the brain of five healthy volunteers. All MR systems fulfilled generally accepted minimal system performance for brain MRS during the entire data acquisition period. The QC procedure of the MR spectra in the database comprised automatic determination of the signal-to-noise ratio (SNR) in a water-suppressed spectrum and of the line width of the water resonance (water band width, WBW) in the corresponding non-suppressed spectrum. Values of SNR > 10 and WBW < 8 Hz at 1.5 T were determined empirically as conservative threshold levels required for spectra to be of acceptable quality. These thresholds only hold for SNR and WBW values using the definitions and data processing described in this article. A final QC check consisted of visual inspection of each clinically validated water-suppressed metabolite spectrum by two, or, in the case of disagreement, three, experienced MR spectroscopists, to detect artefacts such as large baseline distortions, exceptionally broadened metabolite peaks, insufficient removal of the water line, large phase errors, and signals originating from outside the voxel. In the end, 10% of 889 spectra with completed spectroscopic judgement were discarded.

Published
2007
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39. Quantitative Real-Time Legionella PCR for Environmental Water Samples: Data Interpretation

Author

M. Reyrolle, François Vandenesch, Nicole Weill, Jerome Etienne, Janine André, Pierre-Alain Falconnet, Sophie Jarraud, Max Maurin, Philippe Joly, Centre National de Référence des Légionella, Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Bactériologie, CHU Grenoble, CARSO-Laboratoire Santé Environnement Hygiène de Lyon (CARSO-LSEHL), CARSO-LSEHL, Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), and Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)

Subjects
Genus Legionella, Colony Count, Microbial, Fresh Water, Public Health Microbiology, 010501 environmental sciences, 01 natural sciences, Applied Microbiology and Biotechnology, Legionella pneumophila, Polymerase Chain Reaction, law.invention, law, RNA, Ribosomal, 16S, MESH: Water Supply, Polymerase chain reaction, 0303 health sciences, Ecology, biology, MESH: Air Conditioning, Reference Standards, MESH: RNA, Ribosomal, 16S, MESH: Fresh Water, MESH: Laboratories, MESH: Reference Standards, Biotechnology, DNA, Bacterial, Legionella, Sensitivity and Specificity, Microbiology, 03 medical and health sciences, Environmental water, Water Supply, Air Conditioning, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Letters to the Editor, MESH: Colony Count, Microbial, 0105 earth and related environmental sciences, Chromatography, 030306 microbiology, Data interpretation, MESH: Polymerase Chain Reaction, Ribosomal RNA, 16S ribosomal RNA, biology.organism_classification, MESH: DNA, Bacterial, MESH: Legionella pneumophila, MESH: Sensitivity and Specificity, Culture Media, respiratory tract diseases, MESH: Culture Media, Laboratories, Food Science, MESH: Legionella
Abstract

Quantitative Legionella PCRs targeting the 16S rRNA gene (specific for the genus Legionella ) and the mip gene (specific for the species Legionella pneumophila ) were applied to a total of 223 hot water system samples (131 in one laboratory and 92 in another laboratory) and 37 cooling tower samples (all in the same laboratory). The PCR results were compared with those of conventional culture. 16S rRNA gene PCR results were nonquantifiable for 2.8% of cooling tower samples and up to 39.1% of hot water system samples, and this was highly predictive of Legionella CFU counts below 250/liter. PCR cutoff values for identifying hot water system samples containing >10 3 CFU/liter legionellae were determined separately in each laboratory. The cutoffs differed widely between the laboratories and had sensitivities from 87.7 to 92.9% and specificities from 77.3 to 96.5%. The best specificity was obtained with mip PCR. PCR cutoffs could not be determined for cooling tower samples, as the results were highly variable and often high for culture-negative samples. Thus, quantitative Legionella PCR appears to be applicable to samples from hot water systems, but the positivity cutoff has to be determined in each laboratory.

Published
2006
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40. Unique NS5b hepatitis C virus gene sequence consensus database is essential for standardization of genotype determinations in multicenter epidemiological studies

Author

Syria Laperche, Christopher Payan, Catherine Gaudy, Sophie Vallet, Bruno Pozzetto, Jacques Izopet, Catherine Tamalet, Françoise Bouchardeau, Paul Dény, Sophie Alain, Gilles Duverlie, Marie-Laure Chaix, Vincent Thibault, Karine Sauné, Jean-Jacques Lefrère, Françoise Lunel, Jean-Michel Pawlotsky, Centre National de Référence Virus des hépatites B, C et Delta, Institut National de la Transfusion Sanguine [Paris] ( INTS ) -Assistance publique - Hôpitaux de Paris (AP-HP), Université de Limoges ( UNILIM ), Biologie moléculaire et cellulaire des microorganismes ( EA3175 ), Université de Limoges ( UNILIM ) -Génomique, Environnement, Immunité, Santé, Thérapeutique ( GEIST FR CNRS 3503 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire de Virologie [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Groupe Immunité des Muqueuses et Agents Pathogènes ( GIMAP ), Université Jean Monnet [Saint-Étienne] ( UJM ), Laboratoire de Virologie [Toulouse], CHU Toulouse [Toulouse], Institut National de la Transfusion Sanguine [Paris] (INTS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université de Limoges (UNILIM), Biologie moléculaire et cellulaire des microorganismes (EA3175), Université de Limoges (UNILIM)-Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST FR CNRS 3503)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Groupe Immunité des Muqueuses et Agents Pathogènes (GIMAP), and Université Jean Monnet [Saint-Étienne] (UJM)

Subjects
MESH: Sequence Analysis, DNA, Hepacivirus, viruses, MESH : Genotype, Viral Nonstructural Proteins, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, medicine.disease_cause, computer.software_genre, Polymerase Chain Reaction, MESH : Hepacivirus, MESH: Genotype, chemistry.chemical_compound, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genotype, Databases, Genetic, MESH: Hepacivirus, MESH : Viral Nonstructural Proteins, MESH : Polymerase Chain Reaction, MESH: Databases, Genetic, MESH : Consensus Sequence, 0303 health sciences, biology, Database, virus diseases, Hepatitis C, Reference Standards, 3. Good health, [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Laboratories, 030211 gastroenterology & hepatology, MESH: Reference Standards, Microbiology (medical), Hepatitis C virus, MESH : Laboratories, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 03 medical and health sciences, Flaviviridae, Virology, Consensus Sequence, medicine, Consensus sequence, Humans, MESH: Consensus Sequence, MESH : Databases, Genetic, NS5B, 030304 developmental biology, MESH: Hepatitis C, MESH: Humans, MESH : Humans, MESH: Polymerase Chain Reaction, Sequence Analysis, DNA, MESH : Hepatitis C, medicine.disease, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, digestive system diseases, chemistry, MESH : Reference Standards, MESH: Viral Nonstructural Proteins, Laboratories, computer, Reference genome, MESH : Sequence Analysis, DNA
Abstract

A multicenter study of NS5b hepatitis C virus (HCV) genotype determination involving 12 laboratories demonstrates that any laboratory with expertise in sequencing techniques would be able to provide a reliable HCV genotype for clinical and epidemiological purposes as long as they are provided a consensus reference sequence database.

Published
2006
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41. Predicting the clinical outcome of congenital unilateral ureteropelvic junction obstruction in newborn by urinary proteome analysis

Author

Michael Walden, Jean-Loup Bascands, François Bouissou, Joost P. Schanstra, Stefan Wittke, Harald Mischak, Stéphane Decramer, Petra Zürbig, Pharmacologie Moleculaire et Physiopathologie Renale, IFR 31 Louis Bugnard (IFR 31), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Mosaiques Diagnostics & Therapeutics (MOSAIQUES DIAGNOSTICS & THERAPEUTICS), Mosaiques Diagnostics & Therapeutics AG, Bascands, Jean-Loup, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Male, Time Factors, Proteome, 030232 urology & nephrology, Ureteropelvic junction, MESH: Kidney Pelvis, urologic and male genital diseases, [SDV.MHEP.UN]Life Sciences [q-bio]/Human health and pathology/Urology and Nephrology, Severity of Illness Index, Mass Spectrometry, 0302 clinical medicine, MESH: Double-Blind Method, Kidney Pelvis, Prospective Studies, Prospective cohort study, 0303 health sciences, MESH: Infant, Newborn, General Medicine, Reference Standards, Prognosis, MESH: Case-Control Studies, MESH: Infant, MESH: Proteome, MESH: Reproducibility of Results, medicine.anatomical_structure, MESH: Reference Standards, Female, Blinded study, Ureteral Obstruction, medicine.medical_specialty, Urinary system, Urology, General Biochemistry, Genetics and Molecular Biology, MESH: Prognosis, Specimen Handling, 03 medical and health sciences, Double-Blind Method, Severity of illness, medicine, Humans, 030304 developmental biology, Noninvasive biomarkers, MESH: Mass Spectrometry, MESH: Humans, business.industry, Case-control study, MESH: Biological Markers, Infant, Newborn, Infant, Reproducibility of Results, Surgical correction, [SDV.MHEP.UN] Life Sciences [q-bio]/Human health and pathology/Urology and Nephrology, MESH: Prospective Studies, MESH: Male, Surgery, Case-Control Studies, business, MESH: Female, MESH: Severity of Illness, Biomarkers
Abstract

We analyzed urinary polypeptides from individuals with neonatal ureteropelvic junction (UPJ) obstruction to predict which individuals with this condition will evolve toward obstruction that needs surgical correction. We identified polypeptides that enabled diagnosis of the severity of obstruction and validated these biomarkers in urine collected in a prospective blinded study. Using these noninvasive biomarkers, we were able to predict, several months in advance and with 94% precision, the clinical evolution of neonates with UPJ obstruction.

Published
2006
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42. Clinical usefulness of D-dimer testing in cancer patients with suspected pulmonary embolism

Author

Sylvain De Lucia, Marc Philip Righini, Pierre-Marie Roy, Drahomir Aujesky, Grégoire Le Gal, Arnaud Perrier, Guy Meyer, Henri Bounameaux, Calvez, Ghislaine, Service d'angiologie et d'hémostase (MR), Hôpital Universitaire de Genève, Groupe d'Etude de la Thrombose de Bretagne Occidentale (GETBO), Université de Brest (UBO)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO), Centre de Recherche Clinique (CRC Angers), Université d'Angers (UA)-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Department of Internal Medicine (DIM -CHUV), Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), and Service de médecine interne générale (SMIG)

Subjects
Male, MESH: Pulmonary Embolism, 030204 cardiovascular system & hematology, 0302 clinical medicine, Neoplasms, MESH: Neoplasms, 030212 general & internal medicine, MESH: Aged, MESH: Middle Aged, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Respiratory disease, MESH: Enzyme-Linked Immunosorbent Assay, Hematology, Middle Aged, Reference Standards, MESH: Predictive Value of Tests, 3. Good health, Pulmonary embolism, MESH: Reproducibility of Results, Predictive value of tests, Female, MESH: Reference Standards, medicine.medical_specialty, Enzyme-Linked Immunosorbent Assay, Malignancy, Sensitivity and Specificity, Fibrin Fibrinogen Degradation Products, 03 medical and health sciences, Predictive Value of Tests, Internal medicine, D-dimer, MESH: Fibrin Fibrinogen Degradation Products, medicine, Humans, Aged, Models, Statistical, MESH: Humans, business.industry, Vascular disease, Reproducibility of Results, Cancer, Emergency department, medicine.disease, MESH: Sensitivity and Specificity, MESH: Male, Surgery, Pulmonary Embolism, business, MESH: Female, MESH: Models, Statistical, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

SummaryLimited data are available about the diagnostic value of D-dimer testing in cancer patients with clinically suspected pulmonary embolism (PE).Therefore, we evaluated i) the safety and clinical usefulness of an ELISA D-dimer test to rule out PE in cancer patients compared with non-cancer patients and ii) whether adopting a higher D-dimer cut-off value might increase the usefulness of D-dimer in cancer patients. We analysed data from two outcome studies which enrolled 1,721 consecutive patients presenting in the emergency department with clinically suspected PE. Presence of an active malignancy was abstracted from the database. All patients underwent a sequential diagnostic work-up including an ELISA D-dimer test and a 3-month followup. Sensitivity and predictive value (NPV) were 100% in both cancer and non-cancer patients. PE was ruled out by a negative D-dimer test in 494/1,554 (32%) patients without cancer, and in 18/164 (11%) patients witha malignancy. At cut-off values varying from 500 to 900 µg/l, the sensitivity was unchanged (100%, 95% CI: 93% to 100%) and the specificity increased from 16% (95% CI:11% to 24%) to 30% (95% CI:22% to 39%).The 3-month thromboembolic risk was 0% (95 % CI: 0% to 18%) in cancer patients witha negative D-dimer test. ELISA D-dimer appears safe to rule out pulmonary embolism in cancer patients but it is negative in only one of ten patients at the usual cut-off value. Increasing the cut-off value of D-dimer in cancer patients might increase the test’s clinical usefulness.

Published
2006

43. CyProQuant-PCR: a real time RT-PCR technique for profiling human cytokines, based on external RNA standards, readily automatable for clinical use

Author

Boeuf, Philippe, Vigan-Womas, Inès, Jublot, Delphine, Loizon, Séverine, Barale, Jean-Christophe, Akanmori, Bartholomew Dicky, Mercereau-Puijalon, Odile, Behr, Charlotte, Bases génétiques et moléculaires des interactions de la cellule eucaryote (BGMICE), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Structure et régulation de l'expression des anticorps et des récepteurs des lymphocytes T, Immunology Unit, Noguchi Memorial Institute for Medical Research [Accra, Ghana] (NMIMR), University of Ghana-University of Ghana, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Adult, Lipopolysaccharides, lcsh:Immunologic diseases. Allergy, Enzyme-Linked Immunosorbent Assay, Transforming Growth Factor beta1, Automation, MESH: Transforming Growth Factor beta1, MESH: Gene Expression Profiling, Transforming Growth Factor beta, MESH: Automation, MESH: Reverse Transcriptase Polymerase Chain Reaction, MESH: Child, Humans, RNA, Messenger, Malaria, Falciparum, Child, Macrophage Migration-Inhibitory Factors, Cells, Cultured, MESH: Transforming Growth Factor beta, MESH: RNA, Messenger, MESH: Cytokines, MESH: Humans, Reverse Transcriptase Polymerase Chain Reaction, Tumor Necrosis Factor-alpha, Methodology Article, Gene Expression Profiling, MESH: Malaria, Falciparum, MESH: DNA, MESH: Enzyme-Linked Immunosorbent Assay, MESH: Adult, DNA, Reference Standards, MESH: Gene Expression Regulation, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Gene Expression Regulation, MESH: Tumor Necrosis Factor-alpha, MESH: Macrophage Migration-Inhibitory Factors, Cytokines, MESH: Reference Standards, MESH: Lipopolysaccharides, lcsh:RC581-607, MESH: Cells, Cultured
Abstract

Background Real-time PCR is becoming a common tool for detecting and quantifying expression profiling of selected genes. Cytokines mRNA quantification is widely used in immunological research to dissect the early steps of immune responses or pathophysiological pathways. It is also growing to be of clinical relevancy to immuno-monitoring and evaluation of the disease status of patients. The techniques currently used for "absolute quantification" of cytokine mRNA are based on a DNA standard curve and do not take into account the critical impact of RT efficiency. Results To overcome this pitfall, we designed a strategy using external RNA as standard in the RT-PCR. Use of synthetic RNA standards, by comparison with the corresponding DNA standard, showed significant variations in the yield of retro-transcription depending the target amplified and the experiment. We then developed primers to be used under one single experimental condition for the specific amplification of human IL-1β, IL-4, IL-10, IL-12p40, IL-13, IL-15, IL-18, IFN-γ, MIF, TGF-β1 and TNF-α mRNA. We showed that the beta-2 microglobulin (β2-MG) gene was suitable for data normalisation since the level of β2-MG transcripts in naïve PBMC varied less than 5 times between individuals and was not affected by LPS or PHA stimulation. The technique, we named CyProQuant-PCR (Cytokine Profiling Quantitative PCR) was validated using a kinetic measurement of cytokine transcripts under in vitro stimulation of human PBMC by lipopolysaccharide (LPS) or Staphylococcus aureus strain Cowan (SAC). Results obtained show that CyProQuant-PCR is powerful enough to precociously detect slight cytokine induction. Finally, having demonstrated the reproducibility of the method, it was applied to malaria patients and asymptomatic controls for the quantification of TGF-β1 transcripts and showed an increased capacity of cells from malaria patients to accumulate TGF-β1 mRNA in response to LPS. Conclusion The real-time RT-PCR technique based on a RNA standard curve, CyProQuant-PCR, outlined here, allows for a genuine absolute quantification and a simultaneous analysis of a large panel of human cytokine mRNA. It represents a potent and attractive tool for immunomonitoring, lending itself readily to automation and with a high throughput. This opens the possibility of an easy and reliable cytokine profiling for clinical applications.

Published
2005
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44. Data reproducibility in fluorescence image analysis

Author

P. A. Bryon, Catherine Souchier, Christine Brisson, Bernadette Batteux, Michel Robert-Nicoud, Biologie moléculaire et cellulaire de la différenciation, Université Joseph Fourier - Grenoble 1 (UJF)-Institut Albert Bonniot-Institut National de la Santé et de la Recherche Médicale (INSERM), Neurobiologie expérimentale et physiopathologie, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-IFR19-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de cytologie analytique et quantimétrique, Université de Lyon-Université de Lyon, This work was supported by ARC 'Association for Research Cancer' grant, and Souchier, Catherine

Subjects
Spectrum analyzer, MESH: Microscopy, Fluorescence, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Immunofluorescence, Green fluorescent protein, MESH: Calibration, 03 medical and health sciences, MESH: Software, image analysis, medicine, Fluorescence microscope, Image Processing, Computer-Assisted, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, 030304 developmental biology, Fluorescence microscopy, 0303 health sciences, Reproducibility, medicine.diagnostic_test, 030302 biochemistry & molecular biology, Reproducibility of Results, Cell Biology, Reference Standards, cytometry, Fluorescence, MESH: Image Processing, Computer-Assisted, quantification, 3. Good health, MESH: Reproducibility of Results, Microscopy, Fluorescence, Calibration, standards, MESH: Reference Standards, Cytometry, Software, Fluorescence in situ hybridization, Biomedical engineering
Abstract

International audience; Fluorescence image analysis provides quantitative data on fluorescence in situ hybridization signals (FISH), immunofluorescence labelings, Green Fluorescent Protein (GFP) expression and microarrays. It is a valuable tool for decision making in the fields of biology and medicine. The aim of this study was to evaluate the reproducibility of fluorescence intensity measurements and standardization when acquisitions are performed under various but well defined conditions. Fluorescent intensity of standard beads (Inspeck series, Molecular Probes) was repeatedly measured using an image analyzer and automated procedures. Images were acquired using several integration times and neutral filter sets. A standardization procedure was used for expressing the data in a same unit: data were multiplied by the light attenuation factor and were divided by the CCD integration times. Results show that 1) standardization is possible 2) accurate and reliable fluorescence measurements can be obtained and 3) specimens showing large differences in fluorescence intensity can be objectively compared. Moreover fluorescent test slides including fluorochrome solutions and altuglas slides were tested for shading correction and as overall test systems.

Published
2003

45. Real-time PCR for quantification of human herpesvirus 6 DNA from lymph nodes and saliva

Author

Barbara Petit, Sophie Alain, François Denis, Mohamed Touati, Sylvie Ranger-Rogez, Dominique Bordessoule, Sophie Collot, Université de Limoges (UNILIM), Physiologie Moléculaire de la Réponse Immune et des Lymphoproliférations (PMRIL), and Université de Limoges (UNILIM)-Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST FR CNRS 3503)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Saliva, Lymphoma, Herpesvirus 6, Human, MESH: Lymph Nodes, MESH: Base Sequence, medicine.disease_cause, Polymerase Chain Reaction, law.invention, chemistry.chemical_compound, MESH: Lymphoproliferative Disorders, law, Polymerase chain reaction, biology, virus diseases, Reference Standards, Hodgkin Disease, MESH: Hodgkin Disease, Real-time polymerase chain reaction, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH: Lymphoma, T-Cell, MESH: Reference Standards, Human herpesvirus 6, Lymph, MESH: Genome, Viral, MESH: DNA Primers, Microbiology (medical), Adult, NLM, MESH: Leukemia, B-Cell, Lymphoma, B-Cell, Roseolovirus Infections, Genome, Viral, Lymphoma, T-Cell, Sensitivity and Specificity, Herpesviridae, MESH: Roseolovirus Infections, Virology, medicine, Leukemia, B-Cell, Humans, MESH: Saliva, MESH: Lymphoma, B-Cell, DNA Primers, MESH: Humans, Base Sequence, MESH: Adult, MESH: Polymerase Chain Reaction, Assay sensitivity, MESH: Herpesvirus 6, Human, biology.organism_classification, MESH: Sensitivity and Specificity, Lymphoproliferative Disorders, MESH: DNA, Viral, chemistry, DNA, Viral, Lymph Nodes, MESH: Lymphoma, DNA
Abstract

A real-time quantitative PCR assay has been developed to measure human herpesvirus 6 (HHV-6) DNA in biological specimens. The assay sensitivity was 10 copies of DNA per well, with a linear dynamic range of 10 to 10 7 copies of HHV-6 DNA. Intra- and interassay variations were, respectively, 0.88 and 0.8% for samples containing 10 2 DNA copies, 0.99 and 0.96% for samples containing 10 4 copies, and 0.76 and 0.9% for samples containing 10 6 copies. Among 34 saliva samples from healthy subjects, 26 were found to contain HHV-6 DNA (76.5%; median, 23,870 copies/ml), and following a single freeze-thaw cycle, 25 of the same samples were found to be positive for HHV-6 DNA, although at a statistically significantly lower concentration (median, 3,497 copies/ml). The assay enabled detection of HHV-6 DNA in lymph node biopsies from patients with Hodgkin's disease (HD) (13 of 37 patients [35.1%]), B-cell neoplasms (8 of 36 patients [22.2%]), and T- or NK-cell neoplasms (3 of 13 patients [23.1%]), with concentrations ranging from 100 to 864,640 HHV-6 copies per μg of DNA (HHV-6B being found in every case except two). All HD patients infected with HHV-6 presented clinically with the nodular sclerosis subtype of HD. The real-time quantitative PCR assay developed here was simple to perform and was sensitive over a wide range of HHV-6 concentrations. It therefore appears to be of potential value in clinical investigation or diagnosis of HHV-6 infection.

Published
2002
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46. X-ray absorption spectroscopy of a new zinc site in the fur protein from Escherichia coli

Author

Jean-Marc Latour, Jean-Louis Hazemann, Annie Adrait, Daniel Aberdam, Isabelle Michaud-Soret, Lilian Jacquamet, Physiopathologie et biothérapie: cellules souches, développement et cancer, Institut National de la Santé et de la Recherche Médicale (INSERM), IFR50, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Faculté de Médecine Nice, Biologie des Métaux (BioMet), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Nice Sophia Antipolis (... - 2019) (UNS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])

Subjects
Protein Conformation, MESH: Spectrum Analysis, Ligands, Biochemistry, MESH: Zinc, MESH: Recombinant Proteins, MESH: Apoproteins, MESH: Protein Conformation, MESH: Ligands, MESH: Bacterial Proteins, 0303 health sciences, X-ray absorption spectroscopy, Extended X-ray absorption fine structure, Fourier Analysis, MESH: Escherichia coli, Cobalt, Reference Standards, Recombinant Proteins, Zinc, MESH: Repressor Proteins, MESH: Reference Standards, medicine.drug, inorganic chemicals, Absorption spectroscopy, Inorganic chemistry, chemistry.chemical_element, X-ray absorption, 03 medical and health sciences, MESH: X-Rays, Bacterial Proteins, medicine, Escherichia coli, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], 030304 developmental biology, Binding Sites, 030306 microbiology, metalloregulator, Spectrum Analysis, X-Rays, ferric uptake, HEXA, XANES, Repressor Proteins, Crystallography, MESH: Cobalt, chemistry, MESH: Binding Sites, 13. Climate action, metal homeostasis, Ferric, Apoproteins, MESH: Fourier Analysis
Abstract

International audience; The zinc K-edge X-ray absorption spectra of the Fur (ferric uptake regulation) protein isolated from Escherichia coli have been analyzed in frozen solution to determine details of the zinc coordination. The spectra of apoFur and of the cobalt-substituted protein have been analyzed and compared in order to see the influence of the cobalt incorporation on the geometry of the zinc site. EXAFS analysis gave for both samples (apoFur and CoFur) a tetrahedral environment for the zinc atom with two sulfur donor ligands at a distance of 2.3 A from the zinc and two N/O donor ligands at 2.0 A. The two sulfur donor ligands are probably two of the four cysteines present in each Fur monomer and could be Cys92 and Cys95, which are known from mutagenesis studies to be essential for Fur activity [Coy, M., Doyle, C., Besser, J., and Neilands, J. B. (1994) BioMetals 7, 292-298]. The distances obtained from our fits were always too short to be compatible with penta or hexa coordination. The typical pattern observed for the Fourier transform of the EXAFS oscillations suggests the presence of at least one imidazole ligand. The XANES of these two forms of the protein are similar but significantly different. This suggests a change of the conformation of the zinc site upon cobalt incorporation. The present study provides the first unambiguous evidence for the presence of a structural zinc site in the Fur protein from Escherichia coli.

Published
1998
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47. Combined use of hard X-ray phase contrast imaging and X-ray fluorescence microscopy for sub-cellular metal quantification

Author

Heikki Suhonen, Ewelina Kosior, Sylvain Bohic, Asuncion Carmona, Jean Francois Guillet, Florence Marchi, Peter Cloetens, Richard Ortega, Guillaume Devès, Serduc, Raphael, European Synchrotron Radiation Facility (ESRF), INSERM U836, équipe 6, Rayonnement synchrotron et recherche médicale, European Synchrotron Radiation Facility (ESRF)-Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), CP, Physics department - UFR PHITEM, Université Joseph Fourier - Grenoble 1 (UJF)-Université Joseph Fourier - Grenoble 1 (UJF)-Surface Science Laboratory, European Synchrotron Radiation Facility (ESRF)-European Synchrotron Radiation Facility (ESRF), Surface Science Laboratory, and Université Sciences et Technologies - Bordeaux 1-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Analytical chemistry, X-ray fluorescence, Synchrotron radiation, MESH: Microscopy, Fluorescence, 02 engineering and technology, 01 natural sciences, MESH: Zinc, PC12 Cells, law.invention, Structural Biology, law, Microscopy, Fluorescence microscope, MESH: Animals, Microscopy, Phase-Contrast, MESH: Microscopy, Phase-Contrast, Chemistry, Phase-contrast imaging, Reference Standards, 021001 nanoscience & nanotechnology, Synchrotron, Zinc, X-Ray Phase-Contrast Imaging, Calibration, MESH: Reference Standards, Single-Cell Analysis, 0210 nano-technology, Algorithms, MESH: Cell Nucleus, MESH: Rats, MESH: Algorithms, MESH: Trace Elements, [SDV.IB.MN]Life Sciences [q-bio]/Bioengineering/Nuclear medicine, [SDV.IB.MN] Life Sciences [q-bio]/Bioengineering/Nuclear medicine, MESH: Calibration, MESH: X-Rays, Optics, synchrotron, MESH: PC12 Cells, Animals, MESH: Particle Size, Particle Size, Cell Nucleus, business.industry, X-Rays, 010401 analytical chemistry, 0104 chemical sciences, Rats, Trace Elements, Microscopy, Fluorescence, Light sheet fluorescence microscopy, MESH: Potassium, Potassium, business, phase contrast imaging, MESH: Single-Cell Analysis
Abstract

International audience; Hard X-ray fluorescence microscopy and magnified phase contrast imaging are combined to obtain quantitative maps of the projected metal concentration in whole cells. The experiments were performed on freeze dried cells at the nano-imaging station ID22NI of the European Synchrotron Radiation Facility (ESRF). X-ray fluorescence analysis gives the areal mass of most major, minor and trace elements; it is validated using a biological standard of known composition. Quantitative phase contrast imaging provides maps of the projected mass and is validated using calibration samples and through comparison with Atomic Force Microscopy and Scanning Transmission Ion Microscopy. Up to now, absolute quantification at the sub-cellular level was impossible using X-ray fluorescence microscopy but can be reached with the use of the proposed approach.

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