Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge

Motivation: Inferring how humans respond to external cues such as drugs, chemicals, viruses or hormones is an essential question in biomedicine. Very often, however, this question cannot be addressed because it is not possible to perform experiments in humans. A reasonable alternative consists of generating responses in animal models and ‘translating' those results to humans. The limitations of such translation, however, are far from clear, and systematic assessments of its actual potential are urgently needed. sbv IMPROVER (systems biology verification for Industrial Methodology for PROcess VErification in Research) was designed as a series of challenges to address translatability between humans and rodents. This collaborative crowd-sourcing initiative invited scientists from around the world to apply their own computational methodologies on a multilayer systems biology dataset composed of phosphoproteomics, transcriptomics and cytokine data derived from normal human and rat bronchial epithelial cells exposed in parallel to 52 different stimuli under identical conditions. Our aim was to understand the limits of species-to-species translatability at different levels of biological organization: signaling, transcriptional and release of secreted factors (such as cytokines). Participating teams submitted 49 different solutions across the sub-challenges, two-thirds of which were statistically significantly better than random. Additionally, similar computational methods were found to range widely in their performance within the same challenge, and no single method emerged as a clear winner across all sub-challenges. Finally, computational methods were able to effectively translate some specific stimuli and biological processes in the lung epithelial system, such as DNA synthesis, cytoskeleton and extracellular matrix, translation, immune/inflammation and growth factor/proliferation pathways, better than the expected response similarity between species. Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Applications magnétoélectriques des supraconducteurs

La supraconductivité est devenue incontournable, par exemple avec l’IRM qui équipe nos hôpitaux. Elle permet de spectaculaires réalisations tels le LHC du CERN qui a mis en évidence le boson de Higgs, le projet de fusion nucléaire ITER, le train à sustentation magnétique, etc. Ces applications dans divers domaines reposent sur l’aptitude des fils supraconducteurs à transporter de très fortes intensités de courant et sur l’énorme champ magnétique que des bobines supraconductrices peuvent créer. Elles sont l’objet du présent ouvrage avec d’abord l’élaboration des fils supraconducteurs, prouesse technologique tant pour les câbles Nb – Ti et Nb$_{3}$Sn que pour les rubans de cuprates. Ensuite, pour chaque application, sont présentés les phénomènes physiques et le fonctionnement des dispositifs technologiques ; le lecteur peut ainsi acquérir une vision globale des apports scientifiques de ces technologies et de leurs enjeux, scientifiques, médicaux et sociétaux. Trois autres ouvrages de la Collection Grenoble Sciences traitent de la supraconductivité, de ses bases physiques, des matériaux supraconducteurs et des applications de nature électronique

Superconductivity: an introduction

This book proposes a thorough introduction for a varied audience. The reader will master London theory and the Pippard equations, and go on to understand type I and type II superconductors (their thermodynamics, magnetic properties, vortex dynamics, current transport…), Cooper pairs and the results of BCS theory. By studying coherence and flux quantization he or she will be lead to the Josephson effect which, with the SQUID, is a good example of the applications. The reader can make up for any gaps in his knowledge with the use of the appendices, follow the logic behind each model, and assimilate completely the underlying concepts. Approximately 250 illustrations help in developing a thorough understanding. This volume is aimed towards masters and doctoral students, as well as advanced undergraduates, teachers and researchers at all levels coming from a broad range of subjects (chemistry, physics, mechanical and electrical engineering, materials science…). Engineers working in industry will have a useful introduction to other more applied or specialized material. Philippe Mangin is emeritus professor of physics at Mines Nancy Graduate School of Science, Engineering and Management of the University of Lorraine, and researcher at the Jean Lamour Institute in France. He is the former director of both the French neutron scattering facility, Léon Brillouin Laboratory in Orsay, and the Material Physics Laboratory in Nancy, and has taught superconductivity to a broad audience, in particular to engineering students. Rémi Kahn is a retired senior research scientist of the French Alternative Energies and Atomic Energy Commission (CEA-Saclay). He worked at the Léon Brillouin Laboratory and was in charge of the experimental areas of INB 101 (the Orphée research reactor). This work responded to the need to bring an accessible account suitable for a wide spectrum of scientists and engineers

Supraconductivité: introduction

La supraconductivité fait rêver, surtout depuis la découverte de son existence à des températures relativement accessibles. Ses applications sont déjà notables (Imagerie par Résonance Magnétique, futur ITER, NEUROSPIN, SQUID...) et des projets plus futuristes se développent (transport de courant, train en lévitation, moteurs). Le présent ouvrage propose une introduction solide, pour un public assez large. Le lecteur pourra s'initier à la théorie de London et aux équations de Pippard, puis étudier les supraconducteurs de type I et de type II (thermodynamique, magnétisme, dynamique de vortex, transport de courant...), les paires de Cooper et les résultats de la théorie BCS. L'étude de la cohérence et de la quantification du flux conduit à l'effet Josephson qui, avec le SQUID. est un bon exemple d'application. Le lecteur pourra combler certaines de ses lacunes grâce aux compléments, suivre le cheminement d'un modèle et s'approprier les concepts. Environ 250 illustrations en facilitent la compréhension. L'ouvrage est destiné aux étudiants de Master, de préparation aux CAPES et AGREG, aux thésards, et bien sûr aux enseignants, universitaires et chercheurs (chimistes, physiciens, électromécaniciens, spécialistes des matériaux...). Les ingénieurs des entreprises disposeront d'une introduction précieuse pour comprendre d'autres ouvrages plus appliqués ou spécialisés

Comparison of the accuracy of 3-dimensional cone-beam computed tomography and micro-computed tomography reconstructions by using different voxel sizes.

INTRODUCTION: Cone-beam computed tomography (CBCT) data are, in principle, metrically exact. However, clinicians need to consider the precision of measurements of dental morphology as well as other hard tissue structures. CBCT spatial resolution, and thus image reconstruction quality, is restricted by the acquisition voxel size. The aim of this study was to assess geometric discrepancies among 3-dimensional CBCT reconstructions relative to the micro-CT reference. METHODS: A total of 37 permanent teeth from 9 mandibles were scanned with CBCT 9500 and 9000 3D and micro-CT. After semiautomatic segmentation, reconstructions were obtained from CBCT acquisitions (voxel sizes 76, 200, and 300 μm) and from micro-CT (voxel size 41 μm). All reconstructions were positioned in the same plane by image registration. The topography of the geometric discrepancies was displayed by using a color map allowing the maximum differences to be located. RESULTS: The maximum differences were mainly found at the cervical margins and on the cusp tips or incisal edges. Geometric reconstruction discrepancies were significant at 300-μm resolution (P = .01, Wilcoxon test). CONCLUSIONS: To study hard tissue morphology, CBCT acquisitions require voxel sizes smaller than 300 μm. This experimental study will have to be complemented by studies in vivo that consider the conditions of clinical practice

Reorganization of a photosensitive carbo-benzene layer in a triptych nanocatalyst with enhancement of the photocatalytic hydrogen production from water

International audienceThe preparation of a triptych nanomaterial made of TiO2 nanoparticles as semiconductor, Ag plasmonic nanoparticles and a carbo-benzene macrocyclic molecule as photosensitizer is described, and used to produce hydrogen by photo-reduction of pure deionized water under 2.2 bar argon pressure without any electrical input. Silver nanoparticles (~5 nm) are grafted onto the surface of commercial TiO2 nanoparticles (~23 nm) by a photo-deposition process using an original silver amidinate precursor. The thickness of the photosensitive layer (2 nm), which completes the assembly, plays a crucial role in the efficiency and robustness of the triptych nanocatalyst. Thanks to the organic layer reorganization during the first ~24 h of irradiation, it leads to an enhancement of the hydrogen production rate up to 5 times. The amount of silver and carbo-benzene are optimized, along with the mass concentration of nanocatalyst in water and the pH of the aqueous medium, to allow reaching a hydrogen production rate of 22.1 μmol·h−1·gphotocatalyst−1

Transcription profiling by array of normal human and rat bronchial epithelial cells treated with more than 50 different compounds to investigate the ability to translate results from model organisms to humans

Inferring in humans biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to “translate” the results to humans. In this context, the Systems Biology Verification for Industrial Methodology for Process Verification in Research (SBV IMPROVER) initiative had run a Species Translation Challenge for the scientific community to explore and understand the limit of translatability from rodent to human using systems biology. Therefore, a multi-layer omics dataset was generated that comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, the generation, processing and quality control analysis of the multi-layer omics dataset. The datasets are accessible in public repositories could be leveraged for further translation studies